X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4−/− mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.
Hepatitis B envelope antigen (HBeAg) seroconversion represents an endpoint of treatment of chronic hepatitis B virus (HBV) infections. We have studied whether levels of serum HBV RNA during polymerase inhibitor treatment might be helpful for predicting HBeAg seroconversion. HBV RNA levels were determined in serial serum samples from 62 patients with chronic HBV infection (50 HBeAg positive). Patients received antiviral treatment for a mean duration of 30 6 15 (range, 4-64) months. A new rapid amplification of complimentary DNA-ends-based real-time polymerase chain reaction was established for quantitative analysis of polyadenylated full-length (fl) and truncated (tr) HBV RNA. HBV RNA, HBV DNA, and hepatitis B surface antigen (HBsAg) levels as well as presence of HBeAg and hepatitis B envelope antibody were measured at baseline, month 3, month 6, and subsequent time points. Fifteen patients who achieved HBeAg seroconversion after a mean duration of 19 6 14 (range, 3-56) months of antiviral treatment showed a significantly stronger decline in mean HBV flRNA and trRNA levels from baseline to month 3 of 1.0 6 1.4 (range, 21.6-3.4) and 2.1 6 1.4 (range, 0-3.9) and to month 6 of 1.8 6 1.4 (range, 0-4.6) and 3.1 6 1.7 (range, 0-5.1) log 10 copies/mL, respectively, in comparison to 35 HBeAg-positive patients without HBeAg seroconversion (P < 0.001 for months 3 and 6). A similar decline in HBV RNA levels was observed in HBeAg-negative patients. The decline of HBV RNA levels at months 3 and 6 of treatment was to be the strongest predictor of HBeAg seroconversion, when compared to levels of HBV DNA, HBsAg, alanine aminotransferase, and HBV genotype, age, and sex. Conclusion: Serum HBV RNA levels may serve as a novel tool for prediction of serological response during polymerase inhibitor treatment in HBeAg-positive patients. (HEPATOLOGY 2015;61:66-76)
Pausing of transcribing RNA polymerase is regulated and creates opportunities to control gene expression. Research in metazoans has so far mainly focused on RNA polymerase II (Pol II) promoter-proximal pausing leaving the pervasive nature of pausing and its regulatory potential in mammalian cells unclear. Here, we developed a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data and a new native elongating transcript sequencing approach, termed nested NET-seq, that strongly reduces artifactual peaks commonly misinterpreted as pausing sites. Leveraging PDA and nested NET-seq reveal widespread genome-wide Pol II pausing at single-nucleotide resolution in human cells. Notably, the majority of Pol II pauses occur outside of promoter-proximal gene regions primarily along the gene-body of transcribed genes. Sequence analysis combined with machine learning modeling reveals DNA sequence properties underlying widespread transcriptional pausing including a new pause motif. Interestingly, key sequence determinants of RNA polymerase pausing are conserved between human cells and bacteria. These studies indicate pervasive sequence-induced transcriptional pausing in human cells and the knowledge of exact pause locations implies potential functional roles in gene expression.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.