Quantification of differential gene expression by multiplexed targeted resequencing of cDNA

Contains fulltext : 174649.pdf (publisher's version ) (Open Access)Whole-transcriptome or RNA sequencing (RNA-Seq) is a powerful and versatile tool for functional analysis of different types of RNA molecules, but sample reagent and sequencing cost can be prohibitive for hypothesis-driven studies where the aim is to quantify differential expression of a limited number of genes. Here we present an approach for quantification of differential mRNA expression by targeted resequencing of complementary DNA using single-molecule molecular inversion probes (cDNA-smMIPs) that enable highly multiplexed resequencing of cDNA target regions of approximately 100 nucleotides and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. Compared with low-coverage RNA-Seq and a hybridization-based targeted RNA-Seq method, cDNA-smMIPs are a cost-effective high-throughput tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands)

ONECUT transcription factors induce neuronal characteristics and remodel chromatin accessibility

Remodeling of chromatin accessibility is necessary for successful reprogramming of fibroblasts to neurons. However, it is still not fully known which transcription factors can induce a neuronal chromatin accessibility profile when overexpressed in fibroblasts. To identify such transcription factors, we used ATAC-sequencing to generate differential chromatin accessibility profiles between human fibroblasts and iNeurons, an in vitro neuronal model system obtained by overexpression of Neurog2 in induced pluripotent stem cells (iPSCs). We found that the ONECUT transcription factor sequence motif was strongly associated with differential chromatin accessibility between iNeurons and fibroblasts. All three ONECUT transcription factors associated with this motif (ONECUT1, ONECUT2 and ONECUT3) induced a neuron-like morphology and expression of neuronal genes within two days of overexpression in fibroblasts. We observed widespread remodeling of chromatin accessibility; in particular, we found that chromatin regions that contain the ONECUT motif were in- or lowly accessible in fibroblasts and became accessible after the overexpression of ONECUT1, ONECUT2 or ONECUT3. There was substantial overlap with iNeurons, still, many regions that gained accessibility following ONECUT overexpression were not accessible in iNeurons. Our study highlights both the potential and challenges of ONECUT-based direct neuronal reprogramming

Pyrene biotransformation and kinetics in the hepatopancreas of the isopod Porcellio scaber

Various techniques exist for polycyclic aromatic hydrocarbon (PAH) determination in environmental samples, but an adequate risk assessment of PAHs should include aspects such as bioavailability of the contaminant and biotransformation capacity of the species under investigation. In this study, we provided an analysis of the kinetics of pyrene in the terrestrial isopod Porcellio scaber. Isopods were exposed to pyrene in their food (10 μg/g d/w) for 7 days followed by an elimination period of 7 days. The animals were dissected, and the hepatopancreases were analyzed for pyrene biotransformation products; nonmetabolised pyrene in the gut was also monitored. Concentrations of 1-hydroxypyrene in the hepatopancreas were very low. Almost all of the pyrene was found as three conjugates: pyrene-1-glucoside, pyrene-1-sulfate, and a third unknown 1-hydroxypyrene conjugate. Concentrations of the metabolites were extremely variable between individuals because of variable feeding activity. An apparent steady state was reached already after 24 hours of exposure, whereas elimination was complete 48 hours after ending the exposure. This rapid response to changes in the exposure concentration shows that terrestrial isopods have a high biotransformation capacity for PAHs. The data show that concentrations of parent PAHs will not provide a good indication of exposure in rapidly metabolizing invertebrates such as isopods; instead, pyrene metabolites may be considered a promising biomarker for bioavailability of PAH contamination in the field

Sex differences on the WISC-R in Belgium and The Netherlands.

Sex differences on the Dutch WISC-R were examined in Dutch children (350 boys, 387 girls, age 11-13 years) and Belgian children (370 boys, 391 girls, age 9.5-13 years). Multi-group covariance and means structure analysis was used to establish whether the WISC-R was measurement invariant across sex, and whether sex differences on the level of the subtests were indicative of sex differences in general intelligence (g). In both samples, girls outperformed boys on the subtest Coding, while boys outperformed girls on the subtests Information and Arithmetic. The sex differences in the means of these three subtests could not be accounted for by the first-order factors Verbal, Performance, and Memory. Measurement invariance with respect to sex was however established for the remaining 9 subtest. Based on these subtests, no significant sex differences were observed in the means of the first-order factors, or the second-order g-factor. In conclusion, the cognitive differences between boys and girls concern subtest-specific abilities, and these sizeable differences are not attributable to differences in first-order factors, or the second-order factor g. © 2007 Elsevier Inc. All rights reserved