Analyse et Visualisation de structures 2D d’ARN

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(1)Analyse et Visualisation de structures 2D d’ARN Fabrice Leclerc. To cite this version: Fabrice Leclerc. Analyse et Visualisation de structures 2D d’ARN. Master. Paris, France. 2020. �hal-03313812�. HAL Id: hal-03313812 https://hal.archives-ouvertes.fr/hal-03313812 Submitted on 4 Aug 2021. HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. Public. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Domain.

(2) 0 02. 2 A. G B. Analyse et Visualisation de structures 2D d’ARN Fabrice Leclerc, Ph. D., I2BC (Campus d’Orsay) [email protected] 1.

(3) 4SALE. •. •. •. ++. FASTA 4SALE is designed to handle sequence FASTA, and secondary structure information of Output Secondary RNAs synchronously. structure: SVG. •. •. ht 4s. Echelles de taille et complexité Table 3. Structure-aware RNA sequence alignment editors.. 9.8 Figures longueur, repliements (jonctions), interactions à longue distance. Figure 1. Diversity of scales for non protein-coding RNAs. RNAfdl VARNA, S2S, etc With lengths ranging from 20 to 10 000 nucleotides, structurally-resolved RNAs require a (intersection-free) diversity of visualization techniques. 2.

(4) Motifs ARN Représentations 2D. ARN simple brin /ARN double brin fonction / structure 3.

(5) 3. 1. nous regroupons ces jonctions par homologie, nous obtenons 39 classes de jonctions homologues. La table 5.7, page 43, liste les 26 classes contennant plus d’une jonction.. Jonctions: « 3-way » Méthode de prédiction. Processus de prédiction Représentations 2D (3D) Une jonction. Trois empilements. Neuf configurations. Pour chaque configuration, un score Empil. 1 1 1 2 2 2 3 3 3. Famille Score A 2,12 B 0,23 C 0,85 A 1,5 B 0,12 C 0,01 A 1,3 B 0,1 C 1,1. Le meilleur score est notre prédiction. F IGURE 5.2: Processus de prédiction. Une jonction peut avoir trois empilements possibles, et chaque empilement peut ensuite appartenir à trois familles, ce qui 4.

(6) des familles, et encore plus risqué de proposer une méthode de classification. Laing et Schlick [59] définissent neuf familles topologiques, représentées dans la figure 6.3, mais certaines familles ne comportent, si l’on exclut les jonctions homologues, qu’un individu (familles X, cW et ⇡) ou deux (famille cX). Par ailleurs, les familles H et ⇡ sont très proches, la famille ⇡ possédant un empilement de moins, compensé par des interactions tertiaires. En prenant une définition étendue de l’empilement coaxial, comme nous l’avions fait pour les 3-jonctions, ces deux familles sont identiques.. Jonctions: « 4-way » Représentations 2D (3D) Famille H. Famille cK. Famille ⇡. Famille cH. Famille cL. Famille. Famille X. 5. Famille cW. Famille cX.

(7) Structure modulaire. 6.

(8) 0. Motifs: structure & fonction H. Saito, T. Inoue / The International Journal of Biochemistry & Cell Biology 41 (2009) 398–404. 7 Tertiary structures of Watson-Crick base pairs (PDB: 259D), kissing loop (PDB: 1k g. 2. RNA structural motifs: (A) examples of RNA–RNA interacting or structural motifs..

(9) ARNr 16S boucles terminales - boucles internes/bulges - jonctions 3 - jonctions n -. 8.

(10) ARNr 16S. Secondary Structure: small subunit ribosomal RNA A A U G U U G C G C 1100 G C U GC C AA 700 A G A C U A G UG AG U A CGA GC CCUUA UCCUUUGU CC CGG UC CC G G U G G A GA G A A UGC C A UCUGGA G AU G GC G A A U G C U C G G G G G U A G G A A A C GG GCC GG U G A G UC AA A G A A U U UGGA CCUU GA G CG G U GGCG G AA A U G 1150 G U G A U C G A A G C U A G A G C G C A GU G C C G G C G C U U G U A GA G C G C A G U U A G U G C U A A 1200 U A G C G G C U C G A C U A A G G UC U G G C C G A U A C G G C G CU A U G C C G A U A U A G C G A G A C G A A U A U CG U A U G 800 A A A UGA GA A U G C G G U U A G 2 C 1050 C U A G [m G ] C A A A G G C 750 G C C G G A C U U U U G AA G U A U A U G U G AG G C G C G G G G C A A GG 650 U C C U C A U A UA U A C G C C 1000 U UGCA UCUGA CU GGCA A G C A U A C A A CCUGGGA A U C UU G C C G C C G C U G A C U C GGGCCCC C G C G U U A GU GU A GA C U GA U U GU U U GG C C G C GU G C A C G C A U A A A G G G C G A G A A U 600 G A G U A A G AC C G A CUU U U C C C G A G GC A U G A U A G C C G C G A G G G G G 850 A G C C C G UA G U G A G C CG U U U GU C GA CUU A U GCC A A AC U A C ACC G A U A UU G C A A C C G G G A G A C U m7 A A A G C U U CA GCUG C C G G C G C UG A A G U C UG G A A A U A C G C U A G A G C G 1250 G U G A A C G A C G A G UG C A A C G C A U 5 A C 950 U G C U U AAAG G mC 2 U C U G mG G G CA U A U A C C C A G G U U U U CA GU CA G C A A A C C A A G G G G C G C U A U A A ψ A U GGG GGCC G A G U CA G U CGU C C G A U G G A G C G U C A 900 U A A A A G A G CA A G C G CUC UUGG A U GG A C C AAAA G A U A C G U A 450 A A U A C G G U AC A G G G C G G UG C G G C C G G A A A G G A CG G C U U UG A CG GGGCCCG A CA A G C U C A G C G U G C G G G A U A 500 A C CU C U A A C U A A G A U G 550 A C A C U G U U C C G G G C U G G G C G A U A G U 1300 U C A U U U GA C U C U U A G U G C C AG C UAA C G A U G A U C G A A U G U A C A G A U G GGUU GUA C G A G A C C A A G A A 10 C A 1350 G A A A G U 1400 C C G G U A A C U UAUG U CCGG U G U U U G C C A G 400 G C U G 4G U U AGAA G C G G A G mC m A G G A C U A G AU C C C G m3U G G A 2 G A C m C C G G G A C C A C 1500 U A A C C G U A G G A G A U A GCCUG A UGC A G C G G C U G A C U U U G G m6A C A 5C 2 C G G U U G G C G U C C C 5’ m 6 U A C G UA A U G CGGGU G A mA A G 2 A A G U U A AAC G C C G A A C U A U U A C A A C G C G C G A G C C A G C G UA 50 C U G U G U G CA C G C U A C G A G CA U A G A U C G U G U A C G G 350 A U A G A G C U C A G G C C G A C G U 3’ U G U C A C U A CA G GA AA A GUC A U G CAG GUC A CG GU CA G GA A GA A GC G G U U 300 A C G U GU C A A G G U CGG UGA CA GUC UUUCUUCG A U C G AG G G A U G A G A G A AU C A U C G G 100 C A A UC C AG A C UG G C G C A G G U A GU G C CG A A G C A G U U A U C A U A C A G U C GU GU G C G A CG AU U G U G A C G A A G UU G C U A C C G G C G A U G G G C G U G C G C A A U U G A A A A C A C G UG C A U A C G A 250 G G C C G U G 1450 U U U U U C G GC G A G G C G G C C G G U A A U C G U A 150 A U C G C G U GA A A A G CUACUGG GGGG G GG CCUCUU A C G C - Canonical base pair (A-U, G-C) A U CGCC CGA UGGC A U CC GGGGA G A G U A U - G-U base pair A AG UA A U 200 A A G A - G-A base pair A A C C C G U U - Non-canonical base pair A U G C G A Every 10th nucleotide is marked with a tick mark, A C. II. III. I. Escherichia coli. (J01695) 1.cellular organisms 2.Bacteria 3.Proteobacteria 4.gamma subdivision 5. Enterobacteriaceae and related symbionts 6. Enterobacteriaceae 7. Escherichia November 1999 (cosmetic changes July 2001). Symbols Used In This Diagram:. and every 50th nucleotide is numbered.. Tertiary interactions with strong comparative data are connected by solid lines.. 9.

(11) A 74. C. G36. 1. G. C. G. C. A. G. UG C. A C G A C U. C G G C A. E. G A C G U G U A G A G 31 G C G G G G A G G G U A G A C C U C G A U G U C C C G C C C C U C C G AUC U A A G A A G G C G G A U U G A A UA A G G A. A. U. C. A. A. 69. 76. jViz.RNA. RNAplot. G. F. 27. C. 49. D. 50. U U G A A GA C G G U A UA U G U C A A G A U C G G G U A C A AC C G C A U C U G C C G U A G A G C AG A A C A G G U G A C U C CC G C U C G 3 C C G A AA G U G G 1 A G A G G G G G G U 60 A C A 70 U A G C G A U U G C C C G 1 G C G A 76 40. 39. A R U modèles 2D (expérimental: « footprinting », SHAPE, G G A fluorescence, U RR R A CY. C. C A G C G. E. 62. U. A G U C G G R C Y. etc; théoriques: MFold, RNAfold, etc). CCC Y. GGG G. A A G CCU C GRY RU GGA GC G A. représentations 2D à partir de structures 3D d’ARN Y R. C. A. 5' 76. annotations des structures avec des informations: structurales, functionelles, phylogénétiques, etc 10.

(12) G. C. C. G. U. A. G. C13. A. U. UG. C. 85. B S2S/Assemble. C. A. G. G. C. C. G. G G18. A. G. A A A G A 41 G U. U. G 80. U. D. A. 59. G. G. A. C. U C G. U 64. A C. 74. G. 23. A. G. C. U. A. C. E. U. G. A. A. A. 69. 1. C. G. A. G. C. C. G. U. A. G. C 60. G. A. U A. C G. A U. VARNA. C. G. C. G. A. G. A. U G. C G. G. U. 76. G. A. C G36. C. G. C. G. G. U. C. C. 50. U. 62. C. C. 39. 47. A. 27. G C C G G C A U 30 C G G A U A A G G C G G G G GA C G A A A G G U G C G A AU C C G U C C C C G U A C C U G C C U AUC U A G A A G G C G G A A U U A A G A A A U G CG C A 40 G C U G C G U G G A G A C G U A A G G U A A G G U A A A G A G C C A C G UC U G G A 10 C G U C C G A C A C C G U G A A G U G C C G C C C U C 3 A C G U A G A 1 A G G G G G G A G C U U A U A U 70 C G G G C A U C G G C 20 C G A 1 G C U. A 52. A. C. G. G. 5’. 31. 49. A. 3’. A 90 C. G. C. 76. 31. B modèles 2D (expérimental: « footprinting », fluorescence, SHAPE, F etc; théoriques: MFold, RNAfold, etc) 30. G. A. A. G. A. U. A. C. G. G. G. C. G. G. G. 10. C. G. C. G. C. U G 20. A. C. A. A. U. 40. C. G. G. A. U. G. A. C. G. A. C. A. A. C. U C. U. U. 70. G. G. U. C. G. A. G. 50. U. A. C. C. G. U. A. G. C. 60. G. A. U. A. C. G. A U. A G A G U C G G R C Y. R A CCC Y. U A UC Y R G A A G CCU C GRY RU GGA GC G A. RR. GGG G. représentations 2D à partir de structures 3D d’ARN G. 1. C. G. C. Y R. G. C. A. 5'. 76. annotations des structures avec des informations: structurales, functionelles, phylogénétiques, etc 11.

