60 research outputs found
Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes
SummarySomatic mutations in cancer are more frequent in heterochromatic and late-replicating regions of the genome. We report that regional disparities in mutation density are virtually abolished within transcriptionally silent genomic regions of cutaneous squamous cell carcinomas (cSCCs) arising in an XPC−/− background. XPC−/− cells lack global genome nucleotide excision repair (GG-NER), thus establishing differential access of DNA repair machinery within chromatin-rich regions of the genome as the primary cause for the regional disparity. Strikingly, we find that increasing levels of transcription reduce mutation prevalence on both strands of gene bodies embedded within H3K9me3-dense regions, and only to those levels observed in H3K9me3-sparse regions, also in an XPC-dependent manner. Therefore, transcription appears to reduce mutation prevalence specifically by relieving the constraints imposed by chromatin structure on DNA repair. We model this relationship among transcription, chromatin state, and DNA repair, revealing a new, personalized determinant of cancer risk
Chinese journals: a guide for epidemiologists.
Chinese journals in epidemiology, preventive medicine and public health contain much that is of potential international interest. However, few non-Chinese speakers are acquainted with this literature. This article therefore provides an overview of the contemporary scene in Chinese biomedical journal publication, Chinese bibliographic databases and Chinese journals in epidemiology, preventive medicine and public health. The challenge of switching to English as the medium of publication, the development of publishing bibliometric data from Chinese databases, the prospect of an Open Access publication model in China, the issue of language bias in literature reviews and the quality of Chinese journals are discussed. Epidemiologists are encouraged to search the Chinese bibliographic databases for Chinese journal articles.Published versio
Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities
The dose response curve is the gold standard for measuring the effect of a drug treatment, but is rarely used in genomic scale transcriptional profiling due to perceived obstacles of cost and analysis. One barrier to examining transcriptional dose responses is that existing methods for microarray data analysis can identify patterns, but provide no quantitative pharmacological information. We developed analytical methods that identify transcripts responsive to dose, calculate classical pharmacological parameters such as the EC50, and enable an in-depth analysis of coordinated dose-dependent treatment effects. The approach was applied to a transcriptional profiling study that evaluated four kinase inhibitors (imatinib, nilotinib, dasatinib and PD0325901) across a six-logarithm dose range, using 12 arrays per compound. The transcript responses proved a powerful means to characterize and compare the compounds: the distribution of EC50 values for the transcriptome was linked to specific targets, dose-dependent effects on cellular processes were identified using automated pathway analysis, and a connection was seen between EC50s in standard cellular assays and transcriptional EC50s. Our approach greatly enriches the information that can be obtained from standard transcriptional profiling technology. Moreover, these methods are automated, robust to non-optimized assays, and could be applied to other sources of quantitative data
Recommended from our members
Tissue-specific expression of connexin32 from alternate promoters
The gene of the rat connexin32, the gap junction protein found in liver, consists of two exons which are separated by a 6.1-kb intron located within the 5\sp\prime-untranslated region. The promoter of this gene was studied in tissue-culture cells and transgenic mice using reporter gene constructs. Connexin32 transgenes, containing 2.5-kb of sequence upstream from the promoter, exon I, the entire 6.1-kb intron, and the beginning of the coding sequence linked to the coding sequence of the reporter gene luciferase, were found to be expressed in mouse in the same tissue-specific manner as previously reported for the connexin32 gene. Another reporter gene construct lacking the known promoter, but retaining 1.8-kb from the 3\sp\prime-end of the intron, a region containing a potential second promoter, was found to be expressed specifically in the nervous system. This result suggested that a second promoter different from that used in liver drives the expression of the connexin32 gene in nervous tissue. The use of alternate promoters in normal rats was demonstrated by sequence analysis of reverse-transcribed PCR (RT-PCR) products of mRNA obtained from different rat tissues. While an upstream promoter, P1, drives the expression of the gene in liver, the second promoter, P2, drives the synthesis of a second connexin32 mRNA species.In view of the recent finding that mutations in the connexin32 gene have been associated with the X-linked form of the Charcot-Marie-Tooth disease, it was important to determine whether, like in the rat, the human connexin32 gene was transcribed from two alternate promoters. Because the human connexin32 gene had not been isolated, the sequence of the promoter P2 region of the human connexin32 gene was obtained by PCR amplification and sequencing of genomic DNA with primers derived from the known rat sequence. A human brain cDNA library was then screened by PCR using primers that allowed the detection of transcripts originating from either promoter P1 or P2. The analysis showed that the connexin32 mRNA expressed in human brain has a different 5\u27-end than the mRNA isolated from liver. These results were corroborated by RT-PCR amplification of mRNA isolated from human brain and liver. While the liver connexin32 mRNA is initiated from promoter P1, the brain connexin32 mRNA is initiated from promoter P2, located only 550 bases upstream of the start codon.Seven of the 28 reported families with CMT-X disease, however, exhibit no mutations in the connexin32 coding region. If connexin32 mutations are responsible for the CMT-X phenotype, then one would expect that these families exhibit mutations within the promoter region, and these mutations should be present in the promoter P2. DNA samples from patients with CMT-X disease that do not show mutations in the connexin32 coding sequence were obtained. These patients belonged to five different families. The above hypothesis was tested by PCR amplification of the genomic DNA with primers specific for the promoter P2 region. The analysis showed that one of the patients\u27 DNA did not result in the normal PCR amplification pattern, suggesting that a rearrangement or a deletion in the promoter P2 region in this patient\u27s DNA may have occurred. Sequence analysis of the promoter P2 region in these patients is currently under investigation
Recommended from our members
Use of alternate promoters for tissue-specific expression of the gene coding for connexin32
The promoter of rat connexin32 (Cx32), the gap junction protein found in liver, was studied in transgenic mice.
Cx32 transgenes, containing 2.5-kb of sequence upstream from the promoter, exon I, the entire 6.1-kb intron and the beginning of the coding sequence linked to the gene encoding luciferase (Luc), were found to be expressed in mouse in the same tissue-specific manner as previously reported for
Cx32. Another construct lacking the promoter, but retaining 1.8 kb from the 3′ end of the intron, was found to be expressed specifically in the nervous system. This result suggested that a second promoter, different from that used in liver, functions in nervous tissue. The use of this promoter in normal rats was corroborated by sequence analysis of reverse-transcribed PCR products obtained from rat nervous tissue RNA. The second promoter drives the synthesis of a second
Cx32 mRNA species that is processed to remove a small 345-bp intron that shares its acceptor splice site with the large intron. This finding could have implications for the genetic basis of the X-linked form of Charcot-Marie-Tooth disease (CMT-X) in those patients that do not exhibit mutations in the Cx32-coding region
- …