Structured RNAs and synteny regions in the pig genome

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Anthon, Christian ^a   Tafer, Hakim ^b   Havgaard, Jakob H ^a   Thomsen, Bo ^c   Hedegaard, Jakob ^c,d   Seemann, Stefan E ^a   Pundhir, Sachin ^a   Kehr, Stephanie ^b   Bartschat, Sebastian ^b   Nielsen, Mathilde ^c   Nielsen, Rasmus O ^c,e   Fredholm, Merete ^a   Stadler, Peter F ^a,b   Gorodkin, Jan ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c AARHUS UNIVERSITY   (Denmark)

^d AARHUS UNIVERSITY HOSPITAL   (Denmark)

^e GenoSkan A S   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RIBOSOME RNA; RIBOZYME; RNA; SMALL NUCLEOLAR RNA; MICRORNA; UNTRANSLATED RNA;

ANIMAL TISSUE; ARTICLE; CAT; CIS REGULATORY ELEMENT; CONTROLLED STUDY; COW; DNA STRUCTURE; DOG; DOLPHIN; GENE IDENTIFICATION; GENE LIBRARY; GENE LOCUS; GENETIC DATABASE; GENOME ANALYSIS; HEDGEHOG; HORSE; NONHUMAN; PSEUDOGENE; RELIABILITY; RNA GENE; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STRUCTURAL HOMOLOGY; SWINE; SYNTENY; ANIMAL; CHEMISTRY; CLUSTER ANALYSIS; GENETICS; GENOME; HUMAN; METABOLISM; PIG;

SUIDAE;

ANIMALS; CLUSTER ANALYSIS; GENETIC LOCI; GENOME; HUMANS; MICRORNAS; RNA; RNA, RIBOSOMAL; RNA, SMALL NUCLEOLAR; RNA, UNTRANSLATED; SWINE; SYNTENY;

EID: 84905730685     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-459     Document Type: Article

References (68)

1. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome. Nature 2004, 431(7011):931-945. International Human Genome Sequencing Consortium.
2. Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL. De novo prediction of structured RNAs from genomic sequences. Trends Biotech 2010, 28:9-19.
3. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921. International Human Genome Sequencing Consortium.
4. The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE, pilot project. Nature 2007, 447(7146):799-816. The ENCODE Project Consortium.
5. The ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489(7414):57-74. The ENCODE Project Consortium.
6. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2012, 22(9):1760-1774.
7. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res 2009, 37(suppl 1):D136-D140.
8. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 2010, 39(Database issue):D141-D145.
9. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005, 33(Database issue):D121-D124.
10. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA Genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964.
11. Wernersson R, Schierup MH, Jørgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshøj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L. Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 2005, 6:70.
12. Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staefeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, et al. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol 2007, 8(4):R45.
13. Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J. Detection of RNA structures in porcine EST data and related mammals. BMC Genomics 2007, 8:316.
14. Ren H, Li Y, Tang Z, Yang S, Mu Y, Cui W, Ao H, Du L, Wang L, Li K. Genomic structure, chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE libraries. Anim Genet 2009, 40(4):499-508.
15. Xiao B, Zhang X, Li Y, Tang Z, Yang S, Mu Y, Cui W, Ao H, Li K. Identification, bioinformatic analysis and expression profiling of candidate mRNA-like non-coding RNAs in Sus scrofa. J Genet Genomics 2009, 36(12):695-702.
16. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011, 39(Database issue):D146-151.
17. Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Perez-Enciso M. Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. BMC Genomics 2011, 12:552.
18. Yang CX, Du ZQ, Wright EC, Rothschild MF, Prather RS, Ross JW. Small RNA profile of the cumulus-oocyte complex and early embryos in the pig. Biol Reprod 2012, 87(5):117.
19. Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler PF, Rajewsky N, Einspanier R. Deciphering the porcine intestinal microRNA transcriptome. BMC Genomics 2010, 11:275.
20. Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C, Thomsen B. MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing. Anim Genet 2010, 41(2):159-168.
21. Gruber AR, Findeiss S, Waschitl S, Hofacker IL, Stadler PF. RNAZ 2.0 improved noncoding Rna detection. Pac Symp Biocomput 2010, 5:69-79.
22. Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012, 491(7424):393-398.
23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
24. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25(10):1335-1337.
25. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35(9):3100-3108.
26. Bartschat S, Kehr S, Tafer H, Stadler PF, Hertel J. snoStrip: A snoRNA annotation pipeline. Bioinformatics 2014, 30(1):115-116.
27. Yao Z, Weinberg Z, Ruzzo WL. CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics 2006, 22(4):445-452.
28. Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 2012, 40:37-52.
29. Harris RS. Ph.D. Thesis: improved pairwise alignment of genomic DNA. Thesis/dissertation, The Pennsylvania State University 2007,
30. Kent J. UCSC tools. 2011, [http://users.soe.ucsc.edu/~kent/].
31. Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y. In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach. Genomics 2009, 94(2):125-131.
32. Langenberger D, Bartschat S, Hertel J, Hoffmann S, Tafer H, Stadler PF. MicroRNA or Not MicroRNA?. Adv Bioinformatics Comput Biol Lect Notes Comput Sci 2011, 6832:1-9.
33. Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler P. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics 2009, 25:2298-2301.
34. Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics 2012, 28:17-24.
35. Pundhir S, Gorodkin J. MicroRNA discovery by similarity search to a database of RNA-seq profiles. Front Genet 2013, 4:133.
36. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004, 14(4):708-715.
37. Meyers SN, Rogatcheva MB, Larkin DM, Yerle M, Milan D, Hawken RJ, Schook LB, Beever JE. Piggy-BACing the human genome II. A high-resolution, physically anchored, comparative map of the porcine autosomes. Genomics 2005, 86(6):739-752.
38. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blocker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guerin G, et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 2009, 326(5954):865-867.
39. O'Bleness M, Searles VB, Varki A, Gagneux P, Sikela JM. Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet 2012, 13(12):853-866.
40. Havgaard JH, Torarinsson E, Gorodkin J. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput Biol 2007, 3(10):1896-1908.
41. Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res 2006, 16(7):885-889.
42. Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J. Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res 2008, 18(2):242-251.
43. Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 2007, 3(4):e65.
44. Wang AX, Ruzzo WL, Tompa M. How accurately is ncRNA aligned within whole-genome multiple alignments?. BMC Bioinformatics 2007, 8:417.
45. Mosig A, Guofeng M, Stadler BM, Stadler PF. Evolution of the vertebrate Y RNA cluster. Theory Biosci 2007, 126:9-14.
46. Perreault J, Perreault JP, Boire G. Ro-associated Y RNAs in metazoans: evolution and diversification. Mol Biol Evol 2007, 24:1678-1689.
47. Madupu R, Richter A, Dodson RJ, Brinkac L, Harkins D, Durkin S, Shrivastava S, Sutton G, Haft D. CharProtDB: a database of experimentally characterized protein annotations. Nucleic Acids Res 2012, 40(Database issue):D237-D241.
48. Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C. RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA 2011, 17(11):1947-1956.
49. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013, 29:2933.
50. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R. The GENCODE v7 catalog of human long noncoding R N As: analysis of their gene structure, evolution, and expression. Genome Res 2012, 22(9):1775-1789.
51. Podolska A, Anthon C, Bak M, Tommerup N, Skovgaard K, Heegaard PM, Gorodkin J, Cirera S, Fredholm M. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. BMC Genomics 2012, 13:459.
52. Liu Y, Li M, Ma J, Zhang J, Zhou C, Wang T, Gao X, Li X. Identification of differences in microRNA transcriptomes between porcine oxidative and glycolytic skeletal muscles. BMC Mol Biol 2013, 14:7.
53. Hu ZL, Park CA, Wu XL, Reecy JM. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res 2013, 41(Database issue):D871-D879.
54. Nguyen DT, Lee K, Choi H, Choi MK, Le MT, Song N, Kim JH, Seo HG, Oh JW, Lee K, Kim TH, Park C. The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome. BMC Genomics 2012, 13:584.
55. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39(suppl 1):D152-D157.
56. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36(suppl 1):D154-D158.
57. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34(suppl 1):D140-D144.
58. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004, 32(suppl 1):D109-D111.
59. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glo¨ckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35(21):7188-7196.
60. Lestrade L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 2006, 34(suppl 1):D158-D162.
61. Ju¨hling F, Mo¨rl M, Hartmann RK, Sprinzl M, Stadler PF, Pu¨tz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 2009, 37(suppl 1):D159-D162.
62. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R T, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948.
63. Anandam P, Torarinsson E, Ruzzo WL. Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. Bioinformatics 2009, 25(5):668-669.
64. Jiang M, Anderson J, Gillespie J, Mayne M. uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics 2008, 9:192.
65. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008, 26(4):407-415.
66. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31(13):3429-3431.
67. Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 2004, 20(17):2911-2917.
68. Thakur V, Wanchana S, Xu M, Bruskiewich R, Quick WP, Mosig A, Zhu XG. Characterization of statistical features for plant microRNA prediction. BMC Genomics 2011, 12:108.