Structure and functional mapping of the KRAB-KAP1 repressor complex

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.

Pandiloski, NinoslavLund University,Lunds universitet,Institutionen för experimentell medicinsk vetenskap,Medicinska fakulteten,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,Institutionen för laboratoriemedicin,Epigenetik och kromatindynamik,Forskargrupper vid Lunds universitet,Department of Experimental Medical Science,Faculty of Medicine,Stem Cell Center,Division of stem cell research,Department of Laboratory Medicine,Epigenetics and Chromatin Dynamics,Lund University Research Groups(Swepub:lu)ni8740pa (author)
Douse, Christopher HLund University,Lunds universitet,Institutionen för experimentell medicinsk vetenskap,Medicinska fakulteten,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,Institutionen för laboratoriemedicin,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Epigenetik och kromatindynamik,Forskargrupper vid Lunds universitet,Department of Experimental Medical Science,Faculty of Medicine,Stem Cell Center,Division of stem cell research,Department of Laboratory Medicine,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Epigenetics and Chromatin Dynamics,Lund University Research Groups(Swepub:lu)ch2676do (author)
Modis, YorgoUniversity of Cambridge (author)
University of CambridgeInstitutionen för experimentell medicinsk vetenskap (creator_code:org_t)

By the author/editor: Stoll, Guido A; Pandiloski, Nino ...; Douse, Christoph ...; Modis, Yorgo

About the subject

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Medical Genetics

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