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Genetic and functional assessment of human-specific duplicated genes

Award Number: F31HG011205
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 01/12/2021
PERIOD OF PERFORMANCE END DATE: 01/10/2023

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Genetic and functional assessment of human-specific duplicated genes - PROJECT SUMMARY Recent advances in sequencing technologies and bioinformatics have created an emerging picture of structurally dynamic human and non-human primate genomes. In addition to single-nucleotide variants, larger structural variants (SVs; e.g., deletions, duplications, and inversions) are prolific within and between species but are more difficult to study. SVs are often too large to reliably identify with short-read (e.g., Illumina) data and frequently coincide with repetitive elements, making these loci historically difficult to assemble, annotate, and functionally investigate. Despite this, SV-associated rearrangements are known to cause morphological and neurodevelopmental abnormalities in humans, and a handful of human-specific duplicated (HSD) genes have been linked to innovative neurological features. The potential functional impact of SVs is enormous, as single mutational events can rearrange genes and regulatory elements throughout the genome. However, while the genes themselves have received growing attention, the regulatory landscape of SVs remains poorly characterized. Gene expression differences are known to contribute to a variety of human diseases, and are thought to be a major contributor to phenotypic divergence between species. SVs thus represent an understudied and likely impactful set of loci to examine in this light. This is particularly intriguing in the case of HSD genes, which show distinct expression patterns despite having nearly identical sequences. This work will use genomic techniques to investigate the effect of evolutionarily recent SVs on gene expression between humans and chimpanzees. This will be accomplished via three approaches: (1) high-throughput assay of human-duplicated regulatory element activity; (2) identification of differences in the promoter-enhancer connectome across SV breakpoints; and (3) testing for causal relationships between candidate regulatory features and gene expression at SV loci of functional significance. The findings of this research will be the first to characterize hundreds of loci in parallel and will offer insight into the mechanistic basis for regulatory changes between primate species.


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 = $0 )
2024	2022	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR, STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	001	2	2/1/2024	NON-COMPETING CONTINUATION	$0
2024	2022	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	000	2	12/28/2023	NON-COMPETING CONTINUATION	$0
2024	2022	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	002	2	2/26/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $39,176 )
2022	2022	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR, STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	001	2	7/1/2022	NON-COMPETING CONTINUATION	$716
2022	2022	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR, STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	000	2	1/10/2022	NON-COMPETING CONTINUATION	$38,460
														Subtotal = $39,176

Issue Date FY: 2021 ( Subtotal = $38,215 )
2021	2021	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR, STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	002	1	2/9/2021	NEW	$516
2021	2021	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR, STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	000	1	1/12/2021	NEW	$37,699
2021	2021	UNIVERSITY OF CALIFORNIA, DAVIS	1850 RESEARCH PARK DR, STE 300	DAVIS	CA	95618	YOLO	USA	Human Genome Research	001	1	1/12/2021	NEW	$0
														Subtotal = $38,215

Grand Total All Awards = $77,391

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Genetic and functional assessment of human-specific duplicated genes

Award Number: F31HG011205

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 01/12/2021

PERIOD OF PERFORMANCE END DATE: 01/10/2023

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