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An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing

ABSTRACT: Transcriptional coregulators and transcription factors (TFs) contain intrinsically disordered regions (IDRs) that are critical for their partitioning and function in gene regulation. Canonically, IDRs drive coregulator-TF association by directly promoting multivalent protein-protein interactions. Using a chemical genetic approach, we report an unexpected mechanism by which the IDR of the corepressor LSD1 excludes TF association, acting as a dynamic conformational switch that tunes repression of active cis-regulatory elements. Hydrogen-deuterium exchange shows that the LSD1 IDR interconverts between transient open and closed conformational states, the latter of which inhibits partitioning of the proteins structured domains with TF hubs. This autoinhibitory switch controls leukemic differentiation by modulating repression of active cis-regulatory elements bound by LSD1 and master hematopoietic TFs. Together, these studies unveil that the dynamic crosstalk between opposing structured and unstructured regions is an alternative paradigm by which disordered regions can shape coregulator-transcription factor interactions to control cis-regulatory landscapes and cell fate.

INSTRUMENT(S): Q Exactive HF-X, Q Exactive HF, Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Steven A. Carr

PROVIDER: MSV000094239 | MassIVE | Tue Mar 05 11:46:00 GMT 2024

REPOSITORIES: MassIVE

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Project description:Understanding the regulatory genome remains a significant challenge. Annotation of regulatory elements and identification of the transcription factors (TFs) targeting these elements are key steps in understanding how a given cell interprets its genetic blueprint. One goal of the modENCODE (model organism Encyclopedia of DNA Elements) project is to survey a diverse sampling of TFs, both DNA-binding and non-DNA binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also suggest the existence of a partially self-contained Polycomb regulatory network, and highlight the importance of Trithorax-like (Trl) in maintaining hotspots of DNA binding throughout development. Furthermore, the data identify over 5,800 instances in which TFs target DNA regions with demonstrated enhancer activity. Regions of high TF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. A putative regulatory network generated based on these 84 regulators reveals hundreds of co-binding events, thousands of potential regulatory interactions, and distinct regulatory strategies at developmental and housekeeping genes. These data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago.

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An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing

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