50 research outputs found
Computational Micromodel for Epigenetic Mechanisms
Characterization of the epigenetic profile of humans since the initial breakthrough on the human genome project has strongly established the key role of histone modifications and DNA methylation. These dynamic elements interact to determine the normal level of expression or methylation status of the constituent genes in the genome. Recently, considerable evidence has been put forward to demonstrate that environmental stress implicitly alters epigenetic patterns causing imbalance that can lead to cancer initiation. This chain of consequences has motivated attempts to computationally model the influence of histone modification and DNA methylation in gene expression and investigate their intrinsic interdependency. In this paper, we explore the relation between DNA methylation and transcription and characterize in detail the histone modifications for specific DNA methylation levels using a stochastic approach
Exome Sequencing and Genetic Testing for MODY
Context: Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive. Objective: The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results. Research Design and Methods: We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism. Results: On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0–4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively), thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes. Conclusion: Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized
PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality
ABSTRACT:Journal ArticleSCOPUS: ar.jinfo:eu-repo/semantics/publishe
Receptor Complementation and Mutagenesis Reveal SR-BI as an Essential HCV Entry Factor and Functionally Imply Its Intra- and Extra-Cellular Domains
HCV entry into cells is a multi-step and slow process. It is believed that the
initial capture of HCV particles by glycosaminoglycans and/or lipoprotein
receptors is followed by coordinated interactions with the scavenger receptor
class B type I (SR-BI), a major receptor of high-density lipoprotein (HDL), the
CD81 tetraspanin, and the tight junction protein Claudin-1, ultimately leading
to uptake and cellular penetration of HCV via low-pH endosomes.
Several reports have indicated that HDL promotes HCV entry through interaction
with SR-BI. This pathway remains largely elusive, although it was shown that HDL
neither associates with HCV particles nor modulates HCV binding to SR-BI. In
contrast to CD81 and Claudin-1, the importance of SR-BI has only been addressed
indirectly because of lack of cells in which functional complementation assays
with mutant receptors could be performed. Here we identified for the first time
two cell types that supported HCVpp and HCVcc entry upon ectopic SR-BI
expression. Remarkably, the undetectable expression of SR-BI in rat hepatoma
cells allowed unambiguous investigation of human SR-BI functions during HCV
entry. By expressing different SR-BI mutants in either cell line, our results
revealed features of SR-BI intracellular domains that influence HCV infectivity
without affecting receptor binding and stimulation of HCV entry induced by
HDL/SR-BI interaction. Conversely, we identified positions of SR-BI ectodomain
that, by altering HCV binding, inhibit entry. Finally, we characterized
alternative ectodomain determinants that, by reducing SR-BI cholesterol uptake
and efflux functions, abolish HDL-mediated infection-enhancement. Altogether, we
demonstrate that SR-BI is an essential HCV entry factor. Moreover, our results
highlight specific SR-BI determinants required during HCV entry and
physiological lipid transfer functions hijacked by HCV to favor infection