The de novo sequence origin of two long non-coding genes from an inter-genic region

BMC Genomics

Volumn 14, Issue SUPP 8, 2013, Pages

  Dai, Yulin ^a,b   Li, Shengdi ^a,b   Dong, Xiao ^a,b   Sun, Han ^a,b,c   Li, Chao ^a,b   Liu, Zhi ^a,b   Ying, Beili ^d   Ding, Guohui ^a,c   Li, Yixue ^a,c  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^d FUDAN UNIVERSITY   (China)

Author keywords

Conserved Element; Overlapping transcripts; Sequence Origin of Pldi and Ak158810 loci; Substitution rate

Indexed keywords

LONG UNTRANSLATED RNA; PLDI PROTEIN; UNCLASSIFIED DRUG;

AK158810 GENE; ANIMAL TISSUE; ARTICLE; CHROMOSOME REARRANGEMENT; CONSENSUS SEQUENCE; CPG ISLAND; DEMETHYLATION; DNA METHYLATION; EXON; GENE; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; HUMAN; INTRON; LONG INTERSPERSED REPEAT; MOUSE; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PLDI GENE; PROTEIN MOTIF; RNA GENE; SEQUENCE ALIGNMENT; SHORT INTERSPERSED REPEAT; TRANSCRIPTION INITIATION SITE; TRANSPOSON;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, MAMMALIAN; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENETIC LOCI; GENOME; HUMANS; MAMMALS; MICE; MODELS, GENETIC; PHYLOGENY; RNA, LONG NONCODING;

EID: 84889675080     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-S8-S6     Document Type: Article

References (32)

1. Ponting CP, Oliver PL, et al. Evolution and functions of long noncoding RNAs. Cell 2009, 136(4):629-41. 10.1016/j.cell.2009.02.006, 19239885.
2. Mercer TR, Dinger ME, et al. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009, 10(3):155-9. 10.1038/nrg2521, 19188922.
3. Tautz D, Domazet-Loso T. The evolutionary origin of orphan genes. Nat Rev Genet 2011, 12(10):692-702. 10.1038/nrg3053, 21878963.
4. Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res 2010, 20(10):1313-26. 10.1101/gr.101386.109, 2945180, 20651121.
5. Duret L, Chureau C, et al. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 2006, 312(5780):1653-5. 10.1126/science.1126316, 16778056.
6. He S, Liu S, et al. The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol 2011, 11:102. 10.1186/1471-2148-11-102, 3103462, 21496275.
7. Cai J, Zhao R, Jiang H, Wang W. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 2008, 179(1):487-496. 10.1534/genetics.107.084491, 2390625, 18493065.
8. Carvunis AR, Rolland T, Wapinski I, Calderwood MA, et al. Proto-genes and de novo gene birth. Nature 2012, 487(7407):370-4. 10.1038/nature11184, 3401362, 22722833.
9. Derrien T, Johnson R, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012, 22(9):1775-89. 10.1101/gr.132159.111, 3431493, 22955988.
10. Heinen TJ, Staubach F, et al. Emergence of a new gene from an intergenic region. Curr Biol 2009, 19(18):1527-31. 10.1016/j.cub.2009.07.049, 19733073.
11. Katayama S, Tomaru Y, Kasukawa T, et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309(5740):1564-6.
12. Engström PG, Suzuki H, Ninomiya N, et al. Complex Loci in human and mouse genomes. PLoS genetics 2006, 2(4):e47. 10.1371/journal.pgen.0020047, 1449890, 16683030.
13. Dinger ME, Amaral PP, Mercer TR, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Research 2008, 18(9):1433-45. 10.1101/gr.078378.108, 2527704, 18562676.
14. Wheeler DL, Church DM, Federhen S, et al. Database resources of the National Center for Biotechnology. Nucleic Acids Res 2013, 31(1):28-33.
15. Thompson JD, Gibson T, et al. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002, Chapter 2:Unit 2.3.
16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 1987, 4(4):406-425.
17. Blanchette M, Kent WJ, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004, 14(4):708-15. 10.1101/gr.1933104, 383317, 15060014.
18. Sakuraba Y, Kimura T, et al. Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm Genome 2008, 19(10-12):703-12. 10.1007/s00335-008-9152-7, 19015917.
19. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555-6.
20. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996, , http://www.repeatmasker.org
21. Xin Y, O'Donnell AH, Ge Y, Chanrion B, et al. Role of CpG context and content in evolutionary signatures of brain DNA methylation. Epigenetics 2011, 6(11):1308-18. 10.4161/epi.6.11.17876, 3775885, 22048252.
22. Maunakea AK, Nagarajan RP, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010, 466(7303):253-7. 10.1038/nature09165, 20613842.
23. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 2009, 37(18):e123. 10.1093/nar/gkp596, 2764448, 19620212.
24. Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Briefings in bioinformatics 2008, 9(4):326-332. 10.1093/bib/bbn016, 18436575.
25. Lippman Z, Gendrel A V, Black M, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004, 430(6998):471-476. 10.1038/nature02651, 15269773.
26. Prabhakar S, Noonan JP, Pääbo S, Rubin EM. Accelerated evolution of conserved noncoding sequences in humans. Science 2006, 314(5800):786. 10.1126/science.1130738, 17082449.
27. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human Genome Ultraconserved Elements are Ultraselected. Science 2007, 317(5840):915. 10.1126/science.1142430, 17702936.
28. Rosenbloom KR, Dreszer TR, Pheasant M, et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 2012, 40(Database issue):D912-7. 3245183, 22075998.
29. Marques AC, Dupanloup I, Vinckenbosch N, et al. Emergence of young human genes after a burst of retroposition in primates. PLoS biology 2005, 3(11):e357. 10.1371/journal.pbio.0030357, 1251493, 16201836.
30. Long M, Betran E, et al. The origin of new genes: glimpses from the young and old. Nat Rev Genet 2003, 4(11):865-75.
31. Heinen TJ, Staubach F, et al. Emergence of a new gene from an intergenic region. Curr Biol 2009, 19(18):1527-31. (Figure S8), 10.1016/j.cub.2009.07.049, 19733073.
32. Margulies EH, Maduro VVB, Thomas PJ, et al. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(9):3354-3359. 10.1073/pnas.0408539102, 549084, 15718282.