Abstract
Transcription restart after a genotoxic challenge is a fundamental yet poorly understood process. Here, we dissect the interplay between transcription and chromatin restoration after DNA damage by focusing on the human histone chaperone complex HIRA, which is required for transcription recovery post UV. We demonstrate that HIRA is recruited to UV-damaged chromatin via the ubiquitin-dependent segregase VCP to deposit new H3.3 histones. However, this local activity of HIRA is dispensable for transcription recovery. Instead, we reveal a genome-wide function of HIRA in transcription restart that is independent of new H3.3 and not restricted to UV-damaged loci. HIRA coordinates with ASF1B to control transcription restart by two independent pathways: by stabilising the associated subunit UBN2 and by reducing the expression of the transcription repressor ATF3. Thus, HIRA primes UV-damaged chromatin for transcription restart at least in part by relieving transcription inhibition rather than by depositing new H3.3 as an activating bookmark.
Highlights
The maintenance of gene expression programmes established during organism development is critical for preserving cell functions and identities[1]
Consistent with this, we observed that Histone Regulator A (HIRA) knock-down in HeLa and U2OS cells led to a strong down-regulation of Ubinuclein 1 (UBN1) and Calcineurin-binding protein 1 (CABIN1) while Anti-silencing function 1 A (ASF1A) levels remained unaffected
We focused our attention on the Valosin-Containing Protein (VCP) segregase, which promotes the degradation of UV-stalled RNAPII25,26, a critical step in transcription restart[21,22], and which, like HIRA29, is recruited to UVC-damaged chromatin in a ubiquitin-dependent manner in human cells[64]
Summary
The maintenance of gene expression programmes established during organism development is critical for preserving cell functions and identities[1]. Several histone chaperones[39] and modifying enzymes[40] were shown to promote transcription recovery following UVC damage in mammalian cells, including the H3K79 methyltransferase DOT1L28, and the core histone chaperones Facilitate Chromatin Transcription (FACT)[30] and Histone Regulator A (HIRA)[29,41]. In response to UVC irradiation, HIRA is recruited to damaged chromatin regions in a ubiquitin-dependent manner by a mechanism that is not yet fully elucidated, and deposits newly synthesised H3.3 histones[29]. Based on the observation that HIRA was only transiently recruited to damage sites and released long before transcription restart, we proposed a bookmarking mechanism whereby this histone chaperone was priming chromatin for transcription recovery[29]. HIRA-mediated H3.3 deposition plays a critical role in transcriptional reprogramming in Xenopus[48] and mouse cells[49], and is key for reaching the full dynamic range of transcription in mouse developing oocytes[50]
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