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Novel methods to detect and interpret splicing quantitative trait loci - Renewal

Award Number: R01HG011067
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: 12/31/2029

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Novel methods to detect and interpret splicing quantitative trait loci - Renewal - Predicting the effects of noncoding sequence on gene regulation and complex traits remains one of the most important problems in genomics. Many expression quantitative trait loci do not overlap enhancers or promoters. Our previous work showed that about one third of all expression quantitative trait loci likely function after transcription initiation. Further, we have implicated a deep contribution of pre-mRNA splicing to human variation. Assays beyond RNA-seq that report on the pathway of RNA splicing and in a manner independent of decay are sorely lacking, significantly compromising our ability to account for how, and which, genetic variants affect RNA splicing. We have been developing genome-wide assays that explicitly target pre-mRNA splicing. By one assay, we uncovered an under-appreciated mechanism contributing to gene expression and human phenotypic variation: unproductive splicing, which results in transcripts subject to cytoplasmic nonsense- mediated decay. By another assay, we have defined the timing of splicing genome-wide and in doing so discovered an unexpected degree of non-canonical splicing that competes with canonical splicing. In this grant, we propose novel assays to explicitly and efficiently measure canonical and non-canonical splicing. We will develop analytical methods to measure inter-individual variation in these processes and use this variation to study the mechanisms and impact of these regulatory phenotypes. At the end of this project, we will have developed innovative genomic assays that will illuminate novel RNA splicing biology and will have tested hypotheses regarding the function and regulatory mechanisms of RNA splicing. Our work will help improve our understanding of functional gene regulatory variation.


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 = $604,449 )
2025	2025	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	002	5	12/20/2024	COMPETING CONTINUATION	$604,449
2025	2023	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	001	4	12/19/2024	SUPPLEMENT FOR EXPANSION	$0
2025	2023	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	4	12/19/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $604,449

Issue Date FY: 2023 ( Subtotal = $773,379 )
2023	2023	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	4	3/23/2023	NON-COMPETING CONTINUATION	$653,339
2023	2023	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	001	4	3/24/2023	SUPPLEMENT FOR EXPANSION	$120,040
														Subtotal = $773,379

Issue Date FY: 2022 ( Subtotal = $762,742 )
2022	2022	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	3	2/18/2022	NON-COMPETING CONTINUATION	$587,247
2022	2022	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	001	3	5/2/2022	SUPPLEMENT FOR EXPANSION	$110,241
2022	2022	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	002	3	5/3/2022	NON-COMPETING CONTINUATION	$65,254
														Subtotal = $762,742

Issue Date FY: 2021 ( Subtotal = $665,650 )
2021	2021	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	2	2/23/2021	NON-COMPETING CONTINUATION	$665,650
														Subtotal = $665,650

Issue Date FY: 2020 ( Subtotal = $659,505 )
2020	2020	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	1	4/30/2020	NEW	$659,505
														Subtotal = $659,505

Grand Total All Awards = $3,465,725

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Novel methods to detect and interpret splicing quantitative trait loci - Renewal

Award Number: R01HG011067

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: 12/31/2029

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