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Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE58006 | GEO | 2014/10/23

SECONDARY ACCESSION(S): PRJNA248679

REPOSITORIES: GEO

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Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver.

Project description:Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that derepression of the nuclear receptors PPAR?, PPAR?, and LXR? in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix transcription factor Foxa2 and nuclear receptor corepressor Hdac3 exhibit a reciprocal binding pattern at PPAR? targets contributing to gene expression changes that lead to steatosis in aged liver.

| S-EPMC4250828 | biostudies-literature

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-23 | E-GEOD-58006 | biostudies-arrayexpress

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver [ChIP-seq]

Project description:Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that de-repression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and for novel candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix factor Foxa2 and nuclear receptor co-repressor Hdac3 exhibit reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver. Genome-wide location analysis (ChIP-Seq) of Foxa2 and Hdac3 from young (3 months) and old (21 months) mouse livers

2014-10-23 | E-GEOD-60393 | biostudies-arrayexpress

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver [ChIP-seq]

Project description:Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that de-repression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and for novel candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix factor Foxa2 and nuclear receptor co-repressor Hdac3 exhibit reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver.

2014-10-23 | GSE60393 | GEO

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

Project description:Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

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Nucleosome occupancy changes in mammalian cell differentiation and reprogramming

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-07-31 | E-GEOD-59064 | biostudies-arrayexpress

Nucleosome occupancy changes in mammalian cell differentiation and reprogramming

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

2014-07-31 | GSE59064 | GEO

BINOCh: binding inference from nucleosome occupancy changes.

Project description:UnlabelledTranscription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation.AvailabilityThe BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license.

| S-EPMC3117357 | biostudies-literature

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.

Project description:Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that is activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead, there was an increase in the accessibility of nucleosomes, as measured by micrococcal nuclease (MNase) digestion and ATAC-seq (assay for transposase-accessible chromatin [ATAC] using sequencing), that did not result from removal of the nucleosome. Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.

| S-EPMC5393060 | biostudies-literature

Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (microarray)

Project description:Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity. A six chip study using total RNA recovered from three cell types with 2 replicates each

2014-07-31 | E-GEOD-59061 | biostudies-arrayexpress

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