Structure and functional mapping of the KRAB-KAP1 repressor complex
(2022) In EMBO Journal 41(24).- Abstract
Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is... (More)
Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.
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- author
- Stoll, Guido A ; Pandiloski, Ninoslav LU ; Douse, Christopher H LU and Modis, Yorgo
- organization
- publishing date
- 2022-12-15
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- CRISPRi, H3K9me3, heterochromatin, Kr€uppel-associated box, Transposable element
- in
- EMBO Journal
- volume
- 41
- issue
- 24
- article number
- e111179
- pages
- 16 pages
- publisher
- Oxford University Press
- external identifiers
-
- pmid:36341546
- scopus:85141431596
- ISSN
- 1460-2075
- DOI
- 10.15252/embj.2022111179
- language
- English
- LU publication?
- yes
- id
- 9684c3c9-4aff-4939-a65d-15b2023a8610
- date added to LUP
- 2022-11-17 15:19:15
- date last changed
- 2024-06-13 17:44:07
@article{9684c3c9-4aff-4939-a65d-15b2023a8610, abstract = {{<p>Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.</p>}}, author = {{Stoll, Guido A and Pandiloski, Ninoslav and Douse, Christopher H and Modis, Yorgo}}, issn = {{1460-2075}}, keywords = {{CRISPRi; H3K9me3; heterochromatin; Kr€uppel-associated box; Transposable element}}, language = {{eng}}, month = {{12}}, number = {{24}}, publisher = {{Oxford University Press}}, series = {{EMBO Journal}}, title = {{Structure and functional mapping of the KRAB-KAP1 repressor complex}}, url = {{http://dx.doi.org/10.15252/embj.2022111179}}, doi = {{10.15252/embj.2022111179}}, volume = {{41}}, year = {{2022}}, }