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Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses

ABSTRACT: Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which controls developmental gene expression by ubiquitylating the REX1 transcription factor and is mutated in an X-linked intellectual disability disorder. However, the precise mechanisms by which ubiquitylation drives specific transcriptional responses are not known. Here, we show that RNF12 is recruited to specific genomic locations via a consensus sequence motif, which enables co-localisation with REX1 substrate at gene promoters. Surprisingly, RNF12 chromatin recruitment is achieved via a non-catalytic basic region and comprises a previously unappreciated N-terminal autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provide insight into mechanisms by which protein ubiquitylation enables programming of gene expression.

ORGANISM(S): Mus musculus

PROVIDER: GSE236354 | GEO | 2024/01/08

REPOSITORIES: GEO

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Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls gene-specific transcription

Project description:Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which is mutated in an X-linked intellectual disability disorder and controls developmental gene expression by ubiquitylating the REX1 transcription factor. However, the precise mechanisms by which ubiquitylation patterns specific transcriptional programmes are not known. Here, we show that genomic targeting of RNF12 selectively programmes developmental transcription. RNF12 is recruited to specific genomic locations by recognising a distinct consensus sequence motif, which enables co-localisation with REX1. Surprisingly, RNF12 chromatin recruitment is achieved via the non-catalytic basic region (BR) and comprises a previously unappreciated autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provides insight into mechanisms by which spatial control of protein ubiquitylation enables specific programming of gene expression.

2024-01-09 | PXD047197 | Pride

Critical role of the UBL-domain in stimulating the E3 ubiquitin ligase activity of UHRF1 towards chromatin

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The E3 ubiquitin ligase RFWD3 is required for translesion DNA synthesis (total proteome)

Project description:Lesions on DNA can uncouple DNA synthesis from helicase unwinding, generating stretches of unreplicated single stranded DNA (ssDNA) behind the replication fork. These ssDNA gaps need to be filled in to complete DNA duplication and thereby avoid the generation of DNA double-stranded breaks (DSBs), a major source of genomic instability. Gap filling repair involves either translesion DNA synthesis (TLS) or template switching (TS) to bypass the lesion. At the heart of these processes, ubiquitylated PCNA recruits many proteins that dictate pathway choice, but the enzymes regulating PCNA ubiquitylation in vertebrates remain poorly defined. Here we report that the E3 ubiquitin ligase RFWD3 promotes non-specific ubiquitylation of proteins on ssDNA, to enhance protein accumulation and stimulate gap filling repair. The absence of RFWD3 leads to a profound defect in recruitment of key repair and signaling factors to damaged chromatin, including ubiquitin and proteins known to ubiquitylate and interact with ubiquitylated PCNA. As a result, PCNA ubiquitylation is severely inhibited without RFWD3, and TLS across different DNA lesions drastically impaired. We propose that RFWD3 is an essential coordinator of the response to ssDNA gaps, where it triggers non-specific ubiquitylation to drive recruitment of effectors of PCNA ubiquitylation and DNA damage bypass.

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