Monday, June 30, 2025 6/30/2025

Developing and democratizing technologies to study 3D genome organization

Award Number: R35GM137916
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/01/2020
PERIOD OF PERFORMANCE END DATE: 04/30/2030

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Developing and democratizing technologies to study 3D genome organization - PROJECT SUMMARY Each human nucleus contains two meters of DNA that is packaged into an organelle a mere ~10 µm diameter. Despite this dramatic difference in scale, the three-dimensional organization of the genome is non-random and plays a critical functional role in health and disease. My research group is focused on the building robust and scalable methods to study the organization of chromosomes in 3D space, the interactions they participate in with at the inter- and intra-chromosomal level, and the associated RNAs and proteins that occupy functionally relevant sites. The motivation for this work is to better understand the mechanisms by the organization and composition of genomic intervals relevant for health and disease faithfully conduct the essential DNA transactions of transcription, replication, and repair. Our previous studies focused on the development of multiplexed fluorescent in situ hybridization (FISH) methods to map chromosome structure in individual cells and the creation of biochemical screening methods to identify the molecular factors present at the anchor sites for 3D chromosome loops. To this end, we have introduced new multiplexed FISH technologies and adapted these to facilitate proximity labeling and affinity purification of factors from target genomic intervals and chromatin associated RNAs. We now propose to build on these efforts by further developing FISH technologies to support a broader range of questions relevant to chromosome biology and making efforts to speed the adoption of advanced FISH technologies, by extending our proximity labeling approach to more challenging genomic targets important for the regulation of gene expression, and by investigating the position and composition of highly repetitive DNA sequences, which we hypothesize play an integral role in maintaining the structure and stability of the genome. Collectively, the studies proposed here will produce enabling new genomic technologies, produce rich datasets that detail the molecular composition of functionally important genomic loci, and shed light on the function of disease-relevant repetitive sequences within the nucleus.


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: 2025 ( Subtotal = $470,386 )
2025	2025	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	000	6	6/18/2025	COMPETING CONTINUATION	$470,386
														Subtotal = $470,386

Issue Date FY: 2024 ( Subtotal = $498,562 )
2024	2024	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	001	5	7/17/2024	NON-COMPETING CONTINUATION	$370,959
2024	2024	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	000	4	5/1/2024	SUPPLEMENT FOR EXPANSION	$31,901
2024	2024	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	002	5	7/18/2024	SUPPLEMENT FOR EXPANSION	$95,702
														Subtotal = $498,562

Issue Date FY: 2023 ( Subtotal = $370,959 )
2023	2023	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	000	4	7/7/2023	NON-COMPETING CONTINUATION	$370,959
														Subtotal = $370,959

Issue Date FY: 2022 ( Subtotal = $370,959 )
2022	2022	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	000	3	7/28/2022	NON-COMPETING CONTINUATION	$370,959
														Subtotal = $370,959

Issue Date FY: 2021 ( Subtotal = $370,959 )
2021	2021	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	000	2	7/12/2021	NON-COMPETING CONTINUATION	$370,959
														Subtotal = $370,959

Issue Date FY: 2020 ( Subtotal = $370,959 )
2020	2020	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Biomedical Research and Research Training	000	1	7/22/2020	NEW	$370,959
														Subtotal = $370,959

Grand Total All Awards = $2,452,784

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Developing and democratizing technologies to study 3D genome organization

Award Number: R35GM137916

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 08/01/2020

PERIOD OF PERFORMANCE END DATE: 04/30/2030

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