Unraveling determinants of transcription factor binding outside the core binding site

Levo, Michal; Zalckvar, Einat; Sharon, Eilon; Machado, Ana Carolina Dantas; Kalma, Yael; Lotam-Pompan, Maya; Weinberger, Adina; Yakhini, Zohar; Rohs, Remo; Segal, Eran

doi:10.1101/gr.185033.114

Cited by 151 publications

(181 citation statements)

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“…6B), providing further support to the above claims on TATA elements' functionality. Previous studies showed that flanking bases affect in vivo TF binding specificities, possibly through effects on DNA structure (Aow et al 2013;Gordân et al 2013;Rajkumar et al 2013;Levo et al 2015). We thus explored the extent to which the immediate context around the TATA element influences its function by additionally randomizing flanking bases around the TATAAAAA and TATATATA 8-mers inserted into position −98.…”

Section: Wwwgenomeorgmentioning

confidence: 99%

Core promoter sequence in yeast is a major determinant of expression level

et al. 2015

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The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription. Here, we present the first comprehensive study of yeast core promoters, providing massively parallel measurements of core promoter activity and of TSS locations and relative usage for thousands of native and designed sequences. We found core promoter activity to be highly correlated to the activity of the entire promoter and that sequence variation in different core promoter regions substantially tunes its activity in a predictable way. We also show that location, orientation, and flanking bases critically affect TATA element function, that transcription initiation in highly active core promoters is focused within a narrow region, that poly(dA:dT) orientation has a functional consequence at the 3 ′ end of promoters, and that orthologous core promoters across yeast species have conserved activities. Our results demonstrate the importance of core promoters in the quantitative study of gene regulation.[Supplemental material is available for this article.]The RNA polymerase II (Pol II) core promoter is the region to which Pol II and its accompanying general transcription factors are recruited to the DNA, form the pre-initiation complex (PIC), and act to initiate transcription (Smale and Kadonaga 2003). In yeast, the PIC is recruited to a TATA element, either a consensus TATA box or a weaker one with 1-2 mismatches to the consensus (Singer et al. 1990;Basehoar et al. 2004;Sugihara et al. 2011;Rhee and Pugh 2012). In both yeast and metazoans, PIC recruitment to a TATA element leads to promoter DNA melting ∼20 base pairs (bp) downstream from it (Giardina and Lis 1993), with the promoter sequence ∼30 bp downstream from the TATA element located at the Pol II active center (Bushnell et al. 2004;Miller and Hahn 2006). While in metazoans this leads to transcription initiation ∼30 bp downstream from the TATA element, in S. cerevisiae, Pol II performs a downstream scan of the template strand in search of transcription start sites (TSSs) (Giardina and Lis 1993;Kuehner and Brow 2006;Sugihara et al. 2011;Fishburn and Hahn 2012) in a manner that depends on the sequence around and upstream of the TSS (Hahn et al. 1985;Furter-Graves and Hall 1990;Faitar et al. 2001;Zhang and Dietrich 2005;Fishburn and Hahn 2012;Goel et al. 2012). This results in transcription initiation between 40-120 bp downstream from the TATA element and typical core promoter lengths of 100-200 bp (Smale and Kadonaga 2003;Lubliner et al. 2013). To allow access of the PIC to the DNA, core promoters typically contain a nucleosome-free region (NFR) (Field et al. 2008;Kaplan et al. 2009).In the study of regulatory sequences and their effects on expression, core promoter sequences remain relatively understudied, as most efforts are directed at transcription factor (TF) binding sites and their role in determining regulatory logic and expression levels (Levo and Segal 2014). In yeast, many core promoter-related studies revolved around the effec...

