publication . Article . 2016

Intron Length Coevolution across Mammalian Genomes

Peter A. Keane; Cathal Seoighe;
Open Access English
  • Published: 01 Aug 2016 Journal: Molecular Biology and Evolution, volume 33, issue 10, pages 2,682-2,691 (issn: 0737-4038, eissn: 1537-1719, Copyright policy)
  • Publisher: Oxford University Press
Abstract
Although they do not contribute directly to the proteome, introns frequently contain regulatory elements and can extend the protein coding potential of the genome through alternative splicing. For some genes, the contribution of introns to the time required for transcription can also be functionally significant. We have previously shown that intron length in genes associated with developmental patterning is often highly conserved. In general, sets of genes that require precise coordination in the timing of their expression may be sensitive to changes in transcript length. A prediction of this hypothesis is that evolutionary changes in intron length, when they oc...
Subjects
free text keywords: Discoveries, coevolution, introns, transcription, coexpression., Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Intron, Cell Cycle Gene, Gene, Proteome, Transcription (biology), Genome, Alternative splicing, Biology
Funded by
SFI| Cathal Seoighe
Project
  • Funder: Science Foundation Ireland (SFI)
  • Project Code: 07/SK/M1211b
  • Funding stream: SFI Stokes Professorship & Lectureship Programme
39 references, page 1 of 3

Ardehali MB Lis JT.2009 Tracking rates of transcription and splicing in vivo. Nat Struct Mol Biol 16:1123–1124.19888309 [OpenAIRE] [PubMed]

Artieri CG Fraser HB.2014 Transcript length mediates developmental timing of gene expression across Drosophila. Mol Biol Evol 31(11): 2879–2889.25069653 [OpenAIRE] [PubMed]

Batada NN Urrutia AO Hurst LD.2007 Chromatin remodelling is a major source of coexpression of linked genes in yeast. Trends Genet 23:480–484.17822800 [OpenAIRE] [PubMed]

Castillo-Davis CI Mekhedov SL Hartl DL Koonin EV Kondrashov FA.2002 Selection for short introns in highly expressed genes. Nat Genet 31:415–418.12134150 [OpenAIRE] [PubMed]

Chen X Shi S He X.2009 Evidence for gene length as a determinant of gene coexpression in protein complexes. Genetics 183:751–754. 1SI–5SI.19620395 [OpenAIRE] [PubMed]

Chorev M Carmel L.2012 The function of introns. Front Genet 3:55.22518112 [OpenAIRE] [PubMed]

Cunningham F Amode MR Barrell D Beal K Billis K Brent S Carvalho-Silva D Clapham P Coates G Fitzgerald S, 2015 Ensembl 2015. Nucleic Acids Res 43:D662–D669.25352552 [OpenAIRE] [PubMed]

Eisenberg E Levanon EY.2003 Human housekeeping genes are compact. Trends Genet 19:362–365.12850439 [OpenAIRE] [PubMed]

Falcon S Gentleman R.2007 Using GOstats to test gene lists for GO term association. Bioinform Oxf Engl 23:257–258.

Fox-Walsh KL Dou Y Lam BJ Hung S Baldi PF Hertel KJ.2005 The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102:16176–16181.16260721 [OpenAIRE] [PubMed]

Fraser HB Hirsh AE Wall DP Eisen MB.2004 Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci USA 101:9033–9038.15175431 [OpenAIRE] [PubMed]

Gelfman S Burstein D Penn O Savchenko A Amit M Schwartz S Pupko T Ast G.2012 Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res 22:35–50.21974994 [OpenAIRE] [PubMed]

Hubbard TJP Aken BL Ayling S Ballester B Beal K Bragin E Brent S Chen Y Clapham P Clarke L, 2009 Ensembl 2009. Nucleic Acids Res 37:D690–D697.19033362 [OpenAIRE] [PubMed]

Jansen R Greenbaum D Gerstein M.2002 Relating whole-genome expression data with protein-protein interactions. Genome Res 12:37–46.11779829 [OpenAIRE] [PubMed]

