5′-end SAGE for the analysis of transcriptional start sites

Hashimoto, Shinichi; Suzuki, Yutaka; Kasai, Yusuke; Morohoshi, Kei; Yamada, Tomonori; Sese, Jun; Morishita, Shinichi; Sugano, Sumio; Matsushima, Kouji

doi:10.1038/nbt998

Cited by 114 publications

(90 citation statements)

References 18 publications

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“…Indeed, we were amazed at the complex nature of the mammalian transcriptomes, which is being revealed by our and other studies, as well as their flexibility, enabling numerous features unique to each organism. In the present study, we used the 5Ј-end sequences of putative full-length cDNAs and avoided using recently produced and massively compiled data from tag-based approaches, such as CAGE and 5Ј-end SAGE data (Hashimoto et al 2004;. We took this approach because analyses of the latter would require different data processing and analyses, hindering a uniform interpretation of the data.…”

Section: Genome Research 1011mentioning

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: Genome Research 1011mentioning

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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“…In Drosophila melanogaster, we analyzed deep-sequencing serial analysis of gene expression (SAGE) data sets that are derived from a modified protocol that, like CAGE, recognizes and sequences the 59-capped end of full-length RNA transcripts (Hashimoto et al 2004). We considered three libraries generated from different developmental stages (Ahsan et al 2009), finding 27,515 (0.2%) SAGE tags that mapped across EEJs.…”

Section: Post-transcriptional Cleavage Occurs In Lower Eukaryotesmentioning

confidence: 99%

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Mercer¹,

Dinger²,

Bracken³

et al. 2010

Genome Res.

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The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 59 capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genomewide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage-and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.

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“…In addition to alternative splicing, other widespread mechanisms exist that contribute to genome complexity. These include RNA editing (Athanasiadis et al 2004;Blow et al 2004), trans-splicing (Takahara et al 2005), alternative transcription start sites (Hashimoto et al 2004), and alternative polyadenylation transcription termination sites (Beaudoing and Gautheret 2001).…”

mentioning

confidence: 99%

Tandem chimerism as a means to increase protein complexity in the human genome

Parra

Reymond²,

Dabbouseh³

et al. 2005

Genome Res.

184

195

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The "one-gene, one-protein" rule, coined by Beadle and Tatum, has been fundamental to molecular biology. The rule implies that the genetic complexity of an organism depends essentially on its gene number. The discovery, however, that alternative gene splicing and transcription are widespread phenomena dramatically altered our understanding of the genetic complexity of higher eukaryotic organisms; in these, a limited number of genes may potentially encode a much larger number of proteins. Here we investigate yet another phenomenon that may contribute to generate additional protein diversity. Indeed, by relying on both computational and experimental analysis, we estimate that at least 4%-5% of the tandem gene pairs in the human genome can be eventually transcribed into a single RNA sequence encoding a putative chimeric protein. While the functional significance of most of these chimeric transcripts remains to be determined, we provide strong evidence that this phenomenon does not correspond to mere technical artifacts and that it is a common mechanism with the potential of generating hundreds of additional proteins in the human genome

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5′-end SAGE for the analysis of transcriptional start sites

Cited by 114 publications

References 18 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

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Tandem chimerism as a means to increase protein complexity in the human genome

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