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Evolution of new regulatory networks via genetic arms races between KRAB zinc finger proteins and retrotransposons

Award Number: R01HG010329
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 02/12/2019
PERIOD OF PERFORMANCE END DATE: 01/31/2025

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Evolution of new regulatory networks via genetic arms races between KRAB zinc finger proteins and retrotransposons - Project Summary / Abstract This proposal investigates how co-evolution of retrotransposon elements (RTEs) and KRAB zinc finger proteins (KZNFs) have resulted in new gene regulatory modules and how these modules contribute to human embryonic development and pluripotency. KZNFs are the largest family of human transcription factors and have undergone rapid evolution in primates to repress RTE expression. Both RTEs and KZNFs are highly expressed in pluripotent stem cells (PSCs) and are aberrantly expressed in cancers and neurological diseases, suggesting that they play functional roles in these cell types. KZNFs show strong signals of selection and activity even after their target RTEs have lost the ability to mobilize (i.e. generate new insertion events) and therefore no longer pose a threat to their host genome. We hypothesize that over evolutionary time KZNFs are maintained by the host to regulate host gene expression after their job repressing RTEs is finished, and hence tracing the evolution of KZNF-RTE and KZNF-enhancer interactions will not only increase our understanding of the rules governing ZNF-DNA binding, but open a new window on the evolution of and mechanisms in primate/human gene regulatory networks. We will use comparative genomics approaches that take advantage of new, highly contiguous, primate genome assemblies to trace this evolutionary history. This analysis will allow us to apply assays we have developed to dissect the role of evolutionary changes to both KZNFs and their RTE/host targets in controlling transcription in PSCs, and by analogy, in early embryonic cell types. We will focus our experimental analysis on “naive” and “primed” PSCs, which mimic epiblast cells of pre- and post-implantation embryos, respectively. These cell types show high expression of a number of specific RTEs and KZNFs, and these expression signatures differ between closely related species, including between human and non-human apes. Naive and primed PSCs are experimentally tractable and critical for regenerative medicine efforts. We have succeeded in making them in human, chimpanzee and orangutan. We will test the function of KZNF-RTE interactions active in these ape PSCs by modulating both KZNF and RTE expression and will assess the consequences of these manipulations on cell fate specification, maintenance of pluripotency and differentiation potential. By performing these experiments in non-human ape PSCs in addition to human PSCs we can identify conserved and species-specific regulatory programs and dissect the molecular and evolutionary basis for recently evolved differences in pluripotency in humans. The results of this work will reveal how RTEs and KZNFs have influenced human evolution and development and provide important insights into the establishment and maintenance of pluripotent stem cells.


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 = -$16,215 )
2025	2022	UNIVERSITY OF CALIFORNIA SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	4	6/13/2025	NON-COMPETING CONTINUATION	-$16,215
														Subtotal = -$16,215

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2022	UNIVERSITY OF CALIFORNIA SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	4	4/22/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $685,382 )
2022	2022	UNIVERSITY OF CALIFORNIA, SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	4	1/27/2022	NON-COMPETING CONTINUATION	$616,842
2022	2022	UNIVERSITY OF CALIFORNIA, SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	001	4	4/27/2022	NON-COMPETING CONTINUATION	$68,540
														Subtotal = $685,382

Issue Date FY: 2021 ( Subtotal = $685,382 )
2021	2021	UNIVERSITY OF CALIFORNIA, SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	3	3/1/2021	NON-COMPETING CONTINUATION	$685,382
														Subtotal = $685,382

Issue Date FY: 2020 ( Subtotal = $685,382 )
2020	2020	UNIVERSITY OF CALIFORNIA, SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	2	1/24/2020	NON-COMPETING CONTINUATION	$685,382
														Subtotal = $685,382

Issue Date FY: 2019 ( Subtotal = $685,382 )
2019	2019	UNIVERSITY OF CALIFORNIA, SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	1	2/13/2019	NEW	$685,382
														Subtotal = $685,382

Grand Total All Awards = $2,725,313

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Evolution of new regulatory networks via genetic arms races between KRAB zinc finger proteins and retrotransposons

Award Number: R01HG010329

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 02/12/2019

PERIOD OF PERFORMANCE END DATE: 01/31/2025

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