(13) C G31 A G U U G A G. A. 27. U G A G A G A UA GA U A A 50 G G 40 C G U C A C A A U C U G CC C C G U U C C G C G U A C G A G C U U C G A G G G A A C G A G A C UU C C U C 3 G A C G U G C G A G 1 A G G AA 10 AG G G G G C G G G C A C C G A A G U A U U 60 A 70 C G C G A U A U G C G C C G 1 G C C G 1 A 76 G C. A. 39. U. 49. A. U G G A UA. A A A G. F. 62. PseudoViewer. A. R2R A G A G U C G G R C Y. R A CCC Y. U A UC Y R G A A G CCU C U Y R GR A C G G G G A. RR. GGG G. Y R 5'. 76. modèles 2D (expérimental: « footprinting », fluorescence, SHAPE, etc; théoriques: MFold, RNAfold, etc) représentations 2D à partir de structures 3D d’ARN annotations des structures avec des informations: structurales, functionelles, phylogénétiques, etc A G A. R A. Y. RR. A. U G U A CYR 12 A.

(14) RNA 2D Structure by HT-SHAPE. 13.

(15) 14.

(16) 15.

(17) IUPAC nucleotide code /U. /U. / Uracile. /U /U /U /U /U /U /U. 16.

(18) A. Raw Data. All-atoms 3D models RNAML. PDB. Annotation. RNAView MC-Annotate FR3D. (Extended) Secondary Structure File Formats Stockhlom. B. BPSeq. Connect. RNAML. RNA-Aware Tools Interactive Editors. Command-line tools. Web-based tools. VARNA. R-chie. PseudoViewer. xrna. RILogo. R-chie. rnaviz. RNAplot. RILogo. S2S/Assemble. R2R. RNAplot. PseudoViewer. VARNA. RNAMovies. Manual Refinement + Annotations. C. Vienna/DBN. Parameterization Rerun. Post-Processing Vector Graphics Editors Inkscape. Adobe R Illustrator R. Rougier, JDEV2013. D. Rasterization (Optional). Raster Graphics Editors Adobe R Photoshop R. Gimp. 17.

(19) Formats et Outils (Extended) Secondary Structure File Formats Stockhlom. Tools. jViz.RNA. Vienna/DBN. PseudoViewer. PDF. BPSeq. RNAMovies. EPS/PS. RILogo. SVG. R-chie. Connect. RNAML. RNAplot. R2R. PNG. JPG. S2S. GIF. Bitmap Graphics Formats. Vector Graphics Formats. 18. VARNA.

(20) A: FASTA (aligned) B: CLUSTAL. C: Stockholm (RFAM) D: Vienna (RNAfold) E: Pseudobase F: BPSEQ G: CONNECT (CT, CT2) 19.

(21) Notation « dot-bracket » > Rat Alanine tRNA GAGGAUUUAGCUUAAUUAAAGCAGUUGAUUUGCAUUUAACAGAUGUAAGAUAUAGUCUUACAGUCCUUA ((((((...((((.....)))).(((((.......)))))...((((((((...)))))))))))))).. RNAfold. A GU AU GC GC AU U U U GA C A U U C U G A A A U U U C GA U U A UGUA AG A A UA AGC A A G C AG UA UA GU UAU U U A U GC 20. Vienna, DBN.

(22) Format Stockholm U STOCKHOLM 1.0 U=GF ID mir-22 U=GF AC RF00653 ... O.latipes.1 Gasterosteus_aculeat.1 R.esox.1 ... U=GC SS_cons U=GC RF O.latipes.1 Gasterosteus_aculeat.1 R.esox.1 ... U=GC SS_cons U=GC RF //. CGUUG.CCUCACAGUCGUUCUUCA.CUGGCU.AGCUUUAUGUCCCACG.. GGCUG.ACCUACAGCAGUUCUUCA.CUGGCA.AGCUUUAUGUCCUCAUCU AGCUGAGCACA...CAGUUCUUCA.CUGGCA.GCCUUAAGGUUUCUGUAG .<<<<.<<..<<<<<<<<<<<<<<..<<<<..<<<<<<<.<<........ gGccg.acucaCagcaGuuCuuCa.cuGGCA.aGCuuuAuguccuuauaa CCCCACCGUAAAGCU.GC.CAGUUGAAGAGCUGUUGUG..UGUAACC ACCAGC..UAAAGCU.GC.CAGCUGAAGAACUGUUGUG..GUCGGCA ACAGGC..UAAACCU.GC.CAGCUGAAGAACUGCUCUG..GCCAGCU ....>>..>>>>>>>.>>.>>..>>>>>>>>>>>>>>...>>>>>>. acaaac..UaaaGCu.GC.CaGuuGaaGaaCugcuGug..gucggCu. 21.

(23) Stockholm - Ralee (emacs) # STOCKHOLM 1.0 Pho21_215834-215776_-__ Pfu21_163991-163933_-__ Pab21_230575-230517_-__ Consensus #=GC SS_cons //. CGGCCCGGTTCCCGCCCTCTCCGGGGAATCGTGAACCGGGGGTTCCGACCGGGCCGACA GGGCCCGGTTCCCGCCCTCTCCGGGGAATCGTGAACCGGGGGTTCCGACCGGGCCCACA GGGCCCGGCTCCCGCCCTCTCCGGGGAATCGTGAACCGGGGGTTCCGGCCGGGCCTACA GGGCCCGGUUCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCCACA <<<<<<<<<<...<<<<...<<<<...........>>>>>>>>...>>>>>>>>>>.... # STOCKHOLM 1.0 Pab105_1335797-1335648_-__ Pho105_592081-592230_+__ Pfu105_942696-942544_-__ Consensus #=GC SS_cons. CCGCCCGGA-GGCCCGACCGAGGGAGCGTGCCGAGAAAGGCGCGCCATGAACGAGGCGACGTCGCCGGGCGGACAGGGCCCGGTCTCCGGGG CCGCCCGGG-GGCCCGACCGAGGGAGCGTGCCGAGAATGGCGCGCAATGAACGAGGTGACGTCGTCGGGCGGACAGGGCCCGGTCTCCGGGG CCGCCCGGGCGGCCCGACCGAGGGAGCGTGCCGGCAATGGCGCGCGATGAACGAGGTGACGTCTCCGGGCGGACAGGGCCCGGCCTTCGGGG CCGCCCGGG-GGCCCGACCGAGGGAGCGUGCCGAGAAUGGCGCGCAAUGAACGAGGUGACGUCGCCGGGCGGACAGGGCCCGGUCUCCGGGG <<<<<<<<....<<<......>>>.<<<<<<<......>>>>>>>...<<.<<......>>>>.>>>>>>>>...<<<<<<<<<.<<<<.... Pab105_1335797-1335648_-__. CCGCCTGAGGTTGCCGACAACGGCGGGCAATGAGGGCGGGTGGATAAGCCGGGCCTATA-CCGCCTGAGGTTGCCGAGAATGGCGTTCAATGAAGGCGGGCGGATAATCCGGGCCTAAA-CCGCCTGAGGGAGCCGAGAAGGGCAGACGATGAAGGCGGGCGGATAAGCCGGGCCCTCAAA CCGCCUGAGGUUGCCGAGAACGGCGGACAAUGAAGGCGGGCGGAUAAGCCGGGCCUAAA-<<<<<<.....<<<<......>>>>........>>>>>>.>>>>...>>>>>>>>>...... Pfu105_942696-942544_-__ Consensus #=GC SS_cons //. Stockholm 22.

(24) Stockholm - Rfam # STOCKHOLM 1.0 #=GF ID snoR9 #=GF AC RF00065 #=GF DE Small nucleolar RNA snoR9 #=GF AU Bateman A, Daub J #=GF GA 50.0 #=GF NC 49.8 #=GF TC 68.7 #=GF SE Bateman A #=GF SS Published; PMID:12032319 #=GF TP Gene; snRNA; snoRNA; CD-box; #=GF BM cmbuild -F CM SEED; cmcalibrate --mpi -s 1 CM #=GF BM cmsearch -Z 274931 -E 1000000 --toponly CM SEQDB #=GF DR SO:0000593 SO:C_D_box_snoRNA #=GF DR GO:0006396 GO:RNA processing #=GF DR GO:0005730 GO:nucleolus #=GF RN [1] #=GF RM 12032319 #=GF RT Noncoding RNA genes identified in AT-rich hyperthermophiles. #=GF RA Klein RJ, Misulovin Z, Eddy SR; #=GF RL Proc Natl Acad Sci U S A 2002;99:7542-7547. #=GF CC snoRNA R9 is a member of the C/D class of snoRNA which contain #=GF CC the C (UGAUGA) and D (CUGA) box motifs. R9 was identified in a #=GF CC computational screen in AT-rich hyperthermophiles [1]. R9 was #=GF CC found to overlap with the smaller snoRNA R19 which is currently a #=GF CC member of Pyrococcus C/D box snoRNA family Rfam:RF00095. #=GF WK http://en.wikipedia.org/wiki/Small_nucleolar_RNA_snoR9 #=GF SQ 5 #=GS #=GS #=GS #=GS #=GS. Pyrococcus_furiosus Pyrococcus_abyssi_GE Pyrococcus_horikoshi P.furiosus Thermococcus_kodakar. Pyrococcus_furiosus. AC AC AC AC AC. AE009950.1/163991-163864 AJ248283.1/230575-230449 BA000001.2/215834-215709 AF468960.1/1-128 AP006878.1/47908-47779. 23. Stockholm. GGGCCCGGUU.CCCGCCCUCUCCGGGGAAUCGUGAACCGG.

(25) #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF #=GF. DR DR RN RM RT RA RL CC CC CC CC CC WK SQ. GO:0006396 GO:RNA processing GO:0005730 GO:nucleolus [1] 12032319 Noncoding RNA genes identified in AT-rich hyperthermophiles. Klein RJ, Misulovin Z, Eddy SR; Proc Natl Acad Sci U S A 2002;99:7542-7547. snoRNA R9 is a member of the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. R9 was identified in a computational screen in AT-rich hyperthermophiles [1]. R9 was found to overlap with the smaller snoRNA R19 which is currently a member of Pyrococcus C/D box snoRNA family Rfam:RF00095. http://en.wikipedia.org/wiki/Small_nucleolar_RNA_snoR9 5. #=GS #=GS #=GS #=GS #=GS. Pyrococcus_furiosus Pyrococcus_abyssi_GE Pyrococcus_horikoshi P.furiosus Thermococcus_kodakar. Stockholm - Rfam AC AC AC AC AC. AE009950.1/163991-163864 AJ248283.1/230575-230449 BA000001.2/215834-215709 AF468960.1/1-128 AP006878.1/47908-47779. Pyrococcus_furiosus Pyrococcus_abyssi_GE Pyrococcus_horikoshi P.furiosus Thermococcus_kodakar #=GC SS_cons #=GC RF. GGGCCCGGUU.CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGAC GGGCCCGGCU.CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGGC CGGCCCGGUU.CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGAC GGGCCCGGUU.CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGAC GGGCCUGGCGUCCCGCCCUCCCCGGGGAAACGUGAACCGGGGCUUCCUGC <<<<<<<<<........<.<<<<<<<<<.....>>>>>>>>>>.....>> gGGCCCGGcu.CCCgCCCUCUCCGGGGAAUCGUGAACCGGGGGuUCCggC. Pyrococcus_furiosus Pyrococcus_abyssi_GE Pyrococcus_horikoshi P.furiosus Thermococcus_kodakar #=GC SS_cons #=GC RF. CGGGCCCACA..AUGGGAUGAUGACCUUUUGCUUUACUGAACACAUGAUG CGGGCCUACA..G..UUAUGAUGAACUUUUGCUUUGCUGAUGUGGUGAUG CGGGCCGACA..GG.GGAUGAAGAGCUUUUGCUUUGCUGAGCAGAUGAUG CGGGCCCACA..AUGGGAUGAUGACCUUUUGCUUUACUGAACACAUGAUG CAGGCCUACACCGGGGGAUGAAGAGCUUUUGCUUUGCUGAC..UGUGAUG >>>>>>>........................................... CGGGCCcACA..auguuAUGAUGAaCUUUUGCUUUaCUGAagagaUGAUG. Pyrococcus_furiosus Pyrococcus_abyssi_GE Pyrococcus_horikoshi P.furiosus Thermococcus_kodakar #=GC SS_cons #=GC RF. ACCACGCCCUUCGCUGAC.CUAAAUAUUUGAC AGCACGCCCUUCGCUGAUACUCUCUCGUCCAU ACCACGCCCUUCGCUGAC.CU.GCUAUUUGAC ACCACGCCCUUCGCUGAC.CUAAAUAUUUGAC AGCACGCCCUUCACUGACCCCGUAUCAGCUCU ................................ AgCACGCCCUUCGCUGAu.CUaaaUauUugAu. //. Stockholm 24.

