Chromatin modifiers KMT2D, BAF, and p300 are required for <i>de novo</i> binding of transcription factors on enhancers

Transcription factors (TFs) bind to enhancers and recruit H3K4me1 methyltransferase KMT2D, chromatin remodeler BAF, and H3K27 acetyltransferase p300 to activate transcription. However, the role of chromatin modifiers in regulating <i>de novo</i> binding of TFs on enhancers remains unclear. Using a robust nuclear translocation system, we show that the muscle lineage-determining TF MyoD binds to chromatin pervasively within one hour, with half of induced MyoD binding sites co-occupied by KMT2D, BAF, and p300. On the majority of these MyoD<sup>+</sup> enhancers, acute depletion of KMT2D or short-term inhibition of BAF or p300 enzymatic activity markedly reduces <i>de novo</i> binding of MyoD as well as that of KMT2D, BAF, and p300. On enhancers with intact MyoD binding despite these perturbations, we observe a cooperative recruitment among chromatin modifiers. Similar interdependent relationships are observed between the signal-dependent TF Glucocorticoid Receptor and KMT2D, BAF, and p300. Together, our findings show that chromatin modifiers are not only downstream effectors but also required for <i>de novo</i> binding of TFs on enhancers, refining a model of enhancer establishment as a process governed by functional cooperation rather than a strict hierarchy.

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Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2026-01-29
DOI
https://doi.org/10.64898/2026.01.29.702555
Primary Topic
Genomics and Chromatin Dynamics
Type
article
Field-Weighted Citation Impact
0.00

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article

Chromatin modifiers KMT2D, BAF, and p300 are required for de novo binding of transcription factors on enhancers

Hieu T. Van, Young-Kwon Park, Jieun Lee, Shamima Islam et al.
bioRxiv (Cold Spring Harbor Laboratory)
Genomics and Chromatin Dynamics
article

Chromatin modifiers KMT2D, BAF, and p300 are required for de novo binding of transcription factors on enhancers

Hieu T. Van, Young-Kwon Park, Jieun Lee, Shamima Islam, Weiqun Peng, Kai Ge, Vittorio Sartorelli, Chengyu Liu
article en

Abstract

Transcription factors (TFs) bind to enhancers and recruit H3K4me1 methyltransferase KMT2D, chromatin remodeler BAF, and H3K27 acetyltransferase p300 to activate transcription. However, the role of chromatin modifiers in regulating <i>de novo</i> binding of TFs on enhancers remains unclear. Using a robust nuclear translocation system, we show that the muscle lineage-determining TF MyoD binds to chromatin pervasively within one hour, with half of induced MyoD binding sites co-occupied by KMT2D, BAF, and p300. On the majority of these MyoD<sup>+</sup> enhancers, acute depletion of KMT2D or short-term inhibition of BAF or p300 enzymatic activity markedly reduces <i>de novo</i> binding of MyoD as well as that of KMT2D, BAF, and p300. On enhancers with intact MyoD binding despite these perturbations, we observe a cooperative recruitment among chromatin modifiers. Similar interdependent relationships are observed between the signal-dependent TF Glucocorticoid Receptor and KMT2D, BAF, and p300. Together, our findings show that chromatin modifiers are not only downstream effectors but also required for <i>de novo</i> binding of TFs on enhancers, refining a model of enhancer establishment as a process governed by functional cooperation rather than a strict hierarchy.

bioRxiv (Cold Spring Harbor Laboratory)
National Institutes of Health (US), George Washington University (US), National Institute of Arthritis and Musculoskeletal and Skin Diseases (US), National Institute of Diabetes and Digestive and Kidney Diseases (US), National Heart, Lung, and Blood Institute (US)
National Institutes of Health, National Heart, Lung, and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Arthritis and Musculoskeletal and Skin Diseases
Partnerships for the goals
Openalex Percentile: Top 73%
Genomics and Chromatin Dynamics
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