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Structure and functional mapping of the KRAB-KAP1 repressor complex

Stoll, Guido A ; Pandiloski, Ninoslav LU orcid ; Douse, Christopher H LU and Modis, Yorgo (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
; ; and
organization
publishing date
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}},
}