(26) Stockholm - R2R RF00065_seed 4 nt A G G G G C C Y C U C 7-8 nt. R2R. K-Loop. RF00065_seed RF00065_seed Pyrococcus_abyssi_GE RF00 RF00065_seed Pyrococcus_abyssi_GE RF00065_seed Pyrococcus_furiosus 30 4 nt. RF00065_seed Pyrococcus_abyssi. RF00065_seed 4 nt A G G G G C C Y C U C. U G A A C C G G G G. K-Loop. A G G G G C C Y C U C. U G A A C C G G G G. K-Loop 30. 5´. UCG AU C G U K-Loop A G U K-Loop A GA AG GG AA GG CA GG CC CG GC CC GG 8 bp 8 bp 20 UC G G 40 20 CU G G 40 U C G UC G U C CC G C C G UU 5´ guide sequence CG U 3´ guide sequence C 5´ guide sequence C C CC 3´ guide sequence CU C GC C UC G G U CA G 10 10 GG CC 50 CG GC 50 CC GG 99bp bp CC GG C G G C GG CC ANA box GG UC ANA box 5´5´ G CAACC AA. 30. UCG A U K-Loop A G 7-8 nt G A G A G C G C G C C G G Y 5´ A C A base pair annotations 67-70 nt C G 8 bp covarying mutations 20 U G 40 compatible mutations RF00065_seed Pyrococcus_horikoshiRF00065_seed Thermococcus_kodakar RF00 RF00065_seed Pyrococcus_horikoshi RF00065_seed Thermococcus_kodakar RF00065_seed skeleton-with-bp no mutations observed C G U CG A CG C G C A C C U G A U A GU A U C 5 nt nucleotide AU Gnucleotide AA GU U AG G A G U GG AA G A present G G A identity G A A 5´ guide sequence C G C GG CC3´ guide sequence G A C R 97% 75% GG CAN 97% G G C C G 90% 50% GC GCN 90% C C G C C CC GG C CC G G CU C G CC G G C G G 75% C U GN UC G C G G C G UC G U C G C C C C C C C U C U R U U connector length) C(zero G G CC G U G G C U CC U C U 10 CG C U G U C C G C C 50 C C G C C CC C C C C C U CU G C G C U G C GU G CU G C U G CG U A C G U A G C G C G C C G G C C 9 bp G C C G U C A G U A C G C G C G C G C ANA box C G G C G CC G C G C G G G C C G C Y G C G C G C G C G C G C G U ACA G U 5´ G C A C A C G 5´ ACA C G G C ANA 5´ ACA box 5´ ACA 67-70 nt G U RF00065_seed-ILOOP75 RF00065_seed-ILOOP85 RF00065_seed-ILOOP75 RF00065_seed-ILOOP85 subfam_weight=0.696064 subfam_weight=0.303936 5´ ACA 25 subfam_weight=0.696064 subfam_weight=0.303936 U G A A C C G G G G. 75% connector (zero length) variable-length region 5 nt Y R variable-length loop G C G C variable-length stem Y R C G C G modular sub-structure G C ANA box. 30. 30. K-Loop. Y G G Y C C G G G. 30. UCG A U K-Loop A G G A G A G C G C C G C G 8 bp 20 U G 40 C G U 7-8 nt 5 ntC C G U C U G Y R 5´ guide sequence C 3´ guide sequence G C C C G C C CU G Y R C G C G 10 G C G C 50 C G C G G C G C ANA boxC G 9 bp C G G Y 5´ ACA G C 67-70 G C ntANA box G U 5´ ACA. 20. 8 bp 40. 20 20. 30. 30. K-Loop K-Loop. K-Loop. 8 bp , 40 8 bp 40. 8 bp , 40. 5´ guide sequence. 5´ guide sequence. 3´ guide sequence. 10. 9 bp. Stockholm ANA box. 5´ guide sequence. 3´ guide sequence 3´ guide sequence. 5´ guide sequence. 50. 20. 10 10. 3´ guide sequence. 50. 10. 50 9 bp 9 bp. ANA box , 60. ANA box. 50. 9 bp. ANA box , 60. 5´ guid.

(27) C GA U K-Loop U CC G AU G 5´ guide sequence C GC A3´ guide sequence C GC A CU G C GG C 10 G C G C G C C50 G C G 8 bp C G C9 bpG C20 G U G 40 G CC G U G C C CANAGbox U GC U 5´ G ACA U. 5 nt. R C C R G G C C ANA box Y ACA 67-70 nt. Stockholm - R2R. C CC G 5´ guide sequence C C CU U 10 G G C C C G G 5´ guide sequence G 5´. G. A G U U G A guide sequence C 3´G A C G C G. A G C C 50 C C G 9 bp C G G 20 C U C CC C C GANA box CC ACA. C G G G G C. 8 bp , 40. U U C 3´ guide sequ C 5´ guide sequence C C 3´ guide sequence C C C C U _seed Pyrococcus_horikoshiRF00065_seed Thermococcus_kodakarRF00065_seed skeleton-with-bp UGC G CU G U A G C 50 30 30 10 G C 30 CG G C 4 nt A10 C 50 G C U G U A A U K-Loop K-Loop A U K-Loop C G A G C C G 9 bp U U G A G 9 bp G AC G C G G A A G A U K-Loop G AC G G C G A G CG C A G G A G CANA box , 60 G C G C G C G A G A ANA box G C G U C G 5´ ACA C G C G 8 bp , 40 C G G A G C ACA C G 8 bp C5´G. RF00065_seed. G C U G 40 C G C G U C G C U C C G U G Y sequence G ce C C 3´ guide C C C G CU G U U A C G C 10 G C 50 5 C7-8 G nt C G 9 bp Y R C G G C G C G C ANA box G C C G 5´ ACA Y R 20. _seed-ILOOP75C C =0.696064 G G C G C G G 5´. Y R. R2R 5 nt. RF00065_seed Pyrococcus_abyss. RF00065_seed-ILOOP75. nt. G C. C G U G C C C C CU 5´ guide sequence G C G U subfam_weight=0.696064 subfam_weight=0.303936 C 3´ guide sequence C C G 8 bp C C 70% 30% C 20 U G 40 U U GC G C G C G C G 50 G C C G 10 UGC C C C CC G C C C GU G 8 ntC C U A 7 nt C 5 nt9 bp C G U 5 nt G C C G C 5´ guide sequence C C C 3´ guide sequence CU G C U Y R G CANA box , 60 GC G C C G CG U G C CU G 5´ ACA C G 20. G RF00065_seed-ILOOP85 G subfam_weight=0.303936 C 30% C ANA box C G C C C C Y G ACA 8 nt 5 nt 67-70 ntC C C. UGC G. 26. RF00065_seed-ILOOP85. 10. 5´. G G C C C G G G. C C 50 G G 9 bp G C C ANA box U ACA. Stockholm.

(28) Pseudo-nœuds (pseudoknots) U C G A C U G. Définition: structure 2D. G C U G A C. U A. A U A A C A U A U U G G C G C U C A C G G U U U U G U C G C G C G C. d’acide nucléique contenant au moins 2 tige-boucle dans laquelle la moitié de l’une est intercalée entre les 2 autres moitiés de l’autre. Wikipedia 27.

(29) Pseudobase-Pseudoviewer. 15. 1590 1600 1610 1620 1630 # |123456789|123456789|123456789|123456789|123456 $ 1590 AAAAAACUAAUAGAGGGGGGACUUAGCGCCCCCCAAACCGUAACCCC=1636 % 1590 ::::::::::::::[[[[[[:::::(((]]]]]]::::)))::::::. 1. 47. PseudoViewer. A G G G C G G C U A C C A G G U A C U C C A A G C A A C A C G G U U A C A A C A C A C A C A A subs 28. Pseudobase.

(30) Représentations circulaires 50 40 S. C. U. G. G. G. C. A. A. C. A. U. U. C. C. G. W. A. G. G. 60 R. G. R. R. a. S. M. C. M. S. R. Y. a. G. a. G. G. Y. 30. 70. Y. U. Y. G. C. C. C. Y. a. C. c. C. U. U. C. C. G. C. G. R. U. c. 20. A c. 80. A. W. U. C. G Y. G a. C C. D K. A G. A K. g W. 10. M. S. G. S. Y. S. G. G. Y. W. W. S. M. C. M. G. R. G. W. g. g. 90. 1 101. VARNA. Vienna/DBN; Connect 29. jViz.RNA.

(31) Ribozyme HDV (RF00059) 50. 40 S. C. U. G. G. G. C. A. A. C. A. U. U. C. C. G. W. A. G. 60 G. R. G. R. R. a. S. M. C. M. S. R. Y. a. G. a. G. Y. U Y. 30. 70. G Y. G. C. C. C. Y. a. C. c. C. U. U. C. C. G. C. G. R. U. c 20. 80. A c. A. W. U. C. G Y. G a. C C. D K. A G. A K. g W. M. 10. VARNA. S. G. S. Y. S. G. G. Y. S. W. W. 1. 101 100. M. C. M. G. R. G. W. g. g. 90. Vienna/DBN; Stockholm 30. R2R.