Jeffares DC Penkett CJ Bähler J.2008 Rapidly regulated genes are intron poor. Trends Genet 24:375–378.18586348 [OpenAIRE] [PubMed]

39 references, page 1 of 3
Abstract
Although they do not contribute directly to the proteome, introns frequently contain regulatory elements and can extend the protein coding potential of the genome through alternative splicing. For some genes, the contribution of introns to the time required for transcription can also be functionally significant. We have previously shown that intron length in genes associated with developmental patterning is often highly conserved. In general, sets of genes that require precise coordination in the timing of their expression may be sensitive to changes in transcript length. A prediction of this hypothesis is that evolutionary changes in intron length, when they oc...
Subjects
free text keywords: Discoveries, coevolution, introns, transcription, coexpression., Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Intron, Cell Cycle Gene, Gene, Proteome, Transcription (biology), Genome, Alternative splicing, Biology
Funded by
SFI| Cathal Seoighe
Project
  • Funder: Science Foundation Ireland (SFI)
  • Project Code: 07/SK/M1211b
  • Funding stream: SFI Stokes Professorship & Lectureship Programme
39 references, page 1 of 3

Ardehali MB Lis JT.2009 Tracking rates of transcription and splicing in vivo. Nat Struct Mol Biol 16:1123–1124.19888309 [OpenAIRE] [PubMed]

Artieri CG Fraser HB.2014 Transcript length mediates developmental timing of gene expression across Drosophila. Mol Biol Evol 31(11): 2879–2889.25069653 [OpenAIRE] [PubMed]

Batada NN Urrutia AO Hurst LD.2007 Chromatin remodelling is a major source of coexpression of linked genes in yeast. Trends Genet 23:480–484.17822800 [OpenAIRE] [PubMed]

Castillo-Davis CI Mekhedov SL Hartl DL Koonin EV Kondrashov FA.2002 Selection for short introns in highly expressed genes. Nat Genet 31:415–418.12134150 [OpenAIRE] [PubMed]

Chen X Shi S He X.2009 Evidence for gene length as a determinant of gene coexpression in protein complexes. Genetics 183:751–754. 1SI–5SI.19620395 [OpenAIRE] [PubMed]

Chorev M Carmel L.2012 The function of introns. Front Genet 3:55.22518112 [OpenAIRE] [PubMed]

Cunningham F Amode MR Barrell D Beal K Billis K Brent S Carvalho-Silva D Clapham P Coates G Fitzgerald S, 2015 Ensembl 2015. Nucleic Acids Res 43:D662–D669.25352552 [OpenAIRE] [PubMed]

Eisenberg E Levanon EY.2003 Human housekeeping genes are compact. Trends Genet 19:362–365.12850439 [OpenAIRE] [PubMed]

Falcon S Gentleman R.2007 Using GOstats to test gene lists for GO term association. Bioinform Oxf Engl 23:257–258.

Fox-Walsh KL Dou Y Lam BJ Hung S Baldi PF Hertel KJ.2005 The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102:16176–16181.16260721 [OpenAIRE] [PubMed]

Fraser HB Hirsh AE Wall DP Eisen MB.2004 Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci USA 101:9033–9038.15175431 [OpenAIRE] [PubMed]

Gelfman S Burstein D Penn O Savchenko A Amit M Schwartz S Pupko T Ast G.2012 Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res 22:35–50.21974994 [OpenAIRE] [PubMed]

Hubbard TJP Aken BL Ayling S Ballester B Beal K Bragin E Brent S Chen Y Clapham P Clarke L, 2009 Ensembl 2009. Nucleic Acids Res 37:D690–D697.19033362 [OpenAIRE] [PubMed]

Jansen R Greenbaum D Gerstein M.2002 Relating whole-genome expression data with protein-protein interactions. Genome Res 12:37–46.11779829 [OpenAIRE] [PubMed]

Jeffares DC Penkett CJ Bähler J.2008 Rapidly regulated genes are intron poor. Trends Genet 24:375–378.18586348 [OpenAIRE] [PubMed]

39 references, page 1 of 3
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publication . Article . 2016

Intron Length Coevolution across Mammalian Genomes

Peter A. Keane; Cathal Seoighe;