Patterns and rates of intron divergence between humans and chimpanzees

Gazave, Élodie; Marquès-Bonet, Tomàs; Fernando, Olga; Charlesworth, Brian; Navarro, Arcadi

doi:10.1186/gb-2007-8-2-r21

Cited by 87 publications

(102 citation statements)

References 48 publications

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“…In addition, repeats in first introns were associated with greater expression divergence than repeats in other introns. This observation is consistent with previous work showing that most intronic regulatory regions occur in the first intron (Rohrer and Conley 1998), that the first intron has the highest divergence between human and chimpanzees (Gazave et al 2007), and that the first intron influences gene expression more than other introns (Jonsson et al 1992;Charron et al 2007).…”

Section: Discussionsupporting

confidence: 82%

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

et al. 2015

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Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation.

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Section: Discussionsupporting

confidence: 82%

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

et al. 2015

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“…A number of bioinformatic surveys established that the first intron of a eukaryotic gene tends to be longer than subsequent introns [16][17][18][19][20][21][22][23] and in humans and mice the first intron tends to be a little less than three times longer. 16 The huntingtin gene is a dramatic example of this.…”

Section: Architecture Of the Huntingtin Gene And Its Influence On Splmentioning

confidence: 99%

Aberrantly splicedHTT,a new player in Huntington’s disease pathogenesis

et al. 2013

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This discovery spurred our hypothesis that mis-splicing as opposed to proteolysis could be generating the smallest huntingtin fragment. We demonstrated that mis-splicing of mutant huntingtin intron 1 does indeed occur and results in a short polyadenylated mRNA, which is translated into an exon 1 protein.The exon 1 protein fragment is highly pathogenic. Transgenic mouse models containing just human huntingtin exon 1 develop a rapid onset of HD-like symptoms. Our finding that a small, mis-spliced HTT transcript and corresponding exon 1 protein are produced in the context of an expanded CAG repeat has unraveled a new molecular mechanism in HD pathogenesis. Here we present detailed models of how mis-splicing could be facilitated, what challenges remain in this model, and implications for therapeutic studies.

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“…3) All of the Piwi mutations were in the introns. Introns were once considered sequences of indefinite nature, or genome junk, but more and more researchers have realized that introns have important biological functions (Gazave et al, 2007). Intron RNA contains a variety of non-coding RNA (ncRNA), including micro-RNA, small nucleolus RNA, and guidance RNA for RNA editing (Mattick et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphism screening, molecular characterization, and evolutionary aspects of chicken Piwi genes

Wang¹,

Ma²,

Chang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The P-element-induced wimpy testis (Piwi) gene is involved in germline stem cell self-renewal, meiosis, RNA silencing, and transcriptional regulation. Piwi genes are relatively well conserved in many species, but their function in poultry species is unclear. In this study, Piwi genes were sequenced using a target-sequence capture assay in quail and 28 breeds of chicken. Single nucleotide polymorphisms (SNPs) and evolutionary aspects of these chicken breeds were then analyzed. We found that SNP sites existed mainly in the introns of a few chicken breeds, and we selected an SNP on intron 4 for further verification by Sanger sequencing, the results of which were similar to those obtained by the target-capture sequencing assay. The evolutionary analysis revealed that there were more mutations in the Chahua and Leghorn breeds than in the other breeds, and that the phylogenetic tree was divided into four main categories that suggested that Piwi is evolutionarily conserved, and mutations in the introns might be associated with gametogenesis. The screened SNPs can be used as 14803 SNP screening and analysis of chicken Piwi genes ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 14802-14810 (2015) candidate markers for Piwi, and our results provide basic information for the further study of Piwi function in poultry.

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Patterns and rates of intron divergence between humans and chimpanzees

Cited by 87 publications

References 48 publications

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

Aberrantly splicedHTT,a new player in Huntington’s disease pathogenesis

Single nucleotide polymorphism screening, molecular characterization, and evolutionary aspects of chicken Piwi genes

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