(32) ARNr 16S (T. thermophilus) Secondary Structure: small subunit ribosomal RNA A A U G U U G C G C G C U GC CA A A G G C A C A AG U U G U CC A CGA GC G U CCCCG CCGUUA G CC CGG UU G UG G A A UGC G A CCGGGA GGA A C A GC G C A A UGCUCG GGGGA GGCA A UC GG GCC GG U G A G A G C U A A GGCCCUU GG A CG G G C U GGCG C C A AA G A U G U G G C G C G G C A U A A G A G C G C A GU U A C G G C G C U U G U A GA G C U U G C A G U G U G C U A C G A C G G G C A C C G G G A A G G C G C G UC C G G U C G A G C C G G C G G C G C C G C G G C U A C G A G A G A U A G A A A C G G U G C A GC C U GGG GU A U U G C A C A G C A C G C A C G C G C G C G U G G G C C CA A G U U U A U AG G A G C G G G G G A C G CU A GG C U A A A U UA U G C C C A C C G U G G GG GA G C G U G G G A C G C U C A G G C G C U A A A U A UC G C C G GC C C G C U C U C GGCA CCA G U A GUGUA CCCU G C GGGUCCGG C U C G C AG G G G C C C U G G A A G G A A A G C G G U A G C A G A U AU C G A U U CG A C GU C C UA C G C U G A C U G C C G C A G G G G U G A G G C G U G G G G A A U G G GCGCGC G CA A A C GCC A U G U CG A C CC A U A C G C U G A U A C C A A A A CGCGCG C UG G C C C G G C A C A G G A UG A G CG U A G C GA C G A G U A A C A C G G G U G C G G U A G GC C GA C A U G C U C G GA C G G C G G AAA G U G A U A A U C C U U C C CA C C G C A G U AA A GUA G G C A C G A C C G U A U C G U G G G A A GGCC U A C G C C GG C C A G A U U C G C AA G A A G A CAA G C G CUC G A A A UCGG A U U CC C U A A A G A C A G C G U A AU A A G A G G C C G A G G G G G G GG C G C G G CG G C A G A A A C G G C U U U G A C G GGGC C C G AC A G C C C A C U C C G C G GGU CC C A C A C U A CUC G G C A A A U A C U G U U C C G G G C UG GA U G C G G G G U A C A U C U C U U U GA G G U U A G C C A C U U A G G U G C A A G A A C G G C A U G A G GGGU CUCC G U A G C C A A G A G C A G A A G A U A C C A A G A G G U UGC G U CCCG G U U U U U G C A G G U C C U U G AGAA C C A G G G A G G G A G C G AC C C C G C G U U G G G C G C G G C U C G U A G C U G U A C C G A G C G C C A GCCUG CGGA G G G A U N U A C C U U U G A G C A C G C GUCGGCGUGG A C A GCC UC U G CGGGU G U A A G U U AAC 5’ G C A C GA G A C C A C G C C U A CA A C G C G C G A G C A G C C U G A UA C G U A U U G G C C U A G A C G CA A G U A U C G G U U A C G G C G U G A G C U C G C N A G C G A G C N C U G C C A C G CA CG GU A A U G GGC 3’ CCC GUC GCGGGCCGCGGGGU U C G G U U A A GU CA CGGGG A U CGG CGA CUGGUGCCUCA U G AG C G G G GA A G A C G U C C C G G G CG A UC G GC C A A UG G A G G C U G GC A G CG G C A U C A G U C G U G G C A G C G G GCA CU C G C G CG AC C C G A C G A G A G CU G U C G C A C G G A GC G C G G G C C G A C G U A G UG U G C U A A C C G CA U G A G G C C G U C U U A GC G A G G C G G C U G G C A A U C G C G U A U A C G A CA A G G G GG G A CCCGGG G U GCCC A U A CCCC CGGGCUC A U CGGG U C A A UAA U A G A U C G C G U A G C U C G C U G G C G C G C G C U U. Thermus thermophilus (X07998) 1.cellular organisms 2.Bacteria 3.Thermus/Deinococcus group 4.Thermus group 5.Thermus September 2001. jViz.RNA. Vienna/DBN; Connect. Citation and related information available at http://www.rna.icmb.utexas.edu. 31.

(33) Structures 2D alternatives RIBOSWITCH. conformation 1 (ON). Arc. graph. 50. 60. 90. 100. A C U U G U A U A A C C U C A A U A A U A U G G U U U G A G G G U G U C U A C C A G G A A C C G U A A A A U G G U G A U U A C A A A A U U U G U U U A U G A C A U U U U U U G U A A U C A G G A U U U U U U U U 1. 10. VARNA. 20. 30. 40. 70. Vienna/DBN 32. 80. conformation 2 (OFF). 104.

(34) The basic RNAbows tools are extensible to represent any data set with varying coupling strengths and then to highlight differences between conditions. The difference RNAbow juxtaposes arcs and highlights differences with color. The recent. Probabilité de structures 2D mutations, données d’accessibilité with chemical mapping data. base pairing 1. GGaCUCGGCUUGCUGaaGCGCGcACGGCAAGAGGCGAGGGgCGGCgACUGGUGAGuACGCcaaaaAUUUUGACUAGCGgAGGCUAgaAGgAgAgAC GGACUCGGCUUGCUGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAC. base pairing 2 HIV 5' UTR. RNAbows Aalberts & Jannen, RNA, 2013 FIGURE 3. Chemical mapping experiments indicate which bases are 33.

(35) Pseudo-nœuds 88. A. A G C C G C U A C G C G C G A U A G C A C G A G C G A C G U C G C A U G U A C U A U U U C G C G C G C G U G C G C A A U C G G C G C G C G C G C C G G C C G A U G C C CG G U 1 U. B. C. jViz.RNA. PseudoViewer D. U G G C C G G C A U G G U C C C A G C C U C C U C G C U G G C G C C G G C U G G G C A A C A C C A U U G C A C U C C G G U G G U G A A U G G G A C 1. 10. 20. 30. 40. 34. 50. 60. 70. 73. VARNA.

(36) e geometric families, their abbreviations and symbols annotating them in secondary structure diagrams are en in Table 1. To specify a base pair it is necessary to e the base combination (e.g. AU, GU, AG, etc.), as well he geometric family. Thus, cWW UA and tWH UA are erent base pairs even though they entail the same base mbination, UA. Analysis using FR3D (7) of the 3D rRNA structures the 70S ribosomes of E. coli and T. thermophilus and 50S subunit of H. marismortui shows that !59% of bases form canonical WC base pairs, including 7%. pairs. Thus, a significant fraction (27%) of rRNA bases form non-WC base pairs. Furthermore, Table 2 shows that most of the remaining bases, none of which form base pairs, interact with other nucleotides through basestacking or base-phosphate interactions.. Appariements & nomenclature Base pair exemplars and online base pair catalog. To compare base pairs between and within geometric families, we have identified a single representative, called the exemplar, for each base combination (i.e. AA, AC, AG, . . ., UU) that makes a pair in a given geometric. Table 1. The 12 geometric families of RNA base pairs. Downloaded from http://nar.oxfordjournals.org/ at INIST-CNRS on February 22, 2012. Lentos & Westhof, Curr. Opi. Struct. Biol., 2003. Figure 3: Leontis-Westhof nomenclature of RNA base pair interaction types. On the left an example of an RNA base (blue) interacting through each of its 3 edges with 3 other nucleotides illustrating the possible interaction geometries. The right hand side shows a schematic representation with the corresponding graphical notation. minimization procedure to produce a refined structure. The computational efficiency of this method is limited greatly by the of 2009 structural Stombaugh et knowledge al., NAR, constraints Each geometric base pair family is defined by the interacting edges of the bases and the relative orientation of the glycosidic bonds (columns 2-4). Abbreviations and symbols for representing each base pair family in text and secondary. 35. however, MC-Sym was still able to recreate pseudoknotted and.

(37) Motifs ARN & fonction(s) flexibilité nucléotide(s) non appariés, appariements non canoniques. structures et “formes” 3D appariemments canoniques/non-canoniques & sillons. interactions: ARN-ARN, ARN-protéine, ARNligand, … régions simple/double-brin, formes et contacts 36.

(38) Bulges: flexibilité & interaction. Hermann & Patel, Structure, 2000 37.

(39) The secondary structure and constraints for the wild-type RBE determined by covariation of nucleotides among different aptamers are shown on the left. The sequence numbering used is the same as in Giver et al. [4]. Lines between nucleotides indicate Watson–Crick base pairing and dashed lines represent non-Watson–Crick pairing. The primary sequence and secondary structure of the oligonucleotide used in the structure determination study by Battiste et al. [7] are shown on the right. The region of sequence identity is referred to as the core region and is in bold.. energy levels. The compar electrostatic solvation ener their total conformational e only 0.01% (Table 1). The overall energy values are limits of the methodology [9. Appariements & sillons were particularly dissimilar. Figure 3a shows that the deviation of the base moieties of individual nucleotides is. Geometric comparison. Notable geometric differen son of the two structures: t the interproton distances i regions, which were rema NOE values [7]. As seen i. appariements non-canoniques et ouverture du grand sillon Figure 2. The majo A helix (le (middle) SYM (rig using the sequenc NMR stru of nucleo used to c with Wat. petit sillon. grand sillon. appariements NWC. A helix. ⟨JB⟩ structure. ⟨FL⟩ structure. ARN de liaison à la protéine Rev (VIH-1) Leclerc et al., Nat. Struct. Biol., 1994; Leclerc et al., Fold. Des., 1997 38.

(40) on August 6, 2013 - Published by Cold Spring Harbor Laboratory Press. Motifs récurrents. Automated motif extraction and classification. s:. (C-loops, Kly clustered;. bers within a. ngs (Leontis d the same ui 50S (pdb nd Thermus. Djelloul & Denise, RNA, 2008 39.

(41) Motifs ARN 3D & “formes” bioRxiv preprint first posted online Sep. 10, 2019; doi: http://dx.doi.org/10.1101/764449. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.. Watkins & Das, 2019. 1 2. 40 and FARFAR2-Motifs (F-I) benchmarks Figure 2. Cases from the FARFAR2-Classics (A-E).

(42) !"#$ %$ A$-'%!(+F &<+.-<.+$ !"(4+(#& '* <9$ $"49< :;<.+%& *'.%! "% <9$ !"#$%&'#(%)*& PVA (%! -").+%#(/.&,*' @VA &.0.%"< &<+.-<.+$& (%! ( !$+"1$! -'%&$%&.& &$/.$%-$7 89$ %(#$& "%!"-(<$ O9"-9 9$)"= $(-9 $=(#E)$ '* <9$ #'<"* "& *'.%! "%, (--'+!"%4 <' <9$ 9$)"= %.#0$+"%4 &-9$#$ '* X$**$+& +) $,7 25MK>67 A')"! )"%$& +$E+$&$%< H(<&'%IG+"-J E("+"%4& 0$<O$$% 0(&$&, (%! 0)(-J !'<& +$E+$&$%< #"&#(<-9$! 0(&$ E("+"%4&7 Y$))'O &9(!"%4 "%!"-(<$& %.-)$'<"!$& <9(< -'%*'+# <' <9$ !$+"1$! -'%&$%&.& &$/.$%-$7. #'<"*7 A<(0")"R$! 0F ( 9F!+'4$% 0'%! 0$<O$$% <9$ E+'2A6 E9'&E9(<$ '=F4$% '* DMP (%! <9$ ?!;ST '* DMQ, <9$ E9'&E9(<$ 0(-J0'%$ J"%J& 0F U5?V"7 LM> "% <9$ CG;&<$# *'+#& ( %'%;E)(%(+ &9$(+$! 0(&$ E("+ O"<9 DKV, O"<9 LM> (EE+'(-9"%4 DKV (< (% (%4)$ '* UPV"7 DMK &<(-J& 0$%$(<9 DKV (%! E("+& O"<9 L>M, 4"1"%4 +"&$ <' ( -+'&&;&<+(%! (!$%'&"%$ &<(-J (%! ( <FE$ W D;#"%'+ "%<$+(-<"'% 2C"&&$% +) $,7, ?VV567 D% (!!"<"'%() LID E("+ 2L>KIDMM6 -'%; <"%.$& <9$ -'(="() &<(-J 0$*'+$ H(<&'%IG+"-J 0(&$ E("+"%4 "& +$&<'+$! O"<9 L>>IG5VV7. Motif Kink-turn (K-loop). Klein et al., !"#$ &$ A<+.-<.+$ '* :8;>7 2'6 A$-'%!(+F &<+.-<.+$ O"<9 +$&"!.$& "% <9$ G;&<$# )(0$)$! +$! (%! <9$ CG;&<$# 0).$7 89$ 0.)4$! %.-)$'<"!$ "& 4+$$%7 2(6 A-9$#(<"- +$E+$&$%<(<"'% '* <9$ +$)(<"1$ 0(&$;&<(-J"%4 (%! E("+"%4 "%<$+(-<"'%&7 D 0)(-J <+"(%4)$ +$E+$&$%<& (% D;#"%'+ "%<$+(-<"'%7 2)6 89+$$; !"#$%&"'%() +$E+$&$%<(<"'% '* :8;> O"<9 <9$ E9'&E9(<$ 0(-J0'%$ '* <9$ J"%J$! 41 &<+(%! "% '+(%4$ (%! <9$ .%J"%J$! &<+(%! "% F$))'O7 TF!+'4$% 0'%!&. EMBO J., 2001.

