Distribution of miRNA genes in the pig genome

BMC Genetics

Maciej Szydlowski¹  Adrian Grzemski¹  Paulina Paczynska¹ 

[1] Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poland, Wolynska 33, Poznan, 60-637, Poland

关键词: Genomic location;    Pig;    miRNA;   

Others  :  1121330
DOI  :  10.1186/s12863-015-0166-3

 received in 2013-08-13, accepted in 2015-01-16,  发布年份 2015

【 摘 要 】

Background

Recent completion of swine genome may simplify the production of swine as a large biomedical model. Here we studied sequence and location of known swine miRNA genes, key regulators of protein-coding genes at the level of RNA, and compared them to human and mouse data to prioritize future molecular studies.

Results

Distribution of miRNA genes in pig genome shows no particular relation to different genomic features including protein coding genes - proportions of miRNA genes in intergenic regions, introns and exons roughly agree with the size of these regions in the pig genome. Our analyses indicate that host genes harbouring intragenic miRNAs are longer from other protein-coding genes, however, no important GO enrichment was found. Swine mature miRNAs show high sequence similarity to their human and mouse orthologues. Location of miRNA genes relative to protein-coding genes is also similar among studied species, however, there are differences in the precise position in particular intergenic regions and within particular hosts. The most prominent difference between pig and human miRNAs is a large group of pig-specific sequences (53% of swine miRNAs). We found no evidence that this group of evolutionary new pig miRNAs is different from old miRNAs genes with respect to genomic location except that they are less likely to be clustered.

Conclusions

There are differences in precise location of orthologues miRNA genes in particular intergenic regions and within particular hosts, and their meaning for coexpression with protein-coding genes deserves experimental studies. Functional studies of a large group of pig-specific sequences in future may reveal limits of the pig as a model organism to study human gene expression.

【 授权许可】

   
2015 Paczynska et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [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. BioMed Central Full Text
• [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. BioMed Central Full Text
• [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. BioMed Central Full Text
• [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.