The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages

Huang, Zhiqiang; Liang, Ning; Goñi, Saioa; Damdimopoulos, Anastasios; Wang, Cheng; Ballaire, Raphaëlle; Jager, Jennifer; Niskanen, Henri; Han, Hongya; Jakobsson, Tomas; Bracken, Adrian P.; Aouadi, Myriam; Venteclef, Nicolas; Kaikkonen, Minna U.; Fan, Rongrong; Treuter, Eckardt

doi:10.1016/j.molcel.2020.12.040

Cited by 30 publications

(45 citation statements)

References 97 publications

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“…However, sequences with ChIP-seq or ATAC-seq peaks span all four activity categories, consistent with prior reports that that DNA accessibility and TF binding data are not sufficient to identify functional enhancers and silencers (Doni Jayavelu et al, 2020; D. Huang et al, 2019; Z. Huang et al, 2021; Pang & Snyder, 2020; White et al, 2013).…”

Section: Resultssupporting

confidence: 88%

“…Silencers are often enhancers in other cell types (Brand et al, 1987; Doni Jayavelu et al, 2020; Gisselbrecht et al, 2020; Z. Huang et al, 2021; Jiang et al, 1993; Ngan et al, 2020; Pang & Snyder, 2020), reside in open chromatin (Doni Jayavelu et al, 2020; D. Huang et al, 2019; Z. Huang et al, 2021; Pang & Snyder, 2020), sometimes bear epigenetic marks of active enhancers (Fan et al, 2016; Z.…”

Section: Introductionmentioning

confidence: 99%

“…Huang et al, 2021; Jiang et al, 1993; Ngan et al, 2020; Pang & Snyder, 2020), reside in open chromatin (Doni Jayavelu et al, 2020; D. Huang et al, 2019; Z. Huang et al, 2021; Pang & Snyder, 2020), sometimes bear epigenetic marks of active enhancers (Fan et al, 2016; Z. Huang et al, 2021), and can be bound by TFs that also act on enhancers in the same cell type (Alexandre & Vincent, 2003; Grass et al, 2003; Z.…”

Section: Introductionmentioning

confidence: 99%

“…Huang et al, 2021; Pang & Snyder, 2020), sometimes bear epigenetic marks of active enhancers (Fan et al, 2016; Z. Huang et al, 2021), and can be bound by TFs that also act on enhancers in the same cell type (Alexandre & Vincent, 2003; Grass et al, 2003; Z. Huang et al, 2021; Iype et al, 2004; Jiang et al, 1993; Liu et al, 2014; Martínez-Montañés et al, 2013; Peng et al, 2005; Rachmin et al, 2015; Rister et al, 2015; Stampfel et al, 2015; White et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

Friedman¹,

Granas²,

Myers³

et al. 2021

Preprint

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Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF CRX in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences.

show abstract

Section: Resultssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

Friedman¹,

Granas²,

Myers³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…1 ) ( 9 , 28 ). These elements can function additively or synergistically ( 29 ), while some are associated with corepressors and act as silencers to repress transcription of target genes ( 30 ). Enhancer-like elements are also sometimes clustered into super-enhancers ( Fig.…”

Section: Enhancers and Associated Long Non-coding Rnasmentioning

confidence: 99%

Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs

Refael

Melamed

2021

Endocrinology

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The world of long non-coding RNAs (lncRNAs) has opened up massive new prospects in understanding the regulation of gene expression. Not only are there seemingly almost infinite numbers of lncRNAs in the mammalian cell, but they have highly diverse mechanisms of action. In the nucleus, some are chromatin-associated, transcribed from transcriptional enhancers (eRNAs) and/or direct changes in the epigenetic landscape with profound effects on gene expression. The pituitary gonadotrope is responsible for activation of reproduction through production and secretion of appropriate levels of the gonadotropic hormones. As such, it exemplifies a cell whose function is defined through changes in developmental and temporal patterns of gene expression, including those that are hormonally-induced. Roles for diverse distal regulatory elements and eRNAs in gonadotrope biology have only just begun to emerge. Here, we will present an overview of the different kinds of lncRNAs that alter gene expression, and what is known about their roles in regulating some of the key gonadotrope genes. We will also review various screens that have detected differentially expressed pituitary lncRNAs associated with changes in reproductive state, and those whose expression is found to play a role in gonadotrope-derived non-functioning pituitary adenomas. We hope to shed light on this exciting new field, emphasize the open questions, and encourage research to illuminate the roles of lncRNAs in various endocrine systems.

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Transcriptional repression shapes the identity and function of tissue macrophages

2021

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The changing extra‐ and intracellular microenvironment calls for rapid cell fate decisions that are precisely and primarily regulated at the transcriptional level. The cellular components of the immune system are excellent examples of how cells respond and adapt to different environmental stimuli. Innate immune cells such as macrophages are able to modulate their transcriptional programs and epigenetic regulatory networks through activation and repression of particular genes, allowing them to quickly respond to a rapidly changing environment. Tissue macrophages are essential components of different immune‐ and nonimmune cell‐mediated physiological mechanisms in mammals and are widely used models for investigating transcriptional regulatory mechanisms. Therefore, it is critical to unravel the distinct sets of transcription activators, repressors, and coregulators that play roles in determining tissue macrophage identity and functions during homeostasis, as well as in diseases affecting large human populations, such as metabolic syndromes, immune‐deficiencies, and tumor development. In this review, we will focus on transcriptional repressors that play roles in tissue macrophage development and function under physiological conditions.

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The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages

Cited by 30 publications

References 97 publications

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs

Transcriptional repression shapes the identity and function of tissue macrophages

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