Biology subjects

Gaspar, J. M.

Publications and source records attributed to Gaspar, J. M..

4 recordsLinked to original sources

bioRxiv2020

POMC-specific knockdown of Tril reduces body adiposity and increases hypothalamic leptin responsiveness

In a public dataset of transcripts differentially expressed in selected neuronal subpopulations of the arcuate nucleus, we identified TLR4-interactor with leucine-rich repeats (Tril) as a potential candidate for mediating the harmful effects of a high-fat diet in proopiomelanocortin (POMC) neurons. The non-cell-specific inhibition of Tril in the arcuate nucleus resulted in reduced hypothalamic inflammation, protection against diet-induced obesity associated with increased whole-body energy expenditure and increased systemic glucose tolerance. The inhibition of Tril, specifically in POMC neurons, resulted in a trend for protection against diet-induced obesity, increased energy expenditure and increased hypothalamic sensitivity to leptin. Thus, Tril emerges as a new component of the complex mechanisms that promote hypothalamic dysfunction in experimental diet-induced obesity.

neuroscience↗

bioRxiv2019

Short paired-end reads trump long single-end reads for expression analysis

BackgroundTypical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be generated for the same cost, and it is not obvious which strategy should be preferred. Using publicly available data, we test whether short-paired end reads can achieve more robust expression estimates and differential expression results than single-end reads of approximately the same total number of sequenced bases. ResultsAt both the transcript and gene levels, 2x40 paired-end reads unequivocally provide expression estimates that are more highly correlated with 2x125 than 1x75 reads; in nearly all cases, those correlations are also greater than for 1x125, despite the greater total number of sequenced bases for the latter. Across an array of metrics, differential expression tests based upon 2x40 consistently outperform those using 1x75. ConclusionResearchers seeking a cost-effective approach for gene-level expression analysis should prefer short paired-end reads over a longer single-end strategy. Short paired-end reads will also give reasonably robust expression estimates and differential expression results at the isoform level.

bioinformatics↗

bioRxiv2018

Improved peak-calling with MACS2

The computational analyses of genome-enrichment assays, such as ChIP-seq and ATAC-seq, are typically concluded with a peak-calling program that identifies genomic regions that are significantly enriched. The most popular peak-caller, MACS2, assumes that the input alignment files are for single-end sequence reads by default, yet those with paired-end Illumina sequence data frequently use this default setting. This leads to erroneous coverage values and suboptimal peak identification. However, using the correct paired-end mode can introduce another set of artifacts. After thoroughly reviewing the MACS2 source code, we have modified it to limit these and other problems. Our updated version is freely available (https://github.com/jsh58/MACS).

bioinformatics↗

bioRxiv2018

Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos

Heterochromatin formation during early embryogenesis is timed precisely, but it has been elusive how this process is regulated. Here we report the discovery of a histone methyltransferase complex whose nuclear accumulation and activation establishes the onset of heterochromatin formation in C. elegans embryos. We find that the inception of heterochromatin generation coincides with the accumulation of the Histone H3 Lysine 9 (H3K9) methyltransferase MET-2 (SETDB) into nuclear hubs. The absence of MET-2 results in delayed and disturbed heterochromatin formation, whereas accelerated nuclear localization of the methyltransferase leads to precocious H3K9 methylation. We identify two factors that bind to and function with MET-2: LIN-65, which resembles ATF7IP, localizes MET-2 into nuclear hubs, and ARLE-14, orthologous to ARL14EP, promotes stable association of MET-2 with chromatin. These data reveal that nuclear accumulation of MET-2 in conjunction with LIN-65 and ARLE-14 regulates timing of heterochromatin domains during embryogenesis.\n\nONE SENTENCE SUMMARYMET-2/SETDB1 and interactors LIN-65/ATF7IP and ARLE-14/ARL14EP initiate heterochromatin formation during embryogenesis.

developmental biology↗