KAP1 is an antiparallel dimer with a natively functional asymmetry

Fonti, Giulia; Marcaida, M.J.; Bryan, Louise; Traeger, Sylvain; Kalantzi, Alexandra Styliani; Helleboid, Pierre-Yves; Demurtas, Davide; Tully, Mark D.; Grudinin, Sergei; Trono, Didier; Fierz, Beat; Peraro, Matteo Dal

doi:10.1101/553511

Cited by 5 publications

(2 citation statements)

References 107 publications

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“…Mutations at the dimer interface disrupt the formation of KAP1 oligomers without affecting transcriptional silencing, consistent with the data reported herein. A preprint was also published reporting that full-length KAP1 forms elongated dimers with a native asymmetry (45).…”

Section: Methodsmentioning

confidence: 99%

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

Stoll

Oda

Chong

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

102

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Transcription of transposable elements is tightly regulated to prevent genome damage. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, inducing the assembly of an epigenetic silencing complex, with chromatin remodeling activities that repress transcription of the targeted retrotransposon and adjacent genes. Our biophysical and structural data show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevent higher-order oligomerization without significant loss of retrotransposon silencing activity, indicating that, in contrast to other TRIM-family proteins, self-assembly is not essential for KAP1 function. The crystal structure of the KAP1 TRIM dimer identifies the KRAB domain binding site in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 TRIM responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing.

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Section: Methodsmentioning

confidence: 99%

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

Stoll

Oda

Chong

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

102

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“…In addition to the chromatin binding and target gene activation role of the C-terminal PHD-BD cassette, KAP1 contains several domains that could engage in multivalent interactions, including a RING E3 ubiquitin ligase domain (Doyle et al, 2010), two Bboxes and a coiled coil (CC) required for protein-protein interactions and dimerization (Fonti et al, 2019;Peng et al, 2000), a linker involved in heterochromatin protein (HP1) binding (Ryan et al, 1999), and the PHD-BD (Figure 6A).…”

Section: Upon Chromatin Binding Kap1 Scaffolds Rna Pol II and Pause Release Factors At Select Gene Promoters Through Different Protein Domentioning

confidence: 99%

KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs

et al. 2020

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Structure and functional mapping of the KRAB-KAP1 repressor complex

Stoll

Pandiloski

Douse

et al. 2022

Preprint

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Transposable elements (TEs) are a genetic reservoir from which new genes and regulatory elements can emerge. Expression of TEs can be pathogenic, however, and is tightly regulated. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many TEs 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 TE 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 forms the nexus of a transcriptional control axis vital to vertebrates and underpins programmable gene repression by CRISPRi.

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KAP1 is an antiparallel dimer with a natively functional asymmetry

Cited by 5 publications

References 107 publications

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs

Structure and functional mapping of the KRAB-KAP1 repressor complex

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