A matter of time — How transient transcription factor interactions create dynamic gene regulatory networks

Swift, Joseph; Coruzzi, Gloria M.

doi:10.1016/j.bbagrm.2016.08.007

Cited by 64 publications

(58 citation statements)

References 142 publications

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“…Thus, a limited number of Foxa2 molecules per cell will preferentially enrich on a set of binding sites to which Foxa2 has highest affinity. In the cellular context, affinity is not a function of DNA sequence binding alone, but rather represents a combination of different features including DNA shape, DNA methylation, chromatin organization and protein interactions in the vicinity of the binding site (Swift and Coruzzi, 2017). In this context, regions of active chromatin modifications are characterized by higher chromatin dynamics and generally enhanced accessibility, which may favor Foxa2 binding.…”

Section: Discussionmentioning

confidence: 99%

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Cernilogar¹,

Hasenoeder

Wang³

et al. 2019

Preprint

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Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

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Section: Discussionmentioning

confidence: 99%

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Cernilogar¹,

Hasenoeder

Wang³

et al. 2019

Preprint

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“…This is because across eukaryotes, TFs are detectably bound to only a small percentage of their regulated targets, as shown in plants [1][2][3] , yeast 4 , and animals 5,6 . Paradoxically, the very large set of TF-regulated, but unbound genes are typically dismissed as indirect targets, because standard approaches can only identify direct TF targets based on TF binding 7,8 . The alternative hypothesis is that the TF-regulated, but unbound genes are in fact direct targets that are only transiently bound by the TF.…”

mentioning

confidence: 99%

Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

et al. 2020

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Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genomewide can be applied to validate dynamic GRN models for any pathway or organism of interest.

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“…Transcription factors bind to specific DNA sequence and initiate the formation of higher-order complexes with cofactors and epigenetic enzymes, leading to chromosome structure remodeling and recruitment of general transcriptional machinery to initiate and maintain specific transcriptional profiles (1,2). Accurate regulation of transcription factor activation is indispensable for all aspects of development and epistasis.…”

Section: Introductionmentioning

confidence: 99%

Acetylation of Mastermind-like 1 by p300 Drives the Recruitment of NACK to Initiate Notch-Dependent Transcription

et al. 2017

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Although it has long been appreciated that p300 acts as a critical Notch coactivator, the mechanistic details of p300 in Notch-mediated transcription remain unclear. We previously demonstrated that PEAK1-related kinase activating pseudokinase 1 (NACK), also known as SGK223, is a critical coactivator of Notch signaling and binds to the Notch1 ternary complex. Herein we report that p300 and CBP acetylate Mastermind-like 1 (Maml1) on amino acid residues K188 and K189 to recruit NACK to the Notch1 ternary complex, which results in the recruitment of RNA polymerase II to initiate transcription. NACK is recruited to the ternary complexes containing Maml1 and Maml3, but not Maml2. Simultaneous inhibition of p300/ CBP and Notch has a synergistic effect in esophageal adenocarcinoma. In summary, this study provides a deeper mechanistic understanding of the assembly of the Notch transcriptional complex and provides rationale and proof of concept for a combinatorial therapeutic attack on Notch-dependent cancers. Cancer Res; 77(16); 4228-37. Ó2017 AACR.

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A matter of time — How transient transcription factor interactions create dynamic gene regulatory networks

Cited by 64 publications

References 142 publications

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

Acetylation of Mastermind-like 1 by p300 Drives the Recruitment of NACK to Initiate Notch-Dependent Transcription

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