Regional Regulation of Transcription in the Chicken Genome

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2010 Jan 16

PMID 20074332

Citations 6

Authors

Haisheng Nie

Richard P M A Crooijmans

John W M Bastiaansen

Hendrik-Jan Megens

Martien A M Groenen

Affiliations

Soon will be listed here.

Abstract

Background: Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis.

Results: We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes.

Conclusions: Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution.The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108.

Citing Articles

Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos.

Muthusamy M, Ramasamy K, Peters S, Palani S, Gowthaman V, Nagarajan M Metabolites. 2024; 14(12).

PMID: 39728450 PMC: 11678133. DOI: 10.3390/metabo14120669.

Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans.

Gao H, Wang Y, Li W, Gu Y, Lai Y, Bi Y J Exp Bot. 2018; 69(21):5089-5104.

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Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.

Vinuelas J, Kaneko G, Coulon A, Vallin E, Morin V, Mejia-Pous C BMC Biol. 2013; 11:15.

PMID: 23442824 PMC: 3635915. DOI: 10.1186/1741-7007-11-15.

Regional regulation of transcription in the bovine genome.

Kommadath A, Nie H, Groenen M, Te Pas M, Veerkamp R, Smits M PLoS One. 2011; 6(6):e20413.

PMID: 21673989 PMC: 3108615. DOI: 10.1371/journal.pone.0020413.

Neighbourhood continuity is not required for correct testis gene expression in Drosophila.

Meadows L, Chan Y, Roote J, Russell S PLoS Biol. 2010; 8(11):e1000552.

PMID: 21151342 PMC: 2994658. DOI: 10.1371/journal.pbio.1000552.

References

Kielman M, Smits R, Devi T, Fodde R, Bernini L . Homology of a 130-kb region enclosing the alpha-globin gene cluster, the alpha-locus controlling region, and two non-globin genes in human and mouse. Mamm Genome. 1993; 4(6):314-23. DOI: 10.1007/BF00357090. View

Gierman H, Indemans M, Koster J, Goetze S, Seppen J, Geerts D . Domain-wide regulation of gene expression in the human genome. Genome Res. 2007; 17(9):1286-95. PMC: 1950897. DOI: 10.1101/gr.6276007. View

Hurst L, Pal C, Lercher M . The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet. 2004; 5(4):299-310. DOI: 10.1038/nrg1319. View

Rodionov A . [Micro vs. macro: structural-functional organization of avian micro- and macrochromosomes]. Genetika. 1996; 32(5):597-608. View

Castillo-Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F . Selection for short introns in highly expressed genes. Nat Genet. 2002; 31(4):415-8. DOI: 10.1038/ng940. View

Chakalova L, Debrand E, Mitchell J, Osborne C, Fraser P . Replication and transcription: shaping the landscape of the genome. Nat Rev Genet. 2005; 6(9):669-77. DOI: 10.1038/nrg1673. View

Ovcharenko I, Loots G, Nobrega M, Hardison R, Miller W, Stubbs L . Evolution and functional classification of vertebrate gene deserts. Genome Res. 2004; 15(1):137-45. PMC: 540279. DOI: 10.1101/gr.3015505. View

Sproul D, Gilbert N, Bickmore W . The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet. 2005; 6(10):775-81. DOI: 10.1038/nrg1688. View

Singer G, Lloyd A, Huminiecki L, Wolfe K . Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol. 2004; 22(3):767-75. DOI: 10.1093/molbev/msi062. View

10.

Mijalski T, Harder A, Halder T, Kersten M, Horsch M, Strom T . Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc Natl Acad Sci U S A. 2005; 102(24):8621-6. PMC: 1143582. DOI: 10.1073/pnas.0407672102. View

11.

Boutanaev A, Kalmykova A, Shevelyov Y, Nurminsky D . Large clusters of co-expressed genes in the Drosophila genome. Nature. 2002; 420(6916):666-9. DOI: 10.1038/nature01216. View

12.

Versteeg R, van Schaik B, Van Batenburg M, Roos M, Monajemi R, Caron H . The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res. 2003; 13(9):1998-2004. PMC: 403669. DOI: 10.1101/gr.1649303. View

13.

Garcia-Fernandez J . The genesis and evolution of homeobox gene clusters. Nat Rev Genet. 2005; 6(12):881-92. DOI: 10.1038/nrg1723. View

14.

. Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. Nature. 1999; 401(6756):921-3. DOI: 10.1038/44853. View

15.

Habermann F, Cremer M, Walter J, Kreth G, von Hase J, Bauer K . Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res. 2001; 9(7):569-84. DOI: 10.1023/a:1012447318535. View

16.

Falcon S, Gentleman R . Using GOstats to test gene lists for GO term association. Bioinformatics. 2006; 23(2):257-8. DOI: 10.1093/bioinformatics/btl567. View

17.

Amores A, Force A, Yan Y, Joly L, Amemiya C, Fritz A . Zebrafish hox clusters and vertebrate genome evolution. Science. 1998; 282(5394):1711-4. DOI: 10.1126/science.282.5394.1711. View

18.

Morescalchi A, Odierna G, Olmo E . Karyology of the primitive salamanders, family Hynobiidae. Experientia. 1979; 35(11):1434-6. DOI: 10.1007/BF01962768. View

19.

. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004; 432(7018):695-716. DOI: 10.1038/nature03154. View

20.

Bourque G, Zdobnov E, Bork P, Pevzner P, Tesler G . Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 2004; 15(1):98-110. PMC: 540283. DOI: 10.1101/gr.3002305. View