(43) ARNr 16S. 3, No. 8. Secondary Structure: small subunit ribosomal RNA A A U G U U G C G C 1100 G C U GC C AA 700 A G A C U A G UG AG U A CGA GC CCUUA UCCUUUGU CC CGG UC CC G G U G G A GA G A A UGC C A UCUGGA G AU G GC G A A U G C U C G G G G G U A G G A A A C GG GCC GG U G A G UC AA A G A A U U UGGA CCUU GA G CG G U GGCG G AA A U G 1150 G U G A U C G A A G C U A G A G C G C A GU G C C G G C G C U U G U A GA G C G C A G U U A G U G C U A A 1200 U A G C G G C U C G A C U A A G G UC U G G C C G A U A C G G C G CU A U G C C G A U A U A G C G A G A C G A A U A U CG U A U G 800 A A A UGA GA A U G C G G U U A G 2 C 1050 C U A G [m G ] C A A A G G C 750 G C C G G A C U U U U G AA G U A U A U G U G AG G C G C G G G G C A A GG 650 U C C U C A U A UA U A C G C C 1000 U UGCA UCUGA CU GGCA A G C A U A C A A CCUGGGA A U C UU G C C G C C G C U G A C U C GGGCCCC C G C G U U A GU GU A GA C U GA U U GU U U GG C C G C GU G C A C G C A U A A A G G G C G A G A A U 600 G A G U A A G AC C G A CUU U U C C C G A G GC A U G A U A G C C G C G A G G G G G 850 A G C C C G UA G U G A G C CG U U U GU C GA CUU A U GCC A A AC U A C ACC G A U A UU G C A A C C G G G A G A C U m7 A A A G C U U CA GCUG C C G G C G C UG A A G U C UG G A A A U A C G C U A G A G C G 1250 G U G A A C G A C G A G UG C A A C G C A U 5 A C 950 U G C U U AAAG G mC 2 U C U G mG G G CA U A U A C C C A G G U U U U CA GU CA G C A A A C C A A G G G G C G C U A U A A ψ A U GGG GGCC G A G U CA G U CGU C C G A U G G A G C G U C A 900 U A A A A G A G CA A G C G CUC UUGG A U GG A C C AAAA G A U A C G U A 450 A A U A C G G U AC A G G G C G G UG C G G C C G G A A A G G A CG G C U U UG A CG GGGCCCG A CA A G C U C A G C G U G C G G G A U A 500 A C CU C U A A C U A A G A U G 550 A C A C U G U U C C G G G C U G G G C G A U A G U 1300 U C A U U U GA C U C U U A G U G C C AG C UAA C G A U G A U C G A A U G U A C A G A U G GGUU GUA C G A G A C C A A G A A 10 C A 1350 G A A A G U 1400 C C G G U A A C U UAUG U CCGG U G U U U G C C A G 400 G C U G 4G U U AGAA G C G G A G mC m A G G A C U A G AU C C C G m3U G G A 2 G A C m C C G G G A C C A C 1500 U A A C C G U A G G A G A U A GCCUG A UGC A G C G G C U G A C U U U G G m6A C A 5C 2 C G G U U G G C G U C C C 5’ m 6 U A C G UA A U G CGGGU G A mA A G 2 A A G U U A AAC G C C G A A C U A U U A C A A C G C G C G A G C C A G C G UA 50 C U G U G U G CA C G C U A C G A G CA U A G A U C G U G U A C G G 350 A U A G A G C U C A G G C C G A C G U 3’ U G U C A C U A CA G GA AA A GUC A U G CAG GUC A CG GU CA G GA A GA A GC G G U U 300 A C G U GU C A A G G U CGG UGA CA GUC UUUCUUCG A U C G AG G G A U G A G A G A AU C A U C G G 100 C A A UC C AG A C UG G C G C A G G U A GU G C CG A A G C A G U U A U C A U A C A G U C GU GU G C G A CG AU U G U G A C G A A G UU G C U A C C G G C G A U G G G C G U G C G C A A U U G A A A A C A C G UG C A U A C G A 250 G G C C G U G 1450 U U U U U C G GC G A G G C G G C C G G U A A U C G U A 150 A U C G C G U GA A A A G CUACUGG GGGG G GG CCUCUU A C G C - Canonical base pair (A-U, G-C) A U CGCC CGA UGGC A U CC GGGGA G A G U A U - G-U base pair A AG UA A U 200 A A G A - G-A base pair A A C C C G U U - Non-canonical base pair A U G C G A Every 10th nucleotide is marked with a tick mark, A C. II. III. I. Figure 3. Annotated secondary structures of Kink-turn motifs from crystal structures, comparing structural variants to the typical Kink-turn, exemplified by KT-7 from archaeal 23S rRNA. Each characteristic base pair is framed in a different color: The last base pair of the C-stem in orange (base pair 1), the two trans-H/SE base pairs of the NC-stem, base pair 2 in red and base pair 3 in purple, and the two trans-SE/SE, base pair 4 in blue and base pair 5 in green. Each tertiary interaction is represented by a unique symbol indicating the interacting edges of the bases and whether the pair is cis or trans (3).. pair 4 (blue). Even more variation is displayed by the third base pair of the NC-stem, which does not participate directly in K-turn interactions. It is therefore not discussed any further. Besides variations in base-pairing geometry, K-turn structures exhibit variations in the number of nucleotides in the internal loop. Thus, H.m. 23S Kt-38 has one extra nucleotide in the longer strand, which bulges out just above the NC-stem.. This is the most common point of insertion. Bases inserted here have very little effect on the 3D structure of the motif. Insertions also occur in the shorter strand, e.g. 23S Kt-15 (A248), 23S Kt-58 (A1591 and G1592) and 16S Kt-11 (U244 and C245). Unlike the insertions in the longer strand, these usually participate in additional base pairs, as shown in Figure 3.. Escherichia coli. (J01695) 1.cellular organisms 2.Bacteria 3.Proteobacteria 4.gamma subdivision 5. Enterobacteriaceae and related symbionts 6. Enterobacteriaceae 7. Escherichia November 1999 (cosmetic changes July 2001). Symbols Used In This Diagram:. and every 50th nucleotide is numbered.. Tertiary interactions with strong comparative data are connected by solid lines.. 42.

(44) Motifs 2D K-turn Nucleic Acids Research, 2005, Vol. 33, No. 8. Figure 3. Annotated secondary structures of Kink-turn motifs from crystal structures, comparing structural variants to the typical Kink-tu from archaeal 23S rRNA. Each characteristic base pair is framed in a different color: The last base pair of the C-stem in orange (base pair 1), pairs of the NC-stem, base pair 2 in red and base pair 3 in purple, and the two trans-SE/SE, base pair 4 in blue and base pair 5 in green. Ea represented by a unique symbol indicating the interacting edges of the bases and whether the pair is cis or trans (3).. pair 4 (blue). Even more variation is displayed by the third base pair of the NC-stem, which does not participate directly in K-turn interactions. It is therefore not discussed any further. Besides variations in base-pairing geometry, K-turn structures exhibit variations in the number of nucleotides in the internal loop. Thus, 43 H.m. 23S Kt-38 has one extra nucleotide in. This is the most common point of inserti here have very little effect on the 3D stru Insertions also occur in the shorter stran Lescoute et al., (A248), 23S Kt-58NAR, (A15912005 and G1592 (U244 and C245). Unlike the insertions in these usually participate in additional base.

(45) Motifs K-turn & interactions !"# $%&$'()*&+ , &#- ./0 1#23&4,*5 1(*)2()*# 63(%7. !"#$ %$ I&88)+ !"(!"*"+%$%&)+* &+7&1$%&+2 %-" *%!91%9!$# 7&'"!*&%4 ), (!)%"&+K>3%9!+ 1)/(#"="* ,)9+7 &+ %-" *%!91%9!" ), %-" !"#$%&'#(%)*& YPE *989+&%; et al., EMBO T&V ]H? $+7 ]H^ &+%"!$1% .&%- )(()*&%" *&7"* ), ><3O; T'V J"#&1$# ,!$2/"+%* ), ]BP 8&+7 %) %-" 89#2"7 +91#")%&7" &+ ><3?H; T(V Klein ]B^" $+7 ]CO6" /$:" #&/&%"7 &+%"!$1%&)+* .&%- ><3YD; T)V <-" !3"=%"+*&)+ ), ]? &+%"!$1%* %-!)92- %-" .&7"+"7 /$_)! 2!))'" ), ><3?@`* A3*%"/0 .-&#" ]CH" 44 ><3BY .&%- %-" /$_)!&%4 ), &+%"!$1%&)+* &+')#'&+2 -47!)(-)8&1 !"1)2+&\"* &%* :&+:"7 8$1:8)+" $+7 (!)%!97"7 8$*"; T*V ]O6" $+7 ]BY" *9!!)9+7. J., 2001.

(46) Données phylogénétiques R2R. Stockholm; Vienna/DBN. New Hamm. VARNA*. 2D representation (3D). 2D representation. New Hammerhead Ribozymes. New Hammerhead Ribozymes. conservation Perreault et al., PLoS One, 2011. Leclerc, Molecules, 2010 45. * post-processing.

(47) Le ribozyme à tête de marteau. New Hammerhead Riboz. HHR New Hammerhead Ribozymes. New Hammerhead Ribozymes. R2R 46.

(48) Diagrammes Arc covariations, conservation R-Chie 0. 10. 20. Conservation RFAM: RF00065. 30. 40. Covariation. 50. 60. 70. One−sided. Stockholm 47. 80. Invalid. 90. 100. 110. Unpaired. 120. 130. Gap.

(49) Structures 2D conservées. Stockholm 48.

(50) Alignements CLUSTALW. Stockholm 49.

(51) ARN à boîtes C/D RNAz, RNAalifold. D box. _. _. _. _. A AU. CUA AC AAA U. U. U. U. C. A G A A G C U U U G A C A A A A G GG A A C A _ U C C G U C U UC A G A A C C U U GG A C A AA UA C A C’ box A U U U C A C A CCA CG U G A U C GG A U GU A D’ box C A GAA U AU U A A AU U C U GC U U GC U U U C AU AG UC UUA UA C box UU G C C U A Energy = -23.1 kcal/mol A UC. Clustal; Vienna/DBN. 50.

(52) Diagrammes Arc covariations, conservation R-Chie 0. 10. 20. Conservation RFAM: RF00065. 30. 40. Covariation. 50. 60. 70. One−sided. Stockholm 51. 80. Invalid. 90. 100. 110. Unpaired. 120. 130. Gap.

(53) ARN à boîtes C/D RNAz, RNAalifold. Pab C/D sRNA sR1 5’. interORF_Pyro_hori_397 interORF_Pyro_abys_654 interORF_Pyro_furi_347 ruler. C box. D’ box C’ box. D box. 3’. ......(((......((((((.(((((.(((........))).))))).))))))....))). AAAGAAGGCGAUGAUGAAGCCUUCCGCACCUGAAUGAUGAGGAGUGGACGGCUUCCUGAGCCU 63 AUAAAUGGCAAUGAUGAAGCCUUCCGCACCUGAACGGUGAGGAGUGGACGGCUUCCUGAGCCU 63 AGGUAAGGCGAUGAUGAUGCCUUCCGCACCUGAUUGGUGAGGAGUGGACGGCUUCCUGAGCCU 63 ........10........20........30........40........50........60... A AA. Energy = -24.6. A A U AGC GC CG A G G D box A U U C C box GA C UG AU AU GC CG C GC U A U CG kcal/mol CG GU C GA A G C CG UAG U G G A D’ box A U G. 52. C’ box. Clustal; Vienna/DBN.

(54) ARN à boîtes H/ACA RNAz, RNAalifold Pho21_215834-215776_-__ Pfu21_163991-163933_-__ Pab21_230575-230517_-__. Pab-21 H/ACA sRNA ((((((((((...((((...((((...........))))))))...))))))))))... CGGCCCGGUUCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCGACA GGGCCCGGUUCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCCACA GGGCCCGGCUCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGGCCGGGCCUACA A C A ACA box GC GC GC CG stem 1 CG CG GC GC UA C U GC C C internal loop C G UU CG CG UC G stem 2 C U CG CG Energy = -35.1 GC GC G A G A G K-loop AA U UCG. 53. kcal/mol. Clustal; Vienna/DBN.