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Section: Wwwgenomeorgmentioning

confidence: 99%

Core promoter sequence in yeast is a major determinant of expression level

et al. 2015

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“…However, selective binding of motifs by TFs has also been observed in a variety of in vitro experiments (Noyes et al 2008;Badis et al 2009;Berger and Bulyk 2009;Zhao et al 2009;Slattery et al 2011;Enuameh et al 2013;Gordân et al 2013;Jolma et al 2013;Afek et al 2014;Weirauch et al 2014;Abe et al 2015;Levo et al 2015). These in vitro studies show that TFs can bind to different sequences containing a similar motif with a large range of different affinities, which suggests that TF-DNA binding specificity is influenced by the DNA context surrounding the motif.…”

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confidence: 91%

“…These in vitro studies show that TFs can bind to different sequences containing a similar motif with a large range of different affinities, which suggests that TF-DNA binding specificity is influenced by the DNA context surrounding the motif. Indeed, the contribution of the regions directly flanking the motif to binding specificity in vitro has been demonstrated for a small number of TFs (Gordân et al 2013;Afek et al 2014;Yang et al 2014;Levo et al 2015). The sequence environment of a motif has also been shown to contribute to transcriptional regulation by the TF Cone-rod homeobox (CRX) (White et al 2013).…”

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confidence: 99%

A widespread role of the motif environment in transcription factor binding across diverse protein families

et al. 2015

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Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regions. Interestingly, based on a vast amount of data accumulated from genomic assays, it has been shown that only a small fraction of all potential binding sites containing the consensus motif of a given TF actually bind the protein. Recent in vitro binding assays, which exclude the effects of the cellular environment, also demonstrate selective TF binding. An intriguing conjecture is that the surroundings of cognate binding sites have unique characteristics that distinguish them from other sequences containing a similar motif that are not bound by the TF. To test this hypothesis, we conducted a comprehensive analysis of the sequence and DNA shape features surrounding the core-binding sites of 239 and 56 TFs extracted from in vitro HT-SELEX binding assays and in vivo ChIP-seq data, respectively. Comparing the nucleotide content of the regions around the TF-bound sites to the counterpart unbound regions containing the same consensus motifs revealed significant differences that extend far beyond the core-binding site. Specifically, the environment of the bound motifs demonstrated unique sequence compositions, DNA shape features, and overall high similarity to the core-binding motif. Notably, the regions around the binding sites of TFs that belong to the same TF families exhibited similar features, with high agreement between the in vitro and in vivo data sets. We propose that these unique features assist in guiding TFs to their cognate binding sites.

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“…TFs can precisely identify their functional binding sites from among the other 99.8% of putative binding sites in a cellular environment in vivo . Given the multiple layers that contribute to in vivo binding (Levo and Segal 2014;Slattery et al 2014;Mathelier et al 2016;Zentner et al 2015), it is clear that DNA sequence and shape at core binding sites, which in vitro experiments have identified as determinants of DNA binding specificity (Zhao and Stormo 2011;Gordân et al 2013;Zhou et al 2015;Abe et al 2015;Levo et al 2015;Yang et al 2017), are not sufficient to explain TF binding in vivo. An important question is how TFs distinguish their functional binding sites (BSs) in one region of the genome from putative non-BSs with exactly-matched core motifs in other regions in vivo.…”

Section: Introductionmentioning

confidence: 99%

Relationship between histone modifications and transcription factor binding is protein family specific

Xin

Rohs

2018

Genome Res.

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The very small fraction of putative binding sites (BSs) TFs displayed protein family-specific preferences for HM patterns surrounding BSs, with high agreement among cell lines. Moreover, compared to models based on DNA sequence and shape at flanking regions of BSs, HM-augmented quantitative machine-learning methods resulted in increased performance in a TF family-specific manner. Analysis of the relative importance of features in these models indicated that TFs, displaying larger HM pattern differences between BSs and non-BSs, bound DNA in an HM-specific manner on a protein family-specific basis. We propose that TF family-specific HM preferences reveal distinct mechanisms that assist in guiding TFs to their cognate BSs by altering chromatin structure and accessibility.

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Unraveling determinants of transcription factor binding outside the core binding site

Cited by 151 publications

References 50 publications

Core promoter sequence in yeast is a major determinant of expression level

Core promoter sequence in yeast is a major determinant of expression level

A widespread role of the motif environment in transcription factor binding across diverse protein families

Relationship between histone modifications and transcription factor binding is protein family specific

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