Distribution of miRNA genes in the pig genome

BMC Genetics

Volumn 16, Issue 1, 2015, Pages

  Paczynska, Paulina ^a   Grzemski, Adrian ^a   Szydlowski, Maciej ^a  

^a POZNA UNIVERSITY OF LIFE SCIENCES   (Poland)

Author keywords

Genomic location; miRNA; Pig

Indexed keywords

MICRORNA; SPACER DNA; UNTRANSLATED RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA FLANKING REGION; EXON; GENE CONTROL; GENE EXPRESSION PROFILING; GENOME; HUMAN; HUMAN GENOME; INTRON; NONHUMAN; PIG GENOME; PROMOTER REGION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; RNA BINDING; SPECIES COMPARISON; ANIMAL; GENETICS; MOUSE; PHYLOGENY; PIG;

SUIDAE;

ANIMALS; GENOME; HUMANS; MICE; MICRORNAS; PHYLOGENY; SUS SCROFA;

EID: 84924052822     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/s12863-015-0166-3     Document Type: Article

References (24)

1. Lagos-Quintana M. New microRNAs from mouse and human. RNA. 2003;9:175-9.
2. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281-97.
3. Kim VN, Nam JW. Genomics of microRNA. Trends Genet. 2006;22:165-73.
4. Baskerville S, Bartel. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 2005;11:241-7.
5. de Almeida AM, Emøke B. Pig proteomics: a review of a species in the crossroad between biomedical and food sciences. J Proteome. 2012;75:4296-314.
6. Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012;491:393-8.
7. Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, et al. Structured RNAs and synteny regions in the pig genome. BMC Genomics. 2014;15:459-86.
8. Inukai S, de Lencastre A, Turner M, Slack F. Novel microRNAs differentially expressed during aging in the mouse brain. PLoS One. 2012;7:e40028.
9. Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42:D68-D73.
10. Godnic I, Zorc M, Jevsinek Skok D, Calin GA, Horvat S, Dovc P, et al. Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken. PLoS One. 2013;8(6):e65165.
11. Li SC, Tang P, Lin WC. Intronic MicroRNA: discovery and biological implications. DNA Cell Biol. 2007;26:195-207.
12. Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, et al. Birth and expression evolution of mammalian microRNA genes. Genome Res. 2013;23:34-45.
13. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 2005;33:2697-706.
14. He C, Li Z, Chen P, Huang H, Hurst LD, Chen J. Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution. Nucleic Acids Res. 2012;40:4002-12.
15. Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, et al. Transcriptional features of genomic regulatory blocks. Genome Biol. 2009;10:R38.
16. Campo-Paysaa F, Sémon M, Cameron RA, Peterson KJ, Schubert M. microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol Dev. 2011;13:15-27.
17. Sempere LF, Cole CN, McPeek MA, Peterson KJ. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool B Mol Dev Evol. 2006;306B:575-88.
18. Jevsinek Skok D, Godnic I, Zorc M, Horvat S, Dovc P, Kovac M, et al. Genome-wide in silico screening for microRNA genetic variability in livestock species. Anim Genetics. 2013;44:669-77.
19. Hinske LC, Galante PA, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
20. Martini P, Sales G, Brugiolo M, Gandaglia A, Naso F, De Pittà C, et al. Tissue-specific expression and regulatory networks of pig microRNAome. PLoS One. 2014;9(4):e89755.
21. Roux J, Gonzàlez-Porta M, Robinson-Rechavi M. Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res. 2012;40:5890-900.
22. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res. 2014;42(Database issue):D749-55.
23. Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000;16:276-7.
24. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.