Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes

Wolf, Bennett; Zhao, Yanding; McCray, Andrew; Hawk, William H.; Deary, Luke T; Sugiarto, Nicholas W; LaCroix, Ian S; Gerber, Scott A.; Cheng, Chao; Wang, Xiaofeng

doi:10.1038/s41594-022-00880-x

Cited by 32 publications

(19 citation statements)

References 62 publications

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“…Here, using well-controlled synthetic sequences, we clearly demonstrated that the binding of FOXA1 and AP-1 is mutually dependent. This finding, together with a previous proposal that AP-1 may also function as a PF 55 , raises an intriguing possibility that FOXA1 and AP-1 may bind together to achieve sufficient pioneering activities for the invasion and remodeling of closed chromatin in A549, which may contribute to cell-type-specific enhancer selection 56 .…”

Section: Discussionmentioning

confidence: 54%

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

Xu,

Kleinschmidt,

Yang

et al. 2023

Preprint

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Despite the unique ability of pioneer transcription factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called ChIP-ISO to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1. Combining ChIP-ISO within vitroand neural network analyses, we find that 1) FOXA1 binding is strongly affected by co-binding TFs AP-1 and CEBPB, 2) FOXA1 and AP-1 show binding cooperativityin vitro, 3) FOXA1’s binding is determined more by local sequences than chromatin context, including eu-/heterochromatin, and 4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.

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Section: Discussionmentioning

confidence: 54%

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

Xu,

Kleinschmidt,

Yang

et al. 2023

Preprint

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“…In our model, β is related to the turnover of a latent chromatin modification m. Increasing β can occur by increasing its global production (κ 1 ) or decreasing its global removal (κ −1 ). The mechanisms underlying the modification of enhancer chromatin involve the activity of many cellular factors, including chromatin remodelers such as the SWI/SNF, Mi-2/NuRD, SET1/MLL, and Polycomb complexes, and involve various mechanisms including the depletion and modification of histone proteins [78][79][80][81][82]. In addition to these, the methylation of DNA itself can play a role in regulating enhancer function [83].…”

Section: Discussionmentioning

confidence: 99%

EnhancerNet: a model for enhancer selection in dense regulatory networks recapitulates the dynamics of cell type acquisition

Karin

2024

Preprint

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Multicellular organisms are made of many cell types that share a common genetic code. Cell type specification occurs through feedback interactions between transcription factors (TFs) and enhancers, which are regulatory elements with dynamic chromatin that can initiate transcription in distal genes. Understanding the structure and dynamics of these regulatory networks is a key challenge for cell biology. Here, we address this by considering a generic model for a dense feedback network involving TFs and enhancers, where TF binding modulates enhancer activity by adjusting its chromatin state ("EnhancerNet"). We show that experimental observations on autoregulation in these networks provide exacting constraints on the EnhancerNet model. The model recapitulates the dynamics of enhancer selection and cell type specification. EnhancerNet has two pathways for a cell to change its identity - by direct reprogramming or by differentiation through progenitors. These pathways capture the known experimental phenomenology of the corresponding pathways in cells. Moreover, they recapitulate known reprogramming recipes and the complex differentiation hierarchy in hematopoiesis with no fitting parameters. In addition to specific experimental predictions, the EnhancerNet model can explain how new cell types can evolve and highlights the functional importance of various aspects of gene regulation in animals.

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“…New proximity labeling studies from Wolf et al reveal context-dependent interactions between mammalian SWI/SNF (BAF) complexes and the AP-1 complex. Members of the JUN, FOS, ATF, and MAF TF families comprise the dimeric AP-1 complex.…”

Section: Emerging Relationships Among Swi/snf Transcription Factors A...mentioning

confidence: 99%

Functional Epigenomics: Pioneering Changes in Chromatin Structure

Tallan

Hoffman

2023

Biochemistry

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Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes

Cited by 32 publications

References 62 publications

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

EnhancerNet: a model for enhancer selection in dense regulatory networks recapitulates the dynamics of cell type acquisition

Functional Epigenomics: Pioneering Changes in Chromatin Structure

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