Tag: TSS

RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

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Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…

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HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

doi: 10.1093/nar/gkab1221. Online ahead of print. Yang Yang  1   2 , Liwei Zhang  3 , Chaoyang Xiong  2 , Jun Chen  2   4   5 , Li Wang  6 , Zengqi Wen  2   5 , Juan Yu  2 , Ping Chen  4 , Yanhui Xu  6 , Jingji Jin  1   7   8 , Yong Cai …

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Homer finds same peak multiple times

I am using Homer to identify peaks in RNA-seq data and then determine differential expression by counting reads per peak. Homer has a lovely package that does just this: getDifferentialPeaksReplicates.pl. The issue is that for some reason Homer returns the same peak multiple times in its final output (Bonus question:…

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RPKM on TSS using DiffBind

RPKM on TSS using DiffBind 1 Hi everyone, I want to extrapolate RPKM value from Diffbind. Investigated regions are TSS (± 2.5kb) but around 3500 TSS are “lost” because merged. I have read that in the new version of DiffBind is possible to use dbObj_region$config$mergeOverlap with negative value to avoid…

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Determining the microbial and chemical contamination in Ecuador’s main rivers

Bacterial contamination in urban areas of the main Ecuadorian rivers All rivers showed E. coli levels above standard concentrations for bathing-water recommended by the USA, European and Brazilian guidelines (Fig. 1), in concordance with other studies in Latin America, such as Colombia34, Mexico4, and Perú35. Most of the rivers in this…

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Bedfile format deeptools

Bedfile format deeptools 1 Hello everyone, Using deeptools I am trying to plot the enrichment in Genebody and TSS for this we have to give one BED file region of interest in computeMatrix. I am bit confused about the format based on a thread in biostar TSS metaprofile using Deeptoolsbased…

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Senior Bioinformatics Support Scientist | Illumina

Why Us    Illumina are growing at pace, and we are looking for the best customer focused Bioinformatics Support Scientist to join our mission, to improve human health by unlocking the power of the genome. By joining Illumina as a Bioinformatics Support Scientist in our EMEA Head Office, Cambridge UK, you will help support…

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Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files

Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files 0 Hi, I sincerely hope that I am not repeating an already answered question. I couldn’t find the answer to my exact problem. I have three VCF files derived using bcftools (isec). Those…

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computematrix how to set certain TSS

computematrix how to set certain TSS 1 how to set certain TSS deeptools computematrix, I want to visualize the certain gene’s TSS up/downstream instead of whole gene,but how can I do it ? thanks. deeptools • 34 views You probably want the reference-point mode as described here. You will also…

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