(55) ARN à boîtes. n (H/ACA). K-loop K-turn. SSU 891 internal loop. Pab-21 1 motif. Pab-40 3 motifs. Pab-105 2 motifs 54.

(56) ARN à boîtes. 2 (H/ACA) Pab-105 H/ACA sRNA. Pab105_1335797-1335648_-__ Pho105_592081-592230_+__ Pfu105_942696-942544_-__ ruler. ((((((((....(((......))).(((((((......)))))))...((.((......)))).))))))))...(((((((((.((((...((((((.....((((......))))... CCGCCCGGA-GGCCCGACCGAGGGAGCGUGCCGAGAAAGGCGCGCCAUGAACGAGGCGACGUCGCCGGGCGGACAGGGCCCGGUCUCCGGGGCCGCCUGAGGUUGCCGACAACGGCGGGC 119 CCGCCCGGG-GGCCCGACCGAGGGAGCGUGCCGAGAAUGGCGCGCAAUGAACGAGGUGACGUCGUCGGGCGGACAGGGCCCGGUCUCCGGGGCCGCCUGAGGUUGCCGAGAAUGGCGUUC 119 CCGCCCGGGCGGCCCGACCGAGGGAGCGUGCCGGCAAUGGCGCGCGAUGAACGAGGUGACGUCUCCGGGCGGACAGGGCCCGGCCUUCGGGGCCGCCUGAGGGAGCCGAGAAGGGCAGAC 120 ........10........20........30........40........50........60........70........80........90.......100.......110.......120. Pab105_1335797-1335648_-__ Pho105_592081-592230_+__ Pfu105_942696-942544_-__ ruler. .....)))))).))))...)))))))))... AAUGAGGGCGGGUGGAUAAGCCGGGCCUAUA 150 AAUGAAGGCGGGCGGAUAAUCCGGGCCUAAA 150 GAUGAAGGCGGGCGGAUAAGCCGGGCCCUCA 151 .......130.......140.......150.. C G. C A. G internal loop C K-turn AG AUA box A G C G C C G U G G CGG _ C AA A G G G C G C GAG A GGCCCGCC GC A U A UCCGGG U A AC CCGGGCGG C C GA AUA G G AU A GGGCCC GGC A G G G G G U C G A GGA G UCCG A C C A A C C G C G GC A C U GGG C G C C U A A G G UGCC ACA box G G C G AG A G GU G A UG. terminal loop. terminal loop. Energy = -75.8 kcal/mol 55. Clustal; Vienna/DBN.

(57) 3 (H/ACA). ARN à boîtes Pab-40 H/ACA sRNA Pab40_382389-382599_+__ Pho40_1597422-1597634_+__ Pfu40_1732713-1732926_+__ ruler. ((((((((...((...((((((((...........)))))))).))..))))))))....((((((((....(((((...)))))..((((((((.(((.(((((((....))))))))) GCCCCCGCAAGCGAGGGCCUGGUCGA--UUAGUGAGACCAGGUGCGACGCGGGGGCUACAGCCCGGCCUCAGCGAGGUCCCCUCGGUAGGUGCCUUCCGCGUCACGGAGCGCCGUGACCG 118 GCCCCCGCAAGCGAGGGCUUGGCCGAGCUUAAUGAGGCCAGGUGCGACGCGGGGGCGACAGCCCGGCCUUAGCGAGGUCCCCUCGGGAGGCGCCUUCCGCGUCACGGAGUGCCGUGACCG 120 GCCCCCGCAAGCGAGGGCUUGGCUGAUCUUAAUGAGGCCAGGUGCGACGCGGGGGCAACAGCCCGGCCUCAGCGAGGUCCCCUCGGGAGGUGCCUUCCGCGUCACGGAGUGCCGUGACCG 120 ........10........20........30........40........50........60........70........80........90.......100.......110.......120. Pab40_382389-382599_+__ Pho40_1597422-1597634_+__ Pfu40_1732713-1732926_+__ ruler. ))))))..)))))))))))...((((((((((.....((((((((.(((..((......))...)))..))))))))....))))))))))... GGGGUAACCCUGGCCGGGCACAGGCCCGUCUGGGUUAGCCCGCCUGAUCAUGC-CGUUGGCUUAGAUGAAGGCGGGUGUUACGGGCGGGCUACA 211 GGGGUAACCCUGGCCGGGCACAGGCCCGUCUGGGUUAGCCCGCCCAAUUUUGC-CGAGGGCUUAGAUGAGGGCGGGUGUUACGGGCGGGCCACA 213 GGGGUAACCCUGGCCGGGCACAGGCCCACCUGGGUUAGCCCGCCUGAGAAUGCAUACAUGCUACGAUGAGGGCGGGUGUUACGGGUGGGCCACA 214 .......130.......140.......150.......160.......170.......180.......190.......200.......210..... K-loop. U A A U. UC_. A G C GA A G G G A GC G U UC G A C C G GC _ C U G A A U AGU U A A U G C G G G G A G G A U G CU G G GC C G C CGA U G GG CG G A U U CC C A A G C G G A C C C G G U G C G G CU GGU G C C G C GG GU G C AC A CG CC G G C C C GG A A A C C A GC A CG CG CG GC GC CG CGACU G GG C G GA U A C G U GC U GC C G CC C C U AA GU CG CG UG UC G CG GC CG C UA CG AU CG GC GC G A G U. K-turn. internal loop. ACA box3. internal loop. ACA box1. ACA box2. Clustal; Vienna/DBN. 56.

(58) Comparaison 2D. arbre de proximités entre structures 2D. RNAforester. Vienna/DBN 57.

(59) Graphes (((((((..((((........))))((((((.......))))))....(((((.......))))))))))))..... tRNA u. G. 10. A. u. U. G. C. C 1. G. G. C. G. U. A. U. U. A. U. A. A. C. C. Root. A 76. GC. 70. A. C. C. A. CG GC. 60. A. C. U. GU. C. U. C. g. G. A. C. A. C. a. G. A. G. C. c C U. U. G. U. G. C. G. G G. G. A. 20. 30. g. A G g. C. G. C. G. A. U. G. c. A. P. UA 40. c. A g A. AU. P. UA. U g. u 50. U. A. gC. gA. CG. G. g. U. C. CG. cG UA. A. UA CG A. G. u. u. G. G. G. A. CG. GC. AU. UA. Gc. GC. AP. VARNA. c. 58. U. g. A. u A. P g. C A. G. a. U. C. Graphiz (RNAView).

(60) Empreintes B. C. 30 U. C. 20. C. C. U. G. A. A. G. G. A. G. A. G. A. G. A. G. C. G. C. G. C. G. C. C. G. C. G. C. G. C. G. U. G. U. G. C U C. G. C U C. G. occus abyssi GE5 VARNA. 20. 40. U. C U. C. 10. G. G. U C. C C. G. 10. C U. C. G. G. C. G. C. G. C. G. C. C. G. C. G. C. G. C. G. C. G. C. G. G. C. G. C. G. C. G. C. G. U. A. G. U. 59. 1. 1. 50. A. C. 59. G. 50. A. C. A 59. 0.0. 30. U. C. C C. C. 40. G. C. U. U. G. C C. G. A. G. 3' guide sequence. C. A. U. G. chimiques, enzymatiques. 30. 30. 3.0. Vienna/DBN.

(61) Données A. C. functional annotation 20. C. C. Kloop. G. A. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. H/ACA guide RNA (Archaea). U U. C. Internal Loop. C. C C. Kloop. 40. G. 3' guide sequence. C U. 10. VARNA RFAM: RF00065. B. 30 U. 5' guide sequence. 1 fonctionnelles. 5'. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. 5’ guide sequence. 3’ guide sequence. 50. ACA box ANA Loop A. C. A 59. 3'. 60.

(62) Données A. C. functional annotation 20. C. C. Kloop. G. A. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. H/ACA guide RNA (Archaea). target sequence U U. C. Internal Loop. C. C C. Kloop. 40. G. 3' guide sequence. C U. 10. VARNA RFAM: RF00065. B. 30 U. 5' guide sequence. 2 fonctionnelles. 5'. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. 5’ guide sequence. 3’ guide sequence. 50. ACA box ANA Loop A. C. A 59. 3'. 61.

(63) Données A. C. functional annotation 20. C. C. Kloop. G. A. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. H/ACA guide RNA (Archaea). Internal Loop. Nop10. U U. C. C. C C. L7Ae. 40. G. 3' guide sequence. C U. 10. VARNA RFAM: RF00065. B. 30 U. 5' guide sequence. 3 fonctionnelles. 5'. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. Cbf5. 50. ANA Loop A. C. A 59. 3'. 62.

(64) Modifications d’accessibilité 1. RF00065 Pyrococcus abyssi RF00065 Pyrococcus abyssi GE5GE5. B. D. 30 U. C. G. A. 20. C. C. U. U. A. G. G. A. G. A. G. A. G. A. G. A. G. A. G. C. G. C. G. C. G. C. G. C. G. C. C. G. C. G. C. G. C. G. C. G. C. G. U. G. U. G. U. G. C U C. G. C U C. G. C U C. G. G. 40. 20. U. C. G. G. C. G. C. C. G. U. C C. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. C C. G. C U. G. C. G. C. G. C. G. C. G. G. C. G. C. G. G. C. G. C. G. C. G. C. G. C. G. C. A. G. U. A. G. U. A. G. U. 59. 1. 59. 1. 59. 1. G. C. G. C. C. G. G. C. G. C. G. C. G. U. G. C. G. C. C. G. C. 50. 10 50. A. C. 10 50. A. C. U. C. C. C. 10. 40. U. G. G. C. 30. G. G. G. 1. A. C. G. G. C. C. U. C. C U. G. G. C C. G. C U. C. C. A. U. C. VARNA. E. G. 20. 40. C. C U. C. C. A. G. C. C. G. C. U. G. C C. C. 20. 40. U. U. G. C. GE5. A. U. 3.0. 30. G. A. C. 10. C. G. U. U. U. G. 0.0. F. 30. A. C C. C. A. G. ence. E. 30. 59. G. 50. A. C. A 59. Vienna/DBN 63.

(65) Données B. 30 U. C. G. A. accessibility annotation 20. C. C. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. 40. U U. G. guide sequence. C. C. C C 10. VARNA RFAM: RF00065. 1 d’empreintes. C U. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. 50. RNA accessibility A. C. A 59. 64.

(66) 2 RF00065 Pyrococcus abyssi GE5 Données d’empreintes 1. D. 59. 30 U. C. G. A. accessibility annotation 20. C. C. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. 40. U U. G C. C. C C 10. VARNA RFAM: RF00065. C U. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. 50. more accessible A. C. A 59. 65.

(67) Données. abyssi GE5. E. 30 U. C. G. A. accessibility annotation 20. C. C. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. 40. U U. G C. C. C C 10. VARNA RFAM: RF00065. 3 d’empreintes. C U. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. 50. less accessible A. C. A 59. 66.

(68) Données 0.0. F. 3.0. 30 U. C. G. A. accessibility annotation 20. C. C. U A. G. G. A. G. A. G. C. G. C. C. G. C. G. U. G. C U C. G G. 40. U U. G C. C. C C 10. VARNA RFAM: RF00065. 4 d’empreintes. C U. C. G. G. C. G. C. C. G. C. G. C. G. G. C. G. C. G. U. 1. G. 50. A. C. A 59. 67.

