Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA

AbstractTranscription 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.

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Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA

10.1101/2020.09.25.313130 ◽

2020 ◽

Cited By ~ 1

Author(s):

Déborah Bouvier ◽

Juliette Ferrand ◽

Odile Chevallier ◽

Michelle T. Paulsen ◽

Mats Ljungman ◽

...

Keyword(s):

Dna Damage ◽

Histone Chaperone ◽

Canonical Function ◽

Transcription Inhibition ◽

Regulatory Pathways ◽

Local Activity ◽

Genome Wide ◽

A Genome ◽

Chaperone Complex

ABSTRACTTranscription 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 stabilizing 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.

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A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A

Genetics ◽

10.1534/genetics.118.301305 ◽

2018 ◽

Vol 210 (1) ◽

pp. 203-218 ◽

Cited By ~ 9

Author(s):

Sultan Ciftci-Yilmaz ◽

Wei-Chun Au ◽

Prashant K. Mishra ◽

Jessica R. Eisenstatt ◽

Joy Chang ◽

...

Keyword(s):

Budding Yeast ◽

Histone Chaperone ◽

Genome Wide ◽

A Genome ◽

Chaperone Complex

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Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability

10.1101/2021.05.11.443558 ◽

2021 ◽

Author(s):

Marit Geijer ◽

Di Zhou ◽

Kathiresan Selvam ◽

Barbara Steurer ◽

Bastiaan Evers ◽

...

Keyword(s):

Dna Damage ◽

Rna Polymerase Ii ◽

Genome Stability ◽

Genome Instability ◽

Excision Repair ◽

Elongation Factor ◽

Transcription Inhibition ◽

Genome Wide ◽

A Genome ◽

Nucleotide Excision

Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA Polymerase II (Pol II), causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions (TBLs). However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR/cas9 screen, we identified elongation factor ELOF1 as an important new factor in the transcription stress response upon DNA damage. We show that ELOF1 has an evolutionary conserved role in Transcription-Coupled Nucleotide Excision Repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair TBLs and resume transcription. Additionally, ELOF1 modulates transcription to protect cells from transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage by two distinct mechanisms.

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Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library

BMC Genomics ◽

10.1186/1471-2164-13-662 ◽

2012 ◽

Vol 13 (1) ◽

pp. 662 ◽

Cited By ~ 15

Author(s):

Xian Pan ◽

Bingkun Lei ◽

Nan Zhou ◽

Biwei Feng ◽

Wei Yao ◽

...

Keyword(s):

Dna Damage ◽

Schizosaccharomyces Pombe ◽

Dna Damage Response ◽

Novel Genes ◽

Genome Wide ◽

A Genome ◽

Damage Response ◽

Deletion Library

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Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

Biology Direct ◽

10.1186/1745-6150-6-15 ◽

2011 ◽

Vol 6 (1) ◽

pp. 15 ◽

Cited By ~ 35

Author(s):

Evgeny Shmelkov ◽

Zuojian Tang ◽

Iannis Aifantis ◽

Alexander Statnikov

Keyword(s):

Regulatory Pathways ◽

Genome Wide ◽

Transcriptional Regulatory ◽

A Genome ◽

Wide Scale

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Genome-wide transcriptional profiling uncovers a similar oligodendrocyte-related transcriptional response to acute and chronic alcohol drinking in the amygdala

10.1101/2021.09.07.459347 ◽

2021 ◽

Author(s):

Sharvari Narendra ◽

Claudia Klengel ◽

Bilal Hamzeh ◽

Drasti Patel ◽

Joy Otten ◽

...

Keyword(s):

Gene Expression ◽

Alcohol Drinking ◽

Brain Area ◽

Transcriptional Profiling ◽

Expression Patterns ◽

Transcriptional Response ◽

Histone Deacetylation ◽

Regulatory Pathways ◽

Genome Wide ◽

A Genome

AbstractAlcohol intake progressively increases after prolonged consumption of alcohol, but relatively few new therapeutics targeting development of alcohol use disorder (AUD) have been validated. Here, we conducted a genome-wide RNA-sequencing (RNA-seq) analysis in mice exposed to different modes (acute vs chronic) of ethanol drinking. We focused on transcriptional profiles in the amygdala including the central and basolateral subnuclei, a brain area previously implicated in alcohol drinking and seeking, demonstrating distinct gene expression patterns and canonical pathways induced by both acute and chronic intake. Surprisingly, both drinking modes triggered similar transcriptional changes, including up-regulation of ribosome-related/translational pathways and myelination pathways, and down-regulation of chromatin binding and histone modification. Notably, multiple genes that were significantly regulated in mouse amygdala with alcohol drinking, including Atp2b1, Slc4a7, Nfkb1, Nts, and Hdac2, among others had previously been associated with human AUD via GWAS or other genomic studies. In addition, analyses of hub genes and upstream regulatory pathways predicted that voluntary ethanol consumption affects epigenetic changes via histone deacetylation pathways, oligodendrocyte and myelin function, and oligodendrocyte-related transcriptional factor, Sox17.Overall, our results suggest that the transcriptional landscape in the central and basolateral subnuclei of the amygdala is sensitive to voluntary alcohol drinking. They provide a unique resource of gene expression data for future translational studies examining transcriptional mechanisms underlying the development of AUD due to alcohol consumption.

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Genome-wide screening identifies cell cycle control as a synthetic lethal pathway with SRSF2P95H mutation

Blood Advances ◽

10.1182/bloodadvances.2021004571 ◽

2021 ◽

Author(s):

Jane Jialu Xu ◽

Alistair M Chalk ◽

Iva Nikolic ◽

Kaylene Simpson ◽

Monique F Smeets ◽

...

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Cell Lines ◽

Dna Damage Response ◽

Functional Screening ◽

Wild Type ◽

Synthetic Lethal ◽

Genome Wide ◽

A Genome ◽

Damage Response

Current strategies to target RNA splicing mutant myeloid cancers proposes targeting the remaining splicing apparatus. This approach has only been modestly sensitizing and is also toxic to non-mutant bearing wild-type cells. To explore potentially exploitable genetic interactions with spliceosome mutations, we combined data mining and functional screening for synthetic lethal interactions with an Srsf2P95H/+ mutation. Analysis of mis-splicing events in a series of both human and murine SRSF2P95H mutant samples across multiple myeloid diseases (AML, MDS, CMML) was performed to identify conserved mis-splicing events. From this analysis, we identified that the cell cycle and DNA repair pathways were overrepresented within the conserved mis-spliced transcript sets. In parallel, to functionally define pathways essential for survival and proliferation of Srsf2P95H/+ cells, we performed a genome-wide CRISPR loss of function screen using Hoxb8 immortalized R26-CreERki/+ Srsf2P95H/+ and R26-CreERki/+ Srsf2+/+ cell lines. We assessed loss of sgRNA representation at three timepoints: immediately after Srsf2P95H/+ activation, and at one week and two weeks post Srsf2P95H/+ mutation. Pathway analysis demonstrated that the cell cycle and DNA damage response pathways were amongst the top synthetic lethal pathways with Srsf2P95H/+ mutation. Based on the loss of guide RNAs targeting Cdk6, we identified that Palbociclib, a CDK6 inhibitor, showed preferential sensitivity in Srsf2P95H/+ cell lines and in primary non-immortalized lin-cKIT+Sca-1+ cells compared to wild type controls. Our data strongly suggest that the cell cycle and DNA damage response pathways are required for Srsf2P95H/+ cell survival, and that Palbociclib could be an alternative therapeutic option for targeting SRSF2 mutant cancers.

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