A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells

Singh, Gurdeep; Mullany, Shanelle; Moorthy, Sakthi D; Zhang, Richard; Mehdi, Tahmid; Tian, Ruxiao; Duncan, A.; Moses, Alan M.; Mitchell, Jennifer A.

doi:10.1101/gr.272468.120

“…Moreover, these enriched motifs typically belong to cell-type specific TFs that are not expressed in mESCs and are associated with differentiation. Consistent with our findings, a recent study which systematically analyzed the quantity and composition of TF motifs for mESC enhancers described a threshold for the minimal number of TF motifs required for enhancer activity (Singh et al ., 2021).…”

Section: Discussionsupporting

confidence: 91%

“…Low activity enhancers were also enriched for the motif of p53, which was recently found to bind “dormant” enhancers in mESCs that are located in inaccessible chromatin and become activated upon cellular stress or during reprogramming (Peng et al ., 2020). Another plausible explanation for increased activity levels of enhancers could be the absolute number of motifs per enhancer as well as on the diversity of these motifs (Singh et al ., 2021). Accordingly, we found that the high-activity enhancers, on average, contain more motifs (10.6 compared to 9.8 average motifs/enhancer, Fig.…”

Section: Resultsmentioning

confidence: 99%

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Glaser

¹

,

Steiger

²

,

Fuchs

³

et al. 2021

Preprint

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Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess the dynamics of enhancer activity during the early stages of murine ESC differentiation, we analyzed accessible genomic regions using STARR-seq, a massively parallel reporter assay. This resulted in a genome-wide quantitative map of active mESC enhancers, in pluripotency and during the early stages of differentiation. We find that only a minority of accessible regions is active and that such regions are enriched near promoters, characterized by specific chromatin marks, enriched for distinct sequence motifs, and modeling shows that active regions can be predicted from sequence alone. Regions that change their activity upon retinoic acid-induced differentiation are more prevalent at distal intergenic regions when compared to constitutively active enhancers. Further, analysis of differentially active enhancers verified the contribution of individual TF motifs toward activity and inducibility as well as their role in regulating endogenous genes. Notably, the activity of retinoic acid receptor alpha (RARα) occupied regions can either increase or decrease upon the addition of its ligand, retinoic acid, with the direction of the change correlating with spacing and orientation of the RARα consensus motif and the co-occurrence of additional sequence motifs. Together, our genome-wide enhancer activity map elucidates features associated with enhancer activity levels, identifies regulatory regions disregarded by computational prediction tools, and provides a resource for future studies into regulatory elements in mESCs.

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“…Thus, it might be possible that these open but inactive regions become active in upon differentiation. Consistent with our findings, a recent study which systematically analyzed the quantity and composition of TF motifs for mESC enhancers described a threshold for the minimal number of TF motifs required for enhancer activity ( 61 ). Additionally, this finding of motifs adding synergistically to enhancer activity, once passing a threshold of minimal number of motifs, could explain the nature of super-enhancers, regulatory elements that are much larger in size (> 12 kb) and show much higher activity than regular enhancers.…”

Section: Discussionsupporting

confidence: 90%

“…Low activity enhancers were also enriched for the motif of p53, which was recently found to bind ‘dormant’ enhancers in mESCs that are located in inaccessible chromatin and become activated upon cellular stress or during reprogramming ( 45 ). Another plausible explanation for increased activity levels of enhancers could be the absolute number of motifs per enhancer as well as on the diversity of these motifs ( 61 ). Accordingly, we found that the high-activity enhancers, on average, contain more motifs (10.6 compared to 9.8 average motifs/enhancer, Figure 2D ) and were 14% larger than enhancers with low activity (385 bp versus 338 bp for low-activity enhancers, Figure 2E ).…”

Section: Resultsmentioning

confidence: 99%

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Glaser

¹

,

Steiger

²

,

Fuchs

³

et al. 2021

Nucleic Acids Research

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Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess the dynamics of enhancer activity during the early stages of murine ESC differentiation, we analyzed accessible genomic regions using STARR-seq, a massively parallel reporter assay. This resulted in a genome-wide quantitative map of active mESC enhancers, in pluripotency and during the early stages of differentiation. We find that only a minority of accessible regions is active and that such regions are enriched near promoters, characterized by specific chromatin marks, enriched for distinct sequence motifs, and modeling shows that active regions can be predicted from sequence alone. Regions that change their activity upon retinoic acid-induced differentiation are more prevalent at distal intergenic regions when compared to constitutively active enhancers. Further, analysis of differentially active enhancers verified the contribution of individual TF motifs toward activity and inducibility as well as their role in regulating endogenous genes. Notably, the activity of retinoic acid receptor alpha (RARα) occupied regions can either increase or decrease upon the addition of its ligand, retinoic acid, with the direction of the change correlating with spacing and orientation of the RARα consensus motif and the co-occurrence of additional sequence motifs. Together, our genome-wide enhancer activity map elucidates features associated with enhancer activity levels, identifies regulatory regions disregarded by computational prediction tools, and provides a resource for future studies into regulatory elements in mESCs.

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“…As is known, the regulatory regions of the genome represent clusters of the binding sites for sequence-specific transcription factors (TFs). There, the interplay between these TFs and their binding sites ( cis -regulatory elements) as well as the interaction of TFs with one another and the coactivator and chromatin remodeling complexes orchestrate the dynamic and diverse genetic programs, thereby determining the tissue-specific gene expression, spatiotemporal specificity of gene activities during development, and the ability of genes to respond to different external signals [ 7 , 8 , 9 , 10 , 11 , 12 ]. Thus, thanks to the binding to their specific sites on DNA (transcription factor binding sites, TFBSs), TFs directly interpret the regulatory part of the genome, performing the first step in deciphering the DNA sequence [ 13 , 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases

Degtyareva

¹

,

Antontseva

²

,

Merkulova

³

2021

IJMS

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The vast majority of the genetic variants (mainly SNPs) associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites. In this review, we first focus on the history of the discovery of regulatory SNPs (rSNPs) and systematized description of the existing methodical approaches to their study. Then, we brief the recent comprehensive examples of rSNPs studied from the discovery of the changes in the TFBS sequence as a result of a nucleotide substitution to identification of its effect on the target gene expression and, eventually, to phenotype. We also describe state-of-the-art genome-wide approaches to identification of regulatory variants, including both making molecular sense of genome-wide association studies (GWAS) and the alternative approaches the primary goal of which is to determine the functionality of genetic variants. Among these approaches, special attention is paid to expression quantitative trait loci (eQTLs) analysis and the search for allele-specific events in RNA-seq (ASE events) as well as in ChIP-seq, DNase-seq, and ATAC-seq (ASB events) data.

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A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells

Cited by 45 publications

References 78 publications

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases

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