(69) Interactions ARN-ARN A bits 2.0. 5'. 1.0 0.0. R2R*. RILogo. B. GGGCCCGG UCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCG CCGGGCC ACA U C. 1. A G. 10. 20. bits 2.0. 3'. 1.0 0.0. C. 30. 40. GGGGGCGGUUAAGGA 15. 10. U G C. 50. 59. guide. GGG C C C GG C U C C C G C C C U C U C C GGGG A A U C G U G A A C C GGGGG U U C C GG C C GGG C C U A C A. GGG A A GG A A U U GG C GGGGGG A G. 1. 1. 10. 20. guide RNA. RFAM: RF00065. 3 nt. 1. VARNA. 5' guide seq. 30. K-Loop. 4 nt. 3'. 5'. 40. 3' guide seq. 50. 59. ANA Box. 10. 20 22. 5' target seq 3' target seq. Stockholm. G C C C. C. U. 5'. A G G G G C U C C. Y G G C C C G G G. U G A A C C G G G G. R C C G G G C C. K-Loop. guide. G. G. U U C C. 5'. ANA box A C A. C G C C C U. C G C G G U G U C A G A G G G G G target. G U U C C. G U G U C A G A G G G G G A 5' G target. target RNA. Vienna/DBN. * post-processing 68.

(70) Gènes H/ACA. Pyrococcus & Thermococcus 7 H/ACA genes 11 H/ACA motifs Muller et al., NAR, 2008 69.

(71) Fonction des H/ACA. EA 5 ' pré-ARNr 3 '. NY. EA 3 ' EA 5 ' 5'. 5'. NY. EA 3 '. 3'. 5 ' pré-ARNr. 1 4 -1 6 pb. 1 4 -1 6 pb. ANANNA. ACA. Boîte H. Boîte ACA 70. 3'.

(72) Gènes H/ACA. Pyrococcus & Thermococcus 7 H/ACA genes 11 H/ACA motifs Muller et al., NAR, 2008 71.

(73) Repliements H/ACA b) p = 0.618. GGGCCCGGCUCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGGCCGGGCCUACA GGGCCCGGCUCCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGGCCGGGCCUACA. a) p = 0.382 72. Muller et al., NAR, 2008.

(74) H/ACA et leur(s) cible(s). 2466 Nucleic Acids Research, 2008, Vol. 36, No. 8. A. +. 6 bps. Pab21 a). −. K-turn C-G. E U (P.f., P.h.). K-turn. 5 bps. 14 nts. 15 nts. Pab105-1 Pab21 b) 5' C U C C C G CC - GG U U C C U C C C G C C U U C C A C A 3' A C A 3' 2466 Nucleic Acids Research, 2008, Vol. 36, No. 8 3' G G G G C G G A A G G 5' 16S rRNA 3' G G G G G C G U A A G G 5' 16S rRNA UU GU. 5'. 891. B. 892. A K-turn. −. Pab35-1. 4 bps 5' 3'. C-U. CCCG. GGGU. CU. 17 nts. GUGCU. A C A 3'. C A C G G 5' 16S rRNA. C. +. Pab21 a) Pab40-1. + 5' 5'. bps 66bps C-U G G. 5 bps 5'. C-G. CCG. 16 nts. UGCUC. −. 14 nts. UC UG CA C A C A 3'3' AUGCCCGC AGGCGC G A G G G CGGGCGUCCGCG A 3' U 5' 16S C G U U 5' 3' 23SrRNA rRNA AUUU. +. K-turn. − Pab105-1. K-turn K-turn. Pab21 b) 5'. 3'. −. 2588 891. 1122. − Pab35-1. +. K-turn. Pab105-2. (P.h.) C 6 bps et al., NAR, 2008 14Muller nts .U C BPab40-2 a) 5' G G UK-turn C A A C C C U G 3' A C A A C A 3' 73.

(75) 9 H/ACA: Structure-Fonction 8. - Pa21-S892. + Pa21-S891* 30 K-loop. K-loop. UCG A U A G G A G A G C G C 10 bp C G C G 20 U G 40 C G U C G U CC U G C C C C CU G 3' guide sequence C G (5 stacked layers) G C 10 G C 50 C G C G 9 bp C G G C G C ANA box G U 5' ACA. UCG A U A G G A G A G C G C 9 bp CC G 20 U CU G C G 40 C C GG G U C U C C 3´ guide sequence 5´ guide sequence C (5 stacked layers +1nt) (6 stacked layers) CU G C G 10 G C G C 50 C G C G 8-9 bp C G G C G C ANA box G U 5´ ACA. 9. 10. 5' guide sequence (6 stacked layers +1nt). 6. 5. 9. 9. R2R*. 30. Toffano-Nioche et al., NAR, 2015 74.

(76) H/ACA « productifs » Pa21-S891, Ph21-S879, Pf1-S879. Pa21-S891 30. 4 nt A G G G G C C U C 1 nt C C C G C C C U Y G G C C C G G. R2R*. 5'. U G A A C C G G G G G U. R C C G G G C C. K-Loop. U C C G. ANA box. 10. SSU 891,879. G G C G G G G G A G C A. U U. A A G G A A A U U C A A. U C G A U K-Loop A G G A G A G C G C C G C G 20 U G 40 C G U C C G U C U G C C C C C G U C G G C 10 G C 50 C G C G C G G C G C ANA box G U 5' A C A. guide. C G. 5' C C C G C C. UUCC. GGGCGG. ANA. A A G G 5' U U target. E = -28.2 kcal/mol. 5 9. 5'. A C A. SSU 891 G G C G G G G G A G C A. U U. A A G G A A A U U C A A. 5'. Toffano-Nioche et al., NAR, 2015 75.

(77) H/ACA « non-productifs » 9. Pa21-S892,Ph21-S880, Pf1-S880. Pa21-S892 30. 4 nt. 3 nt. G C C C. C. U. 5'. A G G G G C U C C. Y G G C C C G G G. U G A A C C G G G G. R C C G G G C C. K-Loop. 9. SSU 892,880. G. G. U U C C. ANA box. G C G G G G G A G C A C. G U. U A A G G A A A U U C A. U C G A U K-Loop A G G A G A G C G C C C G 20 U C U G C G 40 C G C G G U C U C C C C U G C G 10 G C G C 50 C G C G C G G C G C ANA box G U 5' A C A. guide. C G. 5' U C C C G C. GUUCC. GGGGCG. ANA. U A A G G 5' G U target. E = -24.5 kcal/mol 5'. A C A. R2R*. 6 9. SSU 892 G C G G G G G A G C A C. G U. U A A G G A A A U U C A. 5'. Toffano-Nioche et al., NAR, 2015 76.

(78) 6. Familles H/ACA 28%. R U A G G A. R. 16%. G. Y. 6 nt. 6 nt. 0-1 nt. 10 bp. 0-1 nt. 10. 0-1 nt. Pa_HACA-GUIDE56 subfam_weight=0.215373. 5-6 nt 5. 5-8 nt. 5 nt (6-1) (5 stacked layers). 0-1 nt. ed rs. 9. C G C G 9 bp C G. R2R*. 5'. Y. G Y. R. 6 nt. Y A. U CU G 1 nt G C. 5 nt (6-1). G C C A A. G U C U. A C G C. C G C U C. 5+1 nt 6+1 nt. 1nt. 75% connector (zero length) variable-length region variable-length loop variable-length stem modular sub-structure. C 1 nt C CC G C C C C 1 ntG. G G. G C. 11% U U C C G. 5. 6+2 nt. 5 nt. 9. (3 stacke. 9nucleotide present. C G G C. G C G A C. 5 nt. nucleotide identity 97% 75% N 97% 90% 50% N 90% N 75% 10 bp connector (zero length) Toffano-Nioche et al., NAR, 2015. 10. 77. A G C G. 2 nt. base pair annotations covarying mutations compatible mutations no mutations observed. ACA. 6. C G GGG U. 1. 5 nt. subfam_weight=0.110265. subfam_weight=0.106001. 11%. C. 12%. Pa_HACA-GUIDE85 10 Pa_HACA-GUIDE75 10. 22% C C Y R. subfam_weight=0.120714. G G UG. C. 5 nt. Y R. Y R C G G R Y. subfam_weight=0.163641. subfam_weight=0.284006. 3-21 nt. R2R. Pa_HACA-GUIDE66 Pa_HACA-GUIDE55. Pa_HACA-GUIDE65. Pa_HACA. 9.

(79) Interactions intra-moléculaires A. A. c. a gc. a. u. a. a. a. c. a. g. a ag. a. 30 g. a. gc u. c. c. g. g u. HI. 50 50. cc. gg a. a a aa. g. 50. u. c. c. c c. a g. a. a. g. a. g. a. u. c. u. u. u. u. u. u. c. g. g. a. a. a. g. g. g. a. a. c. a. g. c. c. u. u. u. c. c. c. u. u. u a c. c g. g. ag a. c a. g. ga. c au. aa c. c. g. u. u. u. g. uu. c. c. u. c ac c u a c 10. u. cc. u. u. u. g. u1. g. c. u. g. g. c a. u g. a. c. c. u. u. g 1. g. g. g. g. u. g u 1. c. u. g. Emonomer(25ºC) = -19.4 k c Emonomer(45ºC) = -9.6 k g. intra-molecular base-pairs u. u. c. g u. c. 10 20. nucleotide in tertiary contact cleavage site. 79. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10a. 20a. 30a. monomer 1 HI. 40a. 50a. HII. B. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a. 79a 1b. HIII. 10b. 20b. monomer 2. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. u c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 10a. er 1 HI. 20a. 1a. 79. tertiary or inter-molecular contacts. Emonomer(10ºC) = -26.9 kcal/mol Emonomer(25ºC) = -19.4 kcal/mol Emonomer(45ºC) = -9.6 kcal/mol. u. u. c. 79. u. u. c u c Emonomer(10ºC) = u -26.9 k. a. 10. c. a. g. c. 20. 70. c. a. c. uc. 60. u. a. g. u. g. 20. c. g. c. 70. c a. g. g. ga. u. 70. 60. 60. gg. g. a. g. a. g. a. c a. g. a HII g. 30. 40. a. u. a. a. a. g. g. g. u. a. 40a. ag. u c. VARNA. a. c. HIIIc a. a. g. u. 40. c. a. c. HI 30a. HII. 10a40a. monomer 1 HI. 50a. HIII. 20a. 60a. 70a. 30a. HII 79a 1b. HII. gguu c uu c. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 40a. 10b. monomer 2. 78. HIII 20b. HIII. 50a30b. 40b. 60a. 50b. 60b. 70a. 70b. 79b 1b 79a. monome.

