Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer

Sathira, Nuankanya; Yamashita, Riu; Tanimoto, Kousuke; Kanai, Akinori; Arauchi, Takako; Kanematsu, Soutaro; Nakai, Kenta; Suzuki, Yutaka; Sugano, Sumio

doi:10.1093/dnares/dsq007

Cited by 5 publications

(4 citation statements)

References 45 publications

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“…Publicly available data sets (Sathira et al 2010;Baillat et al 2012;The ENCODE Project Consortium 2012;Fong et al 2017;Davis et al 2018;Woo et al 2018;Choquet et al 2019) used in this study are listed in Supplemental Table S3. Heat maps and average plots were generated using deepTools.…”

Section: Analysis Of Publicly Available Datamentioning

confidence: 99%

Promoter-specific dynamics of TATA-binding protein association with the human genome

Hasegawa

Struhl

2019

Genome Res.

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Transcription factor binding to target sites in vivo is a dynamic process that involves cycles of association and dissociation, with individual proteins differing in their binding dynamics. The dynamics at individual sites on a genomic scale have been investigated in yeast cells, but comparable experiments have not been done in multicellular eukaryotes. Here, we describe a tamoxifen-inducible, time-course ChIP-seq approach to measure transcription factor binding dynamics at target sites throughout the human genome. As observed in yeast cells, the TATA-binding protein (TBP) typically displays rapid turnover at RNA polymerase (Pol) II-transcribed promoters, slow turnover at Pol III promoters, and very slow turnover at the Pol I promoter. Turnover rates vary widely among Pol II promoters in a manner that does not correlate with the level of TBP occupancy. Human Pol II promoters with slow TBP dissociation preferentially contain a TATA consensus motif, support high transcriptional activity of downstream genes, and are linked with specific activators and chromatin remodelers. These properties of human promoters with slow TBP turnover differ from those of yeast promoters with slow turnover. These observations suggest that TBP binding dynamics differentially affect promoter function and gene expression, possibly at the level of transcriptional reinitiation/bursting.

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Section: Analysis Of Publicly Available Datamentioning

confidence: 99%

Promoter-specific dynamics of TATA-binding protein association with the human genome

Hasegawa

Struhl

2019

Genome Res.

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“…We then used HEK293 cells, which do not contain endogenous Ptf1a or Foxa2 but contain ample Rbpj and E proteins (46), to test the individual versus joint contributions of these factors. Each compound site responded to Ptf1a and Foxa2 differently.…”

Section: Figmentioning

confidence: 99%

Program Specificity for Ptf1a in Pancreas versus Neural Tube Development Correlates with Distinct Collaborating Cofactors and Chromatin Accessibility

Meredith

Borromeo

Deering

et al. 2013

Molecular and Cellular Biology

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The lineage-specific basic helix-loop-helix transcription factor Ptf1a is a critical driver for development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. Most regions bound by Ptf1a are specific to each tissue, lie near genes needed for proper formation of each tissue, and coincide with regions of open chromatin. The specificity of Ptf1a binding is encoded in the DNA surrounding the Ptf1a-bound sites, because these regions are sufficient to direct tissue-restricted reporter expression in transgenic mice. Fox and Sox factors were identified as potential lineage-specific modifiers of Ptf1a binding, since binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Of the Fox factors expressed during pancreatic development, Foxa2 plays a major role. Indeed, Ptf1a and Foxa2 colocalize in embryonic pancreatic chromatin and can act synergistically in cell transfection assays. Together, these findings indicate that lineage-specific chromatin landscapes likely constrain the DNA binding of Ptf1a, and they identify Fox and Sox gene families as part of this process.

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“…Moreover, we also developed a method to enable large-scale analysis of transcriptional start sites (which we termed TSS Seq) by combining our full-length cDNA technology (oligo-capping) with massively parallel sequencing. 28 , 29 In this method, a sequence adaptor necessary for the sequencing reaction is introduced into the mRNA as a cap-replacing oligo so that the region immediately downstream of the TSS can be sequenced (TSS tag). 30 We demonstrated that the position of a TSS and its transcriptional level can be analysed at the same time by digital counting of the TSS tags.…”

Section: Introductionmentioning

confidence: 99%

Characterization of STAT6 Target Genes in Human B Cells and Lung Epithelial Cells

et al. 2011

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Using ChIP Seq, we identified 556 and 467 putative STAT6 target sites in the Burkitt's lymphoma cell line Ramos and in the normal lung epithelial cell line BEAS2B, respectively. We also examined the positions and expression of transcriptional start sites (TSSs) in these cells using our TSS Seq method. We observed that 44 and 132 genes in Ramos and BEAS2B, respectively, had STAT6 binding sites in proximal regions of their previously reported TSSs that were up-regulated at the transcriptional level. In addition, 406 and 109 of the STAT6 target sites in Ramos and BEAS2B, respectively, were located in proximal regions of previously uncharacterized TSSs. The target genes identified in Ramos and BEAS2B cells in this study and in Th2 cells in previous studies rarely overlapped and differed in their identity. Interestingly, ChIP Seq analyses of histone modifications and RNA polymerase II revealed that chromatin formed an active structure in regions surrounding the STAT6 binding sites; this event also frequently occurred in different cell types, although neither STAT6 binding nor TSS induction was observed. The rough landscape of STAT6-responsive sites was found to be shaped by chromatin structure, but distinct cellular responses were mainly mediated by distinct sets of transcription factors.

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Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer

Cited by 5 publications

References 45 publications

Promoter-specific dynamics of TATA-binding protein association with the human genome

Promoter-specific dynamics of TATA-binding protein association with the human genome

Program Specificity for Ptf1a in Pancreas versus Neural Tube Development Correlates with Distinct Collaborating Cofactors and Chromatin Accessibility

Characterization of STAT6 Target Genes in Human B Cells and Lung Epithelial Cells

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