Official websites use .gov

A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS

A lock ( 🔒 ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Need Help

Elucidating the interplay between cohesin-mediated loop extrusion and heterochromatin in single cells.

Award Number: F31HG014082
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 01/01/2025
PERIOD OF PERFORMANCE END DATE: 12/31/2027

Group Awards By:

View Award Description

Elucidating the interplay between cohesin-mediated loop extrusion and heterochromatin in single cells. - Project Summary Fragile X Syndrome (FXS) is characterized by the unstable expansion of a CGG short tandem repeat (STR) located in the 5’ untranslated region of the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Expansion of the CGG tract from normal-length (WT, <55 CGG) to mutation-length (ML, >200 CGG) results in silencing of FMR1 transcription and severe loss of the protein it encodes. Textbook models of FXS have long attributed FMR1 silencing to local DNA methylation over the promoter and CGG tract, however removal of methylation is insufficient to reproducibly de-repress the gene in many experiments. Recently, my lab discovered a Megabase- scale domain of H3K9me3 on the X-chromosome and multiple autosomes in FXS induced pluripotent stem cell (iPSC) lines with a mutation-length CGG tract. The H3K9me3 domains encompass repressed synaptic genes, including FMR1, and severe misfolding of the 3D genome. The overall objective of my proposal is to investigate the interplay between cohesin-mediated loop extrusion, H3K9me3, and gene expression in FXS at the resolution of single-cells. Progress toward testing this goal has been limited by the paucity of single-cell approaches for mapping cohesin occupancy and chromatin folding at kilobase-resolution. My central hypothesis is that the FMR1 locus can undergo cohesin-mediated loop extrusion in WT-iPSCs. By contrast, I posit that ML-FXS iPSCs with H3K9me3 domains will exhibit depleted cohesin binding that is functionally linked to severely misfolded topologically associating domains (TADs), subTADs, and loops and silenced FMR1 expression. I generated my hypotheses based on (1) published work demonstrating that depletion of the cohesin unloading factor WAPL causes hyper-extrusion, stabilization of cohesin binding, and loss of H3K9me3 signal, and (2) my own preliminary data showing that loops are abolished at H3K9me3 domains in ML-FXS iPSCs and rescued when H3K9me3 signal is reversed. I will test my hypothesis by employing both single-cell imaging and genomics techniques to map genome folding, immunofluorescence staining of cohesin and H3K9me3, and single-cell TIPseq to assay cohesin binding and H3K9me3 in WT and ML-FXS iPSCs. I will also utilize WAPL degron iPSC lines established in my lab in ML genetic backgrounds to assay changes in genome folding due to loss and gain of cohesin extrusion at the FMR1 locus. Upon successful completion of my experiments, I will have elucidated mechanisms underlying the interplay between chromatin folding and H3K9me3 maintenance in FXS. My work is significant because knowledge generated in this proposal will have impact on our understanding of how heterochromatin disrupts gene expression in a wide range of neurodevelopmental and neurodegenerative disorders. In addition, I will create freely available algorithms to quantify cohesin-mediated loop extrusion from chromatin tracing data.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $49,538 )
2026	2026	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT STREET	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Human Genome Research	000	2	12/15/2025	NON-COMPETING CONTINUATION	$49,538
														Subtotal = $49,538

Issue Date FY: 2025 ( Subtotal = $48,974 )
2025	2025	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Human Genome Research	000	1	11/25/2024	NEW	$48,974
2025	2025	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Human Genome Research	001	1	12/30/2024	NEW	$0
														Subtotal = $48,974

Grand Total All Awards = $98,512

Top

All Categories

About

Search

Reports

Data Submission

Award Information

Elucidating the interplay between cohesin-mediated loop extrusion and heterochromatin in single cells.

Award Number: F31HG014082

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 01/01/2025

PERIOD OF PERFORMANCE END DATE: 12/31/2027

Federal Websites

Department of Health & Human Services

HHS Operating Divisions

HHS Staff Divisions

Download A Document Viewer