(80) a g. 30. a. g. a. a. c 20 u. u. 79c. 10. 20. cleavage site. 79. Interactions inter-moléculaires gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10a. 20a. 30a. 40a. 50a. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. 10b. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. monomer 1 10a HI 1a. monomer 1 B B. HII 30a. 20a. HI. 40a. HIII. HII. 50a. 60a. 20b. monomer 2. 70a. 30b. 40b. 50b. 60b. 70b. 79b. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. HIII. 10b. 20b. 30b. 40b. 50b. 60b. monomer 2. 70b. g. a. g. a. a. 79b. c. H(2)I. H(1)III. a. c. c. c. H(1)I. aa. c. u. u. a u. g. c c10b. 79a. u. a. u. 10b. g. u. g. 20b. c. u. u. u. 30b. g. a. g. g. a. a. a c. a g. c 20b c c. u. H(2)II. a g ga. 30b. c a g a. c. c g c a 40a g a ug c c u c c g u g a u a u u c g 1b a a a c g ca u a g 50a 79a u u u u c g a u u 50b g 70a 60a u c u g g u a c g c g40a u cg a g g c u cg a a c a ua u c g u c c a a a g g 1b a a c a c a a g u c g gu c c g a a a g g g g a a g a c 70a 60b a a a u u u g 50a c u a 50b c 60a g cg g g c g u c c u a g a a g a 40b u c ug a a a g c a a c u c ga ug c c g c gu au au ac g c g c gu a u a u g u a g cg c 70b 60b a ca a g a c c a g c u a c c c g g a c 1a 40b g u Edimer(10ºC) Eint(10ºC) = -9.3 kcal/mol = -47.1 kcal/mol u g a u 70b c a gg a 30a g c c u g u u c u c 10a c u u u g a c a a g u Eint(25ºC) = -8.5 kcal/mol Edimer(25ºC) = -33.6 kcal/mol c u a c g a c 20a 1a u c u u Edimer g E (10ºC) = -9.3 kcal/mol (10ºC) = -47.1 kcal/mol (45ºC) = -5.8 kcal/mol (45ºC) = -15.7 kcal/mol E Edimer u g g c int int 30a 10a a a g 79b u Eint(25ºC) = -8.5 kcal/mol Edimer(25ºC) = -33.6 kcal/mol 20a u c u g c u Eint(45ºC) = -5.8 kcal/mol Edimer(45ºC) = -15.7 kcal/mol 79b u. H(2)III. H(1)II. monomer 1. monomer 2. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10a. 20a. 30a. monomer 1 HI. 40a. 50a. HII. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. HIII. 10b. 1a. 10a. 20a. H(1)I C C. 30a. 40b. 50b. 60b. 50a. 60a. 70a. 79a 1b. 10b. 20b. 30b. monomer 2 H(2)I. 40b. 50b. H(2)III. a. c. 20b. g. c. 40a. a g40a. a. c. u. a. c. u. u c g u Sci. Leclerc et al., Rep., 2016 79a u u. a a g. g 50a a c g. g. c. c a. c. g. 70a. 60a u. 79b. 79. u. u. g. u. u. c. g. u. 1b. 79a u g g. c u. u. a. 70b. a. 79b. 30b. g. g. a. a30b g a a g 10b a g c a c a u g a u u u a c u a c a u c c g g c c 10b g g c g c c u a a u c c a a u u g a a g a u u c c a u c a g 40b 50b cc u g a g g c20b c. g. u. 70b. 60b. u. IntaRNA a. 30b. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. HII HIII H(1)II H(1)III. monomer 1 HI. a. 40a. 20b. monomer 2. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. a. g g. a. c. VARNA.

(81) a. c. a. a. g. g. c a. c. u. u. u. c. g. a. g. a. c. u a c. c. 30a. c. u. u. u. c. u. 79b g. g. u. u. 70b. a. g. 1a. Eint(10ºC) = -9.3 kcal/mol Eint(25ºC) = -8.5 kcal/mol Eint(45ºC) = -5.8 kcal/mol. g. 10a. u. 20a. c. u. u. u. c. g. c. Edimer(10ºC) = -47.1 kcal/mol Edimer(25ºC) = -33.6 kcal/mol Edimer(45ºC) = -15.7 kcal/mol. Interactions inter-moléculaires 79b. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10a. 20a. 30a. 40a. monomer 1 HI. C. 50a. HII. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. HIII. 10b. H(1)III 10a. 20a. monomer 1 HI. c. a a. u. g. u. c c ag. c. g. u. a a. c. a. g. g a40a g. 30a. c. a. aa. a. H(1)II g. u. c. c. a. g. g. a. g. u. a. a. a. g. g. g. a. a. a. g. a. c. u. u. u. c. c. c. u. u. u a c. a. a. c a. c. g. a. a. a. g. c. c. u. u. u. c. 70b. g. a. c. c. u. u. g. g. u c. g. g. a. a. c. c. u. u. c a. u a c. u. c. u. u. u. c. g. g. 1a. g u. g. a. c. c 79b. u. u. g. g. u. g. c. u. c c. 1b. 30b. a. u. 50b. u. u. c. a. a u. c a. a. c g. a. a70b c. c. c. u. u. u. c. g. 60b. c. u. 79b g. g. c a. a. 30b. g. g. u. u. g. a. g. H(2)III. u gc. u. u. 40b. a aa g c 20b g a g a a u a u 40b a 50b g u c c a a g a g c g c g c a 60b10b a c c c ac u a= u-53.7 kcal/mol u g a a u u E (10ºC) c u dimer c g 79a c 70b c ag Edimer (25ºC) = -38.9 kcal/mol c g c g c u a 1b u E a a (45ºC) = -19.2 kcal/mol c dimer g a u u a u a g g g 40b 50b g u a c a g c a g a c 60b c c a u Edimer(10ºC) = -53.7 kcal/mol g u 70b c a E (25ºC) = -38.9 kcal/mol g. g. g. c. a. 79b. H(2)II. u. 30b. 79a. g. 70a. c. monomer 1 g. g. u. 10a60a. g. 60b. 10b. c. c g. 30a. c. g. u. 50b. 20b. H(2)I. 20b. monomer 2. u. u. 10b. g. 70a. c. g. a. 79a 1b. u. g. 50a u c 20a. 40b. g c a g a c c u g g u u u ac g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a agg u c g g a a g. g. 60a. cg. a. a. 70a. H(1)I u. ca. c. 60a. HIII. 50a. u. 50a. HII. g. g. a. 40a. a. a. a. 30a. g. c. 40a. C. a. c. 30b. monomer 2. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 20b. 1a. dimer. 10a. Edimer(45ºC) = -19.2 kcal/mol. monomer 2. g. 20a. c. u. g. c. u. u. u. 79b. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10a. 20a. monomer 1 HI. 30a. 40a. 50a. HII. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. HIII. 10a. H(1)I. 20a. monomer 1 HI. IntaRNA. 30a. 40a. 20b. 30b. 40b. 50b. 60b. 70b. 79b. monomer 2. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10b. 50a. H(1)II H(1)III HII HIII. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. 10b. H(2)I. monomer 2. Leclerc et al., Sci. Rep., 2016 80. 20b. 30b. H(2)II. 40b. 50b. H(2)III. 60b. 70b. 79b. VARNA.

(82) Interactions inter-moléculaires H(1)I:H(2)I. 79a g. u. c. c. g. g. u. u. c. u. u. c. c. u u. c u. g. g. c. 20b. 10b. 1b. a. g. u. a c. a. a. g. g. u a. u a. u a. c g. a a. c c. g u. 50a. a. g c. a u. g a. c. a. a. g. a. a. a a. g. u. a. c. 40b c. g g. g. H(2)III. Eint(10ºC) = -12.0 kcal/mol Eint(25ºC) = -9.6 kcal/mol Eint(45ºC) = -5.9 kcal/mol. g. c. u. 60a. 70a. 30b a. c c. c. a. g. u. c a u. g. H(1)III. a. c. H(1)I:H(2)I. g. a. a. 50b. u. g. u. c. a. c. g. u. c. g. g. a. a. a. g. g. g. a. a. u. g. c. a. g. c. c. u. u. u. c. c. c. u. u. a. g a. c. 40a. g. a. 70b. 60b. c. c a. u g. a. c. c. u. u. g 1a. g. g. g. u. u u c. a. a. u a c. c g. 30a. a. a. g. u. c. g c. 10a 20a. 79b. Edimer(10ºC) = -54.8 kcal/mol Edimer(25ºC) = -40.7 kcal/mol Edimer(45ºC) = -22.0 kcal/mol. H(1)II:H(2)II. u. inter-molecular base-pairs intra-molecular base-pairs tertiary contacts nucleotide in tertiary contact cleavage site. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c 1a. 10a. 20a. monomer 1 HI. IntaRNA. monomer 1 30a. HII. 40a. 50a. HIII. 60a. 70a. gguu c uu c c c a u c uuu c c c ug a a g a g a c g a a g c a a gu c g a a a c u c a g a gu c gg a a a gu c gg a a c a g a c c ugguuu c gu c. 79a 1b. 10b. monomer 2. 20b. monomer 2. Leclerc et al., Sci. Rep., 2016 81. 30b. 40b. 50b. 60b. 70b. 79b. VARNA.

(83) Conclusions représentations standardisées et personnalisées (édition, annotation) gain de temps pour la génération de représentations multiples gain de temps pour la mise à jour de structures consensus outils qualitatif (quantitatif) pour évaluer des modèles structurefunction. 82.

(84) Outils & Ressources RFAM (VARNA), Comparative RNA Web Site & Project (RNA2DMap, CT, BPSEQ), The RNA Mapping Database RMDB (RDAT, RNAstructure), ... packages: Vienna Package (RNAfold, RNAalifold, etc), Boulder Alignment Editor (VARNA), SAVor (RNAfold, RNAplot), S2S/Assemble 2D & 3D, Jalview 2D & 3D (VARNA, Jmol), ... outils récents: long RNAs: RNAfdl, pairing probabilities (alternative conformations): RNAbow, RNAllViewer, ... 83.

(85) Références. Ponty Y. & Leclerc F., Drawing and editing the Secondary Structures of RNA(s), Methods in Molecular Biology, 2015. Aigner K. et al., Chapitre 9. Visualizing RNA sequence and structure, 2011.. 84.

(86) Acknowledgments Institute for Integrative Biology of the Cell. 85.

(87) De la séquence au 2D (((( ((( GCUG UUAGG GGA GUUUUA GCCG UUAGG GGA GUUUCA GUUG UAGG GGA GUCUCA GCUG GAGG GAA GC AA ACUU CAGU GGA GC AA ACUU CAGU GGA GC AA GAUG GAGG UUG G AAA GGGC CAGG GGU G AAA GGCC UAGG UCG G AAA GGCC CAGG UCG G AAA GGCC CAGG UCG G AAA GGCC CAGG UCG G AAA GGCC CAGG UCG G AAA. ))) UCC UCC UCC UUC UCC UCC CAA ACC CGG CGG CGG CGG CGG. AGCGU AGCGA AGCA AGCA AGCA AGCA UGCA AGCA AGCA AGCA AGCA AGCA AGCA. )))-) CAG-C UGG-C CAA-C CAG-C GAGAU GAGAU CAU-C GCC-A GGU-C GGU-C GGU-C GGU-C GGU-C. 1D 3D. 2D. Westhof, 2015 86.

(88) De la structure 2D à 3D la structure 2D: une contrainte géométrique. (((( ((( GCUG UUAGG GGA GUUUUA GCCG UUAGG GGA GUUUCA GUUG UAGG GGA GUCUCA GCUG GAGG GAA GC AA ACUU CAGU GGA GC AA ACUU CAGU GGA GC AA GAUG GAGG UUG G AAA GGGC CAGG GGU G AAA GGCC UAGG UCG G AAA GGCC CAGG UCG G AAA GGCC CAGG UCG G AAA GGCC CAGG UCG G AAA GGCC CAGG UCG G AAA. “forte” appariements non-. ))) UCC UCC UCC UUC UCC UCC CAA ACC CGG CGG CGG CGG CGG. AGCGU AGCGA AGCA AGCA AGCA AGCA UGCA AGCA AGCA AGCA AGCA AGCA AGCA. )))-) CAG-C UGG-C CAA-C CAG-C GAGAU GAGAU CAU-C GCC-A GGU-C GGU-C GGU-C GGU-C GGU-C. 1D 3D. canoniques et motifs pseudonœuds et. 2D. interactions tertiaires … 87.

(89) RNA Puzzles tester les capacités de prédiction de structures 3D d’ARN compétition entre modélisateurs ARN compétition à “l’aveugle”: structures 3D d’ARN non publiques. 88.

(90) RNA Puzzle: T-Box/tRNA Problem 10. • The T-box riboswitch in complex with tRNA. 89. •. PDB: 4LCK. • •. Resolution: 3.20Å Avg B = 128 Å2. • •. tRNA: 75nt T-box : 96nt. •. Clash score: 2.28. •. Some small fragments solved by NMR before. tRNA structure known..

(91) RNA Puzzle: T-Box/tRNA Table*of*results*(Problem*10*T7box) 5.96. 90.

(92) RNA Puzzle: T-Box/tRNA. H1. H2. H3. L1 H4 L2 H4 H3. H2 H1. L3. D-domain & anticodon stem. T-domain. Deforma(on*proﬁle*Das*model*#1*. H1. H2. H3. L1 H4 L2 H4 H3. H2 H1. L3. D-domain & T-domain anticodon stem. 91.