Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures DOI Creative Commons
Joshua Justice, Todd M. Greco, Josiah E. Hutton

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 11, 2024

Abstract Huntington’s disease (HD) is a debilitating neurodegenerative disorder affecting an individual’s cognitive and motor abilities. HD caused by mutation in the huntingtin gene producing toxic polyglutamine-expanded protein (mHTT) leading to degeneration striatum cortex. Yet, molecular signatures that underlie tissue-specific vulnerabilities remain unclear. Here, we investigate this aspect leveraging multi-epitope interaction assays, subcellular fractionation, thermal proteome profiling, genetic modifier assays. Use of human cell, mouse, fly models afforded capture distinct pools epitope-enriched tissue-dependent interactions linked dysregulated cellular pathways relevance. We established HTT association with nearly all subunits transcriptional regulatory Mediator complex (20/26), preferential enrichment MED15 tail domain. Using KO models, find modulates localization assembly Mediator. demonstrated striatal enriched functional regulators calcium homeostasis chromatin remodeling, whose relevance was supported modifiers Altogether, offer insights into tissue- localization-dependent (m)HTT functions pathobiology.

Language: Английский

Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics DOI Creative Commons

Wilfried Engl,

Aliz Kunstar-Thomas,

Si‐Yi Chen

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 2, 2024

Despite their prevalent cancer implications, the in vivo dynamics of SWI/SNF chromatin remodelers and how misregulation such underpins remain poorly understood. Using live-cell single-molecule tracking, we quantify intranuclear diffusion chromatin-binding three key subunits common to all major human remodeler complexes (BAF57, BAF155 BRG1), resolve two temporally distinct stable binding modes for fully assembled complex. Super-resolved density mapping reveals heterogeneous, nanoscale "hotspots" across nucleoplasm where multiple events (especially longer-lived ones) preferentially cluster. Importantly, uncover roles bromodomain modulating binding/targeting a DNA-accessibility-dependent manner, pointing model successive within leads sustained productive remodeling. Finally, systematic comparison six BRG1 mutants implicated various cancers unveils alterations unique each mutant, shedding insight into multi-modal landscape regulating spatio-temporal organizational remodelers. Live-cell imaging complex cell nucleus, uncovers aberrations DNA associated with cancers.

Language: Английский

Citations

2
Mechanistic basis of gene regulation by SRCAP and H2A.Z DOI Open Access
Armelle Tollenaere, Enes Ugur, Cédric Deluz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 7, 2024

Summary A central problem in gene regulation is to discriminate regulatory functions of chromatin composition from the one chromatin-modifying complexes. This question has been virtually unexplored context H2A.Z histone variant and its incorporation into nucleosomes by Snf2 Related CREBBP Activator Protein (SRCAP) complex. Here we combine rapid SRCAP depletion, a mutant lacking deposition activity, quantitative genome-wide approaches dissect how regulate transcription pluripotent stem cells. We find that exhibits essential H2A.Z-independent preventing DNA binding lineage-specific factors at enhancers stimulating factor promoters. In contrast, acts mainly as transcriptional repressor requires dynamic reloading throughout cell cycle. Our study demonstrates SRCAP-H2A.Z axis broadly orchestrates promote self-renewal, inhibit differentiation, maintain plasticity

Language: Английский

Citations

1
The SWI/SNF PBAF complex facilitates REST occupancy at repressive chromatin DOI Creative Commons
Elena Grossi,

Christie B. Nguyen,

Saul Carcamo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

Summary Multimeric SWI/SNF chromatin remodelers assemble into discrete conformations with unique complex functionalities difficult to dissect. Distinct cancers harbor mutations in specific subunits, altering the landscape, such as PBAF-specific component ARID2 melanoma. Here, we performed comprehensive epigenomic profiling of complexes and their associated states melanoma melanocytes uncovered a subset PBAF-exclusive regions that coexist PRC2 repressive chromatin. Time-resolved approaches revealed PBAF are generally less sensitive ATPase-mediated remodeling than BAF sites. Moreover, PBAF/PRC2-bound loci enriched for REST, transcription factor represses neuronal genes. In turn, absence consequent disruption hinders ability REST bind inactivate its targets, leading upregulation synaptic transcripts. Remarkably, this gene signature is conserved patients mutations. sum, demonstrate role generating accessibility silencing at repressed chromatin, important implications disease.

Language: Английский

Citations

1
Intrinsically Disordered Regions Define Unique Protein Interaction Networks in CHD Family Remodelers DOI Creative Commons
Mehdi Sharifi Tabar, Chirag Parsania, Caroline Giardina

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 25, 2024

Abstract Chromodomain helicase DNA-binding (CHD1-9) enzymes reposition nucleosomal DNA for transcription, recombination, and replication. They possess highly conserved ATPase domains flanked by poorly characterised N- C-termini, which are enriched with intrinsically disordered regions (IDRs) short aggregation-prone (APRs). The roles of IDRs APRs in CHD function has remained elusive. Here, integrating proteomics AlphaFold Multimer analysis, we defined the protein-protein interaction (PPI) networks within C-termini all CHDs. We generated a comprehensive map CHD1-9-specific binding proteins, revealing dozens novel interactions transcription regulators. identified APR that contribute to PPI formation demonstrated C-terminus CHD4 is critical its nucleosome remodeling deacetylase (NuRD), as well CHD, ADNP, HP1 (ChAHP) complexes. Further analysis unravels regulatory role gene during erythrocyte formation. Our results emphasize chromatin remodelers establish drive unique transcriptional programs.

Language: Английский

Citations

1
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures DOI Creative Commons
Joshua Justice, Todd M. Greco, Josiah E. Hutton

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 11, 2024

Abstract Huntington’s disease (HD) is a debilitating neurodegenerative disorder affecting an individual’s cognitive and motor abilities. HD caused by mutation in the huntingtin gene producing toxic polyglutamine-expanded protein (mHTT) leading to degeneration striatum cortex. Yet, molecular signatures that underlie tissue-specific vulnerabilities remain unclear. Here, we investigate this aspect leveraging multi-epitope interaction assays, subcellular fractionation, thermal proteome profiling, genetic modifier assays. Use of human cell, mouse, fly models afforded capture distinct pools epitope-enriched tissue-dependent interactions linked dysregulated cellular pathways relevance. We established HTT association with nearly all subunits transcriptional regulatory Mediator complex (20/26), preferential enrichment MED15 tail domain. Using KO models, find modulates localization assembly Mediator. demonstrated striatal enriched functional regulators calcium homeostasis chromatin remodeling, whose relevance was supported modifiers Altogether, offer insights into tissue- localization-dependent (m)HTT functions pathobiology.

Language: Английский

Citations

1