Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs

Genome Biology and Evolution

Volumn 6, Issue 6, 2014, Pages 1387-1392

  Zhou, Zhong Yin ^a,b   Li, Ai Min ^c   Adeola, Adeniyi C ^b,d   Liu, Yan Hu ^e   Irwin, David M ^b,f,g   Xie, Hai Bing ^b   Zhang, Ya Ping ^a,b,e  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c XI'AN UNIVERSITY OF TECHNOLOGY   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^e YUNNAN UNIVERSITY   (China)

^f UNIVERSITY OF TORONTO   (Canada)

^g UNIVERSITY OF TORONTO   (Canada)

Author keywords

Domestication; LincRNA; Pig

Indexed keywords

LONG UNTRANSLATED RNA;

ANIMAL; DOMESTIC ANIMAL; GENE EXPRESSION PROFILING; GENETICS; GENOME; HUMAN; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SWINE;

ANIMALS; ANIMALS, DOMESTIC; BASE SEQUENCE; GENE EXPRESSION PROFILING; GENOME; HUMANS; MICE; MOLECULAR SEQUENCE DATA; RNA, LONG NONCODING; SEQUENCE ALIGNMENT; SUS SCROFA;

EID: 84902950819     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu113     Document Type: Article

References (37)

1. Albert FW, et al. 2012. A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genet. 8:e1002962.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol. 11:R106.
3. Borsani G, et al. 1991. Characterization of a murine gene expressed from the inactive X chromosome. Nature 351: 325-329.
4. Brockdorff N, et al. 1992. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71: 515-526.
5. Brown CJ, et al. 1992. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71: 527-542.
6. Cabili MN, et al. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25: 1915-1927.
7. Derrien T, et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22: 1775-1789.
8. Fang M, Larson G, Ribeiro HS, Li N, Andersson L. 2009. Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet. 5:e1000341.
9. Farajzadeh L, et al. 2013. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level. Biochem Biophys Res Commun. 438: 346-352.
10. Fujii J, et al. 1991. Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Science 253: 448-451.
11. Groenen MA, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398.
12. Guttman M, et al. 2010. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 28: 503-510.
13. Guttman M, et al. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477: 295-300.
14. Harrow J, et al. 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22: 1760-1774.
15. Huarte M, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419.
16. Hung T, et al. 2011. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 43: 621-629.
17. Jia H, et al. 2010. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16: 1478-1487.
18. Khalil AM, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 106: 11667-11672.
19. Kong L, et al. 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35:W345-W349.
20. LaPlant Q, et al. 2010. Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat Neurosci. 13: 1137-1143.
21. Liu J, et al. 2012. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24: 4333-4345.
22. Martianov I, Ramadass A, Barros AS, Chow N, Akoulitchev A. 2007. Repression of the human dihydrofolate reductase gene by a noncoding interfering transcript. Nature 445: 666-670.
23. Mercer TR, Dinger ME, Mattick JS. 2009. Long non-coding RNAs: insights into functions. Nat Rev Genet. 10: 155-159.
24. Mikawa S, et al. 2007. Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1). Genome Res. 17: 586-593.
25. Mitchell Guttman IA, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
26. Orom UA, et al. 2010. Long noncoding RNAs with enhancer-like function in human cells. Cell 143: 46-58.
27. Payer B, Lee JT. 2008. X chromosome dosage compensation: how mammals keep the balance. Annu Rev Genet. 42: 733-772.
28. Price EO. 1999. Behavioral development in animals undergoing domestication. Appl Anim Behav Sci. 65: 245-271.
29. Ravasi T, et al. 2006. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res. 16: 11-19.
30. Rinn JL, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129: 1311-1323.
31. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
32. Trapnell C, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28: 511-515.
33. Trapnell C, et al. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 7: 562-578.
34. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. 2011. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147: 1537-1550.
35. Van Laere A-S, et al. 2003. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425: 832-836.
36. Wang KC, et al. 2011. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472: 120-124.
37. Xie C, et al. 2014. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 42:D98-D103.