Cockayne syndrome group B protein (CSB) plays a general role in chromatin maintenance and remodeling

Abstract

Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair-and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. Using expression microarrays and a unique method for comparative expression analysis called L2L, we sought to define this defect in cells lacking a functional CS group B (CSB) protein, the SWI͞SNF-like ATPase responsible for most cases of CS. Remarkably, many of the genes regulated by CSB are also affected by inhibitors of histone deacetylase and DNA methylation, as well as by defects in poly(ADP-ribose)-polymerase function and RNA polymerase II elongation. Moreover, consistent with these microarray expression data, CSB-null cells are sensitive to inhibitors of histone deacetylase or poly(ADP-ribose)-polymerase. Our data indicate a general role for CSB protein in maintenance and remodeling of chromatin structure and suggest that CS is a disease of transcriptional deregulation caused by misexpression of growthsuppressive, inflammatory, and proapoptotic pathways.DNA repair ͉ L2L ͉ microarray ͉ transcription C ockayne syndrome (CS) is a devastating inherited disease characterized by severe postnatal growth failure and progressive neurological dysfunction, along with a variety of symptoms reminiscent of aging, including retinal degeneration, sensorineural hearing loss, cataracts, and loss of subcutaneous fat (1). The nature of the molecular defect that causes CS remains elusive, although CS has been intensively studied for many years, and much is known about the cellular functions of the five genes responsible for the disease. Most cases of CS are caused by defects in two genes: CS groups A (CSA) and B (CSB). The CSB protein is a SWI͞SNF-like DNA-dependent ATPase (2-4) that can wind DNA (5) and remodel chromatin in vitro (6). CSB is required for translocation of the CSA protein to the nuclear matrix after DNA damage (7). Rare alleles of three xeroderma pigmentosum (XP) genes (XPB, XPD, and XPG) are responsible for the remaining cases of CS; these patients usually lack the severe predisposition to skin cancer typical of XP (8). CS genes have been implicated, alone or in various combinations, in transcription-coupled repair (TCR) of UV-induced DNA lesions (9, 10), repair of oxidative DNA damage (11), transcription initiation by RNA polymerase I (pol I; refs. 12 and 13) and RNA polymerase II (pol II; ref. 14), elongation by pol II (15, 16), transcription of induced genes (17), protein ubiquitination (18), and metaphase chromosome condensation (19).To understand how CSB defects cause CS, we characterized the array of genes regulated by CSB. Previous expression array studies, although encouraging, had not been conclusive (20) or had focused on the role of CS genes in the transcriptional response to oxidative (17) or ultraviolet (21) DNA damage. Our hope was to work backwards from effect to cause, deducing the biochemical functions of CSB from genes it...

The role of CSA in the response to oxidative DNA damage in human cells

“…The similar impairment of 8-OH-Gua repair reported in the absence of CSB (reviewed by Licht et al, 2003) or CSA (this study) suggests that these proteins act in the same pathway. We favor the hypothesis that the acceleration of repair at early repair times mediated by CSB (Osterod et al, 2002) or CSA (this study) reflects the role of CS proteins in the regulation of chromatin structure (for instance by ubiquitination and/or acetylation of histones) (Citterio et al, 2000;Groisman et al, 2003;Newman et al, 2006). CS-mediated chromatin remodeling activity might increase the accessibility of DNA damage to the repair machinery.…”

Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects

“…Different approaches provide evidence that CSB might have an impact on transcription itself. Transcriptome analysis of CS-B cells revealed deregulation of gene expression similar to that caused by agents that disrupt chromatin structure [35]. When added to a stalled RNAPIIo (at a CPD photolesion) CSB can stimulate transcription elongation by addition of one nucleotide to the nascent transcript, but not bypass of the lesion [36].…”

The role of Cockayne Syndrome group B (CSB) protein in base excision repair and aging

“…A study by Egly and co-workers (Proietti-De-Santis et al, 2006) supports a role for CSB in regulating the transcription pattern after UV damage as they found a function for CSB in transcription from some but not other promoters. Another comparative gene expression study established that CSB is involved in transcription of genes involved in chromatin maintenance and remodeling (Newman et al, 2006). CS cells display a stronger apoptotic response to DNA damaging agents than normal cells Laposa et al, 2007;Liu et al, 2006), which in part could explain why no cancer is seen in the patients.…”

“…When compared to CSB deficient cells, the transcription from chromatin in wild type cells was more resistant to the detergent Triton X-100, indicating that the transcription machinery is less tightly associated with chromatin in CSB deficient cells compared to wild type cells (Balajee et al, 1997). A study by Weiner and coworkers found that the transcription pattern of CSB deficient cells had a significant overlap with the transcription pattern of cells treated with the histone deacetylase (HDAC) inhibitor trichostatin A (TSA), indicating that CSB could play a role in chromatin maintenance (Newman et al, 2006). The similarity of HDAC inhibited cells to CSB deficient cells indicates that a role of CSB is to decrease the amount of histone acetylation.…”