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Interdependence between histone marks and steps in Pol II transcription [Antczak.submission]

ABSTRACT: ChRO-seq provides quantative information about gene expression levels in liver tissue taken at necropsy from two healthy Quarter Horse mares.

ORGANISM(S): Equus caballus

PROVIDER: GSE163048 | GEO | 2020/12/12

REPOSITORIES: GEO

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Interdependence between histone marks and steps in Pol II transcription

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-12 | GSE163049 | GEO

Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

Project description:We trained sensitive machine learning models that decompose maps of primary transcription into ChIP-seq profiles representing 9 distinct histone modifications. We show that transcription measured using precision run-on and sequencing (PRO-seq) can recover the pattern of active histone modifications at nucleosome resolution and with an accuracy that rivals the correlation between independent ChIP-seq experiments in holdout cell types. To define the nature of the causal relationship between histone modifications and transcription, we perturbed transcription and examined the genomic distribution of four active and one repressive histone modification: H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K27me3.

2020-12-12 | GSE163043 | GEO

Interdependence between histone marks and steps in Pol II transcription

Project description:Interdependence between histone marks and steps in Pol II transcription

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Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

Project description:Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

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Interdependence between histone marks and steps in Pol II transcription [Antczak.submission]

Project description:Interdependence between histone marks and steps in Pol II transcription [Antczak.submission]

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Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes.

Project description:Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of protein-coding gene expression, the transcription of noncoding RNA genes by RNA polymerase III (Pol III) is less well characterized. Here we profile the epigenetic features of Pol III target genes throughout the human genome. This reveals that the chromatin landscape of Pol III-transcribed genes resembles that of Pol II templates in many ways, although there are also clear differences. Our analysis also uncovered an entirely unexpected phenomenon: namely, that Pol II is present at the majority of genomic loci that are bound by Pol III.

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Methylation studies in horses

Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. cricoarytenoideus dorsalis muscle), liver, lung, mammary gland, mitral valve of the heart, skeletal muscle (gluteal muscle and longissimus muscle), occipital cortex, ovary, parietal cortex, pituitary, sacrocaudalis dorsalis muscle, skin, spinal cord (C1 and T8), spleen, suspensory ligament, temporal cortex, tendon (deep digital flexor tendon and superficial digital flexor tendon), uterus.

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Identification of genomic loci associated with Rhodococcus equi susceptibility in foals

Project description:aCGH performed to identify copy number variants in Quarter Horses and perform casec-control GWAS Two-condition experiment, All samples were compared to a single Quarter Horse reference to identify copy number variants to be used in the CNV GWAS

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The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation.

Project description:Enhancers play a central role in precisely regulating the expression of developmentally regulated genes. However, the machineries required for enhancer-promoter communication have remained largely unknown. We have found that Ell3, a member of the Ell (eleven-nineteen lysine-rich leukemia gene) family of RNA Pol II elongation factors, occupies enhancers in embryonic stem cells. Ell3's association with enhancers is required for setting up proper Pol II occupancy at the promoter-proximal regions of developmentally regulated genes and for the recruitment of the super elongation complex (SEC) to these loci following differentiation signals. Furthermore, Ell3 binding to inactive or poised enhancers is essential for stem cell specification. We have also detected the presence of Pol II and Ell3 in germ cell nuclei. These findings raise the possibility that transcription factors could prime gene expression by marking enhancers in ES cells or even as early as in the germ cell state.

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Project description:The signal for maternal recognition of pregnancy (MRP) has still not been identified in the horse. Endometrial biopsies, uterine fluid, embryonic tissues and yolk sac fluid were collected 13 days after ovulation during pregnant and control cycles from the same mares. Micro-RNA-Sequencing was performed on all collected samples and mRNA-Sequencing was conducted on the same endometrial and embryonic tissue samples

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