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Transcriptional consequences of XPA disruption in human cell lines

Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activate...

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Autores principales: Manandhar, Mandira, Lowery, Megan G., Boulware, Karen S., Lin, Kevin H., Lu, Yue, Wood, Richard D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731452/
https://www.ncbi.nlm.nih.gov/pubmed/28704716
http://dx.doi.org/10.1016/j.dnarep.2017.06.028
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author Manandhar, Mandira
Lowery, Megan G.
Boulware, Karen S.
Lin, Kevin H.
Lu, Yue
Wood, Richard D.
author_facet Manandhar, Mandira
Lowery, Megan G.
Boulware, Karen S.
Lin, Kevin H.
Lu, Yue
Wood, Richard D.
author_sort Manandhar, Mandira
collection PubMed
description Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage. We then analyzed four genetically matched human cell line pairs deficient or proficient in XPA. Of the ∼14,000 genes transcribed in each cell line, 325 genes (2%) had a significant XPA-dependent directional change in gene expression that was common to all four pairs (with a false discovery rate of 0.05). These genes were enriched in pathways for the maintenance of mitochondria. Only 27 common genes were different by more than 1.5-fold. The most significant hits were AKR1C1 and AKR1C2, involved in steroid hormone metabolism. AKR1C2 protein was lower in all of the immortalized XPA-deficient cells. Retinoic acid treatment led to modest XPA-dependent activation of some genes with transcription-related functions. We conclude that XPA status does not globally influence human gene transcription. However, XPA significantly influences expression of a small subset of genes important for mitochondrial functions and steroid hormone metabolism. The results may help explain defects in neurological function and sterility in individuals with xeroderma pigmentosum.
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spelling pubmed-57314522017-12-15 Transcriptional consequences of XPA disruption in human cell lines Manandhar, Mandira Lowery, Megan G. Boulware, Karen S. Lin, Kevin H. Lu, Yue Wood, Richard D. DNA Repair (Amst) Article Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage. We then analyzed four genetically matched human cell line pairs deficient or proficient in XPA. Of the ∼14,000 genes transcribed in each cell line, 325 genes (2%) had a significant XPA-dependent directional change in gene expression that was common to all four pairs (with a false discovery rate of 0.05). These genes were enriched in pathways for the maintenance of mitochondria. Only 27 common genes were different by more than 1.5-fold. The most significant hits were AKR1C1 and AKR1C2, involved in steroid hormone metabolism. AKR1C2 protein was lower in all of the immortalized XPA-deficient cells. Retinoic acid treatment led to modest XPA-dependent activation of some genes with transcription-related functions. We conclude that XPA status does not globally influence human gene transcription. However, XPA significantly influences expression of a small subset of genes important for mitochondrial functions and steroid hormone metabolism. The results may help explain defects in neurological function and sterility in individuals with xeroderma pigmentosum. 2017-06-29 2017-09 /pmc/articles/PMC5731452/ /pubmed/28704716 http://dx.doi.org/10.1016/j.dnarep.2017.06.028 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/BY-NC-ND/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) ).
spellingShingle Article
Manandhar, Mandira
Lowery, Megan G.
Boulware, Karen S.
Lin, Kevin H.
Lu, Yue
Wood, Richard D.
Transcriptional consequences of XPA disruption in human cell lines
title Transcriptional consequences of XPA disruption in human cell lines
title_full Transcriptional consequences of XPA disruption in human cell lines
title_fullStr Transcriptional consequences of XPA disruption in human cell lines
title_full_unstemmed Transcriptional consequences of XPA disruption in human cell lines
title_short Transcriptional consequences of XPA disruption in human cell lines
title_sort transcriptional consequences of xpa disruption in human cell lines
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731452/
https://www.ncbi.nlm.nih.gov/pubmed/28704716
http://dx.doi.org/10.1016/j.dnarep.2017.06.028
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