Biology subjects

Huseyin, M. K.

Publications and source records attributed to Huseyin, M. K..

6 recordsLinked to original sources

bioRxiv2026

Dissection of Polycomb complexes reveals canonical PRC1-independent 3D chromatin interactions

The Polycomb system is an essential regulator of developmental genes which controls chromatin state through histone modifications and 3D chromatin organization. Although Polycomb-mediated histone modification is well understood, how Polycomb-mediated 3D chromatin interactions form remains unclear. To address this gap, we combine comprehensive Polycomb subunit degrons with Region Capture Micro-C, ChIP-seq, nascent transcriptomics, and live-cell imaging of DNA loci and Polycomb bodies. We find that, within canonical Polycomb repressive complex 1 (cPRC1), polyhomeotic proteins are the primary contributors to interactions. In surprising contrast to existing models, we find that Polycomb-mediated interactions persist in the absence of cPRC1, and combined depletion of cPRC1 with individual variant PRC1 and PRC2 complexes indicates that the remaining interactions do not depend on a single complex. These results raise the previously unexplored possibility of a more general mechanism for Polycomb-mediated interactions not requiring cPRC1.

genomics↗

bioRxiv2026

Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation

Enhancers are key regulators of mammalian gene expression, yet how they interact with promoters in space (contact vs. action-at-a-distance) and in time (transient vs. stable) remains poorly understood. Recent studies suggest that enhancers can activate promoters across distances exceeding 200 nanometers, challenging classical contact models, but limited spatiotemporal resolution has obscured the mechanistic details of enhancer-promoter (E-P) interactions and their link to transcription. Here, we engineered a synthetic biology platform optimized for the simultaneous visualization of E-P 3D distance and nascent transcription using super-resolution live-cell imaging. By applying five complementary approaches integrating imaging, 3D genomics, and gene expression data across cell lines, we estimate that transcriptional activation is mediated by [~]25-42 nanometer contacts on the seconds timescale. Our results support a transient contact mechanism for E-P-mediated gene activation.

biophysics↗

bioRxiv2022

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

Although enhancers are central to the regulation of mammalian gene expression, the mechanisms underlying Enhancer-Promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively capture large-scale 3D genome structure but struggle to achieve the depth necessary to resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining MNase-based 3C with a tiling region-capture approach and generate the deepest 3D genome maps reported thus far with only modest sequencing. By applying RCMC in mouse embryonic stem cells and reaching the genome-wide equivalent of [~]200 billion unique contacts, RCMC reveals previously unresolvable patterns of highly nested and focal 3D interactions, which we term microcompartments. Microcompartments frequently connect enhancers and promoters and are largely robust to loss of loop extrusion and inhibition of transcription. We therefore propose that many E-P interactions form through a compartmentalization mechanism, which may explain why acute cohesin depletion only modestly affects global gene expression.

genomics↗

bioRxiv2020

BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications that are found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A mono-ubiquitylation (H2AK119ub1) which is enriched at Polycomb-repressed gene promoters, but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we discover that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 represses gene expression by counteracting transcription initiation from gene regulatory elements, causing reductions in transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes leading to their derepression, therefore explaining the original genetic characterisation of BAP1 as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification, without the need for elaborate gene-specific targeting mechanisms.

molecular biology↗

bioRxiv2020

Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy

Polycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. However, how PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We reveal that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits surprisingly low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, and suggests that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.

molecular biology↗

bioRxiv2019

PRC1 catalytic activity is central to Polycomb system function.

The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how its target genes are selected and whether its histone modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. We demonstrate that a mutation widely used to disrupt PRC1 catalysis is hypomorphic, complicating the interpretation of previous studies. To overcome this, we develop a new inducible mutation system in embryonic stem cells that completely ablates PRC1 catalytic activity, revealing that catalysis by PRC1 drives Polycomb chromatin domain formation and higher-order chromatin interactions. In the absence of catalysis, we uncover the primary DNA-based targeting determinants that direct Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling new evidence supporting a PRC1-initiated pathway for Polycomb system function in gene regulation.

molecular biology↗