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Genetic effects on chromatin accessibility during human neuronal differentiation

ABSTRACT: Genetic effects on chromatin accessibility during human neuronal differentiation

PROVIDER: PRJNA598745 | ENA |

REPOSITORIES: ENA

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Genetic effects on chromatin accessibility during human neuronal differentiation

Project description:Genetic effects on chromatin accessibility during human neuronal differentiation

| PRJNA598746 | ENA

Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation.

Project description: Not available

| S-EPMC8254789 | biostudies-literature

Chromatin accessibility profiling of developing cerebellar granule neurons identifies novel neuronal enhancers and reveals a role for Zic transcription factors in neuronal maturation

Project description:To identify chromatin mechanisms of neuronal differentiation, we characterized the relationship between chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to globally map accessibility of cis-regulatory elements and RNA-seq to profile transcript abundance at key points in postnatal neuronal differentiation in vivo and in culture. We observed thousands of chromatin accessibility changes as CGNs differentiated and determined that many of these regions function as stage-specific neuronal enhancers. Motif discovery within differentially accessible chromatin regions suggested a novel role for the Zic family of transcription factors in CGN maturation, and we confirmed the association of Zic with these elements by ChIP-seq. Knockdown of Zic1 and Zic2 indicated Zic transcription factors are required to coordinate mature neuronal gene expression patterns. These data reveal chromatin dynamics at thousands of gene regulatory elements that facilitate gene expression patterns necessary for neuronal differentiation and function. Biological triplicate DNase-seq and RNA-seq samples from 3 in vivo cerebellum developmental stages (P7, P14, P60) and 3 cultured CGN stages (isolated granule neuron precursors, +3DIV, and +7DIV) obtained. Zic1 and Zic2 were separately knocked down by lentiviral shRNA in cultured CGNs followed by RNA-seq (2 biological replicates per KD and 2 controls). Zic1/2 ChIP-seq was performed with in vivo cerebellum at two developmental stages (P7 and P60) in duplicate with matching input and IgG controls.

2015-02-27 | E-GEOD-60731 | biostudies-arrayexpress

Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome

Project description:Compartmentalisation of the genome as topologically associating domains (TADs) may have a regulatory role in development and cellular functioning, but the mechanism involved in TAD establishment is still unclear. Here, we present the first high-resolution contact map of Drosophila melanogaster neuronal cells (BG3) and identify different classes of TADs by comparing this to genome organisation in embryonic cells (Kc167). We find new interactions during differentiation in neuronal cells, which are reflected as enhanced long-range interactions. This is supported by pronounced enrichment of CTCF at TAD borders. Furthermore, we observed strong divergent transcription, together with RNA Polymerase II occupancy, and an increase in DNA accessibility at the TAD borders. Interestingly, TAD borders that are specific to neuronal cells are enriched in enhancers controlled by neuronal specific transcription factors. Our results suggest that TADs are dynamic across developmental stages and reflect the interplay between insulators, transcriptional states and enhancer activities.

2019-01-18 | GSE122603 | GEO

Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling.

Project description:We report the 4C-seq data and ChIP-seq to study Shep regulation of chromatin looping. We also reported ATAC-seq and CUT&Tag data on sorted neurons that reveal chromatin accessibility and states during the neuronal remodeling of Drosophila melanogaster

2021-08-30 | GSE154645 | GEO

Conserved exchange of paralog proteins during neuronal differentiation

Project description:Gene duplication enables the emergence of new functions by lowering the general evolutionary pressure. Previous studies have highlighted the role of specific paralog genes during cell differentiation, e.g., in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological functions and whether the regulation of paralog genes is conserved across species. Here, we analyze the expression of paralogs across human tissues, during development and neuronal differentiation in fish, rodents and humans. While ~80% of paralog genes are co-regulated, a subset of paralogs shows divergent expression profiles, contributing to variability of protein complexes. We identify 78 substitutions of paralog eggNOG pairs that occur during neuronal differentiation and are conserved across species. Among these, we highlight a substitution between the paralogs Sec23a and Sec23b subunits of the COPII complex. Altering the ratio between these two genes via silencing-RNA knockdown was able to influence neuronal differentiation in different ways. We propose that remodeling of the vesicular transport system via paralog substitutions is an evolutionary conserved mechanism enabling neuronal differentiation.

2022-03-07 | PXD027195 | Pride

Conserved exchange of paralog proteins during neuronal differentiation

2022-03-07 | PXD027191 | Pride

ZNF281 inhibits neuronal differentiation

Project description:ZNF281 inhibits neuronal differentiation

| PRJNA438998 | ENA

Neuronal differentiation of DFATs

Project description:Neuronal differentiation of DFATs

| PRJNA417063 | ENA

Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling.

Project description:Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling.

| PRJNA646944 | ENA