Alu -mediated phylogenetic novelties in gene regulation and development 1 1Edited by J. Karn

Hamdi, Hamdi; Nishio, Hisahide; Tavis, Jeffrey H; Zielinski, Rita; Dugaiczyk, Achilles

doi:10.1006/jmbi.2000.3795

Cited by 63 publications

(51 citation statements)

References 27 publications

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“…Especially, the so-called retroelement-type repetitive elements, such as L1 and Alu, mostly accounted for this differential distribution. There are a number of reported examples in which such classes of retroelements were integrated in the vicinity of future TSSs and acquired transcriptional regulatory activities via slight changes in their sequences (Norris et al 1995;Vansant and Reynolds 1995;Hamdi et al 2000). Considering that L1 and Alu spread throughout the human genome after the human and mouse lineages separated, integration of those elements could explain the generation of species-specific promoters.…”

Section: Possible Origin Of the "Non-conserved" Papsmentioning

confidence: 99%

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

et al. 2007

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Although recent studies have revealed that the majority of human genes are subject to regulation of alternative promoters, the biological relevance of this phenomenon remains unclear. We have also demonstrated that roughly half of the human RefSeq genes examined contain putative alternative promoters (PAPs). Here we report large-scale comparative studies of PAPs between human and mouse counterpart genes. Detailed sequence comparison of the 17,245 putative promoter regions (PPRs) in 5463 PAP-containing human genes revealed that PPRs in only a minor fraction of genes (807 genes) showed clear evolutionary conservation as one or more pairs. Also, we found that there were substantial qualitative differences between conserved and non-conserved PPRs, with the latter class being AT-rich PPRs of relative minor usage, enriched in repetitive elements and sometimes producing transcripts that encode small or no proteins. Systematic luciferase assays of these PPRs revealed that both classes of PPRs did have promoter activity, but that their strength ranges were significantly different. Furthermore, we demonstrate that these characteristic features of the non-conserved PPRs are shared with the PPRs of previously discovered putative non-protein coding transcripts. Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. BP870448-BP873619 and BP244227-BP249739.]With the completion of the human and mouse genome sequencing projects (Waterston et al. 2002; International Human Genome Sequencing Consortium 2004) as well as the large-scale compilation of full-length cDNA information (Zhang et al. 2000;Okazaki et al. 2002;Strausberg et al. 2002;Imanishi et al. 2004;Ota et al. 2004), it has gradually become clear that the genome systems in higher mammals are far more complex than previously thought. Now, the once-dominant static view that a single locus corresponds to only one transcript and one protein has been shown to be of very limited validity. Rather, it is more common for a single locus to produce several transcript variants. In about half of human genes, on average, four different transcripts are produced by alternative splicing and as a consequence translated into proteins of divergent biological functions (Modrek and Lee 2002;Imanishi et al. 2004). Similarly, recent studies also demonstrated that diversification via transcriptional regulation is no less common in human genes (Landry et al. 2003). By use of alternative promoters (APs), which consist of different modules of transcriptional regulatory elements, diversified transcriptional regulation is enabled within a single locus (Landry et al. 2003;Carninci et al. 2005;Cheng et al. 2005;Kim et al. 2005;Kimura et al. 2006).The functional diversification of a single gene enabled by the use of alternative splices (ASs) and APs ...

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Section: Possible Origin Of the "Non-conserved" Papsmentioning

confidence: 99%

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

et al. 2007

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“…Diverged genomes with different silencing and expression patterns may exhibit incompatibilities when joined. For example, transposons inserted next to genes can alter their expression pattern (Martienssen 1998;Hamdi et al 2000;Kashkush et al 2003). The regulatory novelty provided by the transposon can be recruited to build promoters with new advantageous specificities.…”

Section: Mechanismsmentioning

confidence: 99%

Do the different parental ‘heteromes’ cause genomic shock in newly formed allopolyploids?

Comai

Madlung

Josefsson

et al. 2003

Phil. Trans. R. Soc. Lond. B

159

132

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Allopolyploidy, the joining of two parental genomes in a polyploid organism with diploid meiosis, is an important mechanism of reticulate evolution. While many successful long-established allopolyploids are known, those formed recently undergo an instability phase whose basis is now being characterized. We describe observations made with the Arabidopsis system that include phenotypic instability, gene silencing and activation, and methylation changes. We present a model based on the epigenetic destabilization of genomic repeats, which in the parents are heterochromatinized and suppressed. We hypothesize that loss of epigenetic suppression of these sequences, here defined as the heterome, results in genomic instability including silencing of single-copy genes.

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“…Repetitive elements at the boundaries of the blocks could contribute to such modifications. There are a number of examples in which retroelements integrated in the vicinity of TSSs became involved in transcriptional regulation via changes in their sequences (Norris et al 1995;Vansant and Reynolds 1995;Hamdi et al 2000). It is likely that such variations have accumulated during evolution and have laid the genetic background to drive speciation during certain periods of time.…”

Section: Genome Research 1715mentioning

confidence: 99%

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

Suzuki¹,

Yamashita²,

Shirota³

et al. 2004

Genome Res.

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Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the upstream putative promoter sequences over the 1-kb proximal regions and found that the sequence conservation could not be further extended at, on average, 510 bp upstream positions of the TSSs. This discontinuous manner of the sequence conservation revealed a "block" structure in about one-third of the putative promoter regions. Consistently, we also observed that G+C content and CpG frequency were significantly different inside and outside the blocks. Within the blocks, the sequence identity was uniformly 65% regardless of their length. About 90% of the previously characterized transcription factor binding sites were located within those blocks. In 46% of the blocks, the 5Ј ends were bounded by interspersed repetitive elements, some of which may have nucleated the genomic rearrangements. The length of the blocks was shortest in the promoters of genes encoding transcription factors and of genes whose expression patterns are brain specific, which suggests that the evolutional diversifications in the transcriptional modulations should be the most marked in these populations of genes.

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Alu -mediated phylogenetic novelties in gene regulation and development 1 1Edited by J. Karn

Cited by 63 publications

References 27 publications

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Do the different parental ‘heteromes’ cause genomic shock in newly formed allopolyploids?

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

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