Monday, November 3, 2025 11/3/2025

Systematic mapping and prediction of gene-enhancer connections

Award Number: R00HG009917
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 05/01/2020
PERIOD OF PERFORMANCE END DATE: 02/28/2023

Group Awards By:

View Award Description

Systematic mapping and prediction of gene-enhancer connections - A fundamental challenge in modern biology is to identify the noncoding regulatory elements (REs) that control gene expression, which could inform the interpretation of the thousands of noncoding genetic variants associated with human diseases through genome-wide association studies (GWAS). Interpreting the functions of REs and noncoding genetic variants has been challenging because we have lacked the ability to systematically perturb REs in their native locations in the genome. To address this challenge, I recently developed a high-throughput method to map the functions of thousands of REs in their native genomic contexts and measure their quantitative effects on gene expression (CRISPRi tiling). I also developed a novel analytical approach to model and predict gene-RE connections based on maps of chromatin state and 3D folding. Together, these advances motivate a strategy to allow systematic mapping of all of the REs that control any given gene in any given cell type. In the K99 phase, I propose to: (i) apply CRISPRi tiling to map ~6,000 additional gene-RE connections, and (ii) use these data to extend and optimize a model to predict gene-RE connections from chromatin state. I will use human immune cells as a model system to compare predictions across cell types. In the R00 phase, I will apply these tools to (iii) characterize the network architecture of gene-RE connections across hundreds of cell types, and (iv) edit single-nucleotide variants identified by the model in cellular models to characterize their effects on gene expression. Together, these aims will provide insights into the mechanisms and architecture of gene-RE connectivity, generate tools for mapping gene-RE connectivity in any cell type, and reveal mechanisms underlying common diseases. Stanford University is an ideal environment for my independent laboratory, providing all of the facilities needed for the proposed research and a rich interdisciplinary environment for collaborative studies. Together, these aims will launch my independent scientific career at the interface of regulatory genomics and disease genetics.


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: 2024 ( Subtotal = -$1,060 )
2024	2022	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	5	12/6/2023	SUPPLEMENT FOR EXPANSION	-$79
2024	2022	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	5	12/6/2023	NON-COMPETING CONTINUATION	-$982
														Subtotal = -$1,060

Issue Date FY: 2022 ( Subtotal = $260,700 )
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	5	2/25/2022	SUPPLEMENT FOR EXPANSION	$17,374
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	5	2/24/2022	NON-COMPETING CONTINUATION	$217,253
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	002	5	4/28/2022	NON-COMPETING CONTINUATION	$24,142
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	003	5	4/29/2022	SUPPLEMENT FOR EXPANSION	$1,931
														Subtotal = $260,700

Issue Date FY: 2021 ( Subtotal = $286,114 )
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	4	3/5/2021	NON-COMPETING CONTINUATION	$284,628
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	3	2/18/2021	SUPPLEMENT FOR EXPANSION	$1,486
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	003	4	6/7/2021	NON-COMPETING CONTINUATION	$0
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	002	3	6/4/2021	SUPPLEMENT FOR EXPANSION	$0
														Subtotal = $286,114

Issue Date FY: 2020 ( Subtotal = $250,060 )
2020	2020	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	3	4/30/2020	EXTENSION WITH OR WITHOUT FUNDS	$249,000
2020	2020	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	3	9/2/2020	EXTENSION WITH OR WITHOUT FUNDS	$1,060
														Subtotal = $250,060

Grand Total All Awards = $795,814

Top

All Categories

About

Search

Reports

Data Submission

Award Information

Systematic mapping and prediction of gene-enhancer connections

Award Number: R00HG009917

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 05/01/2020

PERIOD OF PERFORMANCE END DATE: 02/28/2023

Federal Websites

Department of Health & Human Services

HHS Operating Divisions

HHS Staff Divisions

Download A Document Viewer