Chromatin rewiring in endothelial cells upon cohesin reduction redistributes genome-wide FLI1 binding
11 affiliations
- 1Versiti Blood Research Institute, Milwaukee, WI, USA
- 2Department of Physiology, University of Arizona, Tucson, AZ, USA
- 3Amrita School of Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ernakulam, India
- 4Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- 5Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- 6Division of Biostatistics, Data Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
- 7Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- 8Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
- 9Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- 10The Jackson Laboratory, Bar Harbor, ME, USA
- 11Department of Pediatrics, Section of Hematology/Oncology/Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA
Abstract
Three-dimensional genome organization is crucial for gene regulation and cell identity. The architectural proteins CTCF and the cohesin complex mediate chromatin looping, shaping cell-type-specific transcription. While their functions have been extensively characterized in embryonic stem cells and other proliferative systems, the regulation of transcription by these two ubiquitously expressed factors in terminally differentiated cells, such as endothelial cells (ECs), remains poorly understood. Moreover, interpretation of prior studies is further complicated by the essential requirement of CTCF and cohesin for cell viability, as most rely on near-complete depletion. Consequently, the extent to which CTCF and cohesin function redundantly, cooperatively, or independently to regulate cell-type-specific programs in differentiated cells remains a major knowledge gap. To address this, we reduced CTCF or the core cohesin subunit RAD21 to approximately 50% protein levels in an isogenic system of human induced pluripotent stem cells (iPSCs) and iPSC-derived endothelial cells (iEcs), enabling direct comparison between undifferentiated and lineage-committed cell states. CUT&Tag and RNA sequencing revealed a striking, EC-specific loss of CTCF and RAD21 occupancy at gene promoters following partial depletion; RAD21 reduction had a more pronounced impact on endothelial gene expression than CTCF depletion. RAD21 loss also led to a marked redistribution of FLI1 binding, a transcription factor essential for endothelial identity and function. Collectively, our findings highlight critical contributions of RAD21 in EC-specific gene expression through coordinated control of chromatin architecture and modulating transcription factor occupancy, providing mechanistic insight into cohesin-dependent regulation of vascular transcriptional programs.
Related
- Human FACT complex coordinates cohesin and transcription on chromatin
- Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization.
- Loss of cohesin deacetylation through KDAC8 inactivation leads to altered cohesin complex expression and chromosomal instability
- Region-specific generation and retention of acetylated cohesin shape the genome-wide pattern of sister chromatid cohesion
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells
BibTeX
@article{ray2026chromatin,
title = {{Chromatin rewiring in endothelial cells upon cohesin reduction redistributes genome-wide FLI1 binding}},
author = {Atrayee Ray and Rajan Pandey and Daniel Bennett Chrisenberry and Josiah D. Murray and Cary Stelloh and Pengyuan Liu and Yong Liu and Qiongzi Qiu and Alison E. Meyer and Monika Tutaj and Chien-Wei Lin and Khanmi Kasomva and Michael Sadowski and Paul Auer and Michael E. Widlansky and Aron M. Geurts and Allen W. Cowley and Anne E. Kwitek and Andrew S. Greene and Mingyu Liang and Sridhar Rao},
journal = {Epigenetics},
year = {2026},
month = oct,
doi = {10.1080/15592294.2026.2749250},
url = {https://doi.org/10.1080/15592294.2026.2749250},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Chromatin rewiring in endothelial cells upon cohesin reduction redistributes genome-wide FLI1 binding
AU - Atrayee Ray
AU - Rajan Pandey
AU - Daniel Bennett Chrisenberry
AU - Josiah D. Murray
AU - Cary Stelloh
AU - Pengyuan Liu
AU - Yong Liu
AU - Qiongzi Qiu
AU - Alison E. Meyer
AU - Monika Tutaj
AU - Chien-Wei Lin
AU - Khanmi Kasomva
AU - Michael Sadowski
AU - Paul Auer
AU - Michael E. Widlansky
AU - Aron M. Geurts
AU - Allen W. Cowley
AU - Anne E. Kwitek
AU - Andrew S. Greene
AU - Mingyu Liang
AU - Sridhar Rao
PY - 2026
DA - 2026/10/23
JO - Epigenetics
DO - 10.1080/15592294.2026.2749250
UR - https://doi.org/10.1080/15592294.2026.2749250
AB - Three-dimensional genome organization is crucial for gene regulation and cell identity. The architectural proteins CTCF and the cohesin complex mediate chromatin looping, shaping cell-type-specific transcription. While their functions have been extensively characterized in embryonic stem cells and other proliferative systems, the regulation of transcription by these two ubiquitously expressed factors in terminally differentiated cells, such as endothelial cells (ECs), remains poorly understood. Moreover, interpretation of prior studies is further complicated by the essential requirement of CTCF and cohesin for cell viability, as most rely on near-complete depletion. Consequently, the extent to which CTCF and cohesin function redundantly, cooperatively, or independently to regulate cell-type-specific programs in differentiated cells remains a major knowledge gap. To address this, we reduced CTCF or the core cohesin subunit RAD21 to approximately 50% protein levels in an isogenic system of human induced pluripotent stem cells (iPSCs) and iPSC-derived endothelial cells (iEcs), enabling direct comparison between undifferentiated and lineage-committed cell states. CUT&Tag and RNA sequencing revealed a striking, EC-specific loss of CTCF and RAD21 occupancy at gene promoters following partial depletion; RAD21 reduction had a more pronounced impact on endothelial gene expression than CTCF depletion. RAD21 loss also led to a marked redistribution of FLI1 binding, a transcription factor essential for endothelial identity and function. Collectively, our findings highlight critical contributions of RAD21 in EC-specific gene expression through coordinated control of chromatin architecture and modulating transcription factor occupancy, providing mechanistic insight into cohesin-dependent regulation of vascular transcriptional programs.
SN - 1559-2294
SN - 1559-2308
ER -