Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse (MNase-seq)

ABSTRACT: Chromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using low-input MNase-seq. We observed distinct features of inheritance and reconstruction of nucleosome position in both male and female genomes. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 hour after the injection of sperm. The nucleosome positioning pattern was continually rebuilt to form nucleosome depletion regions (NDRs) at promoters and transcription factor (TF) binding sites. NDRs formed more quickly on the promoters of genes involved in zygotic genome activation (ZGA), and their formation is closely connected with histone acetylation, but not transcription elongation or DNA replication. Importantly, we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA. Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA, respectively. Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei following fertilization, but also provide an efficient method for identifying key transcription regulators during development.

ORGANISM(S): Mus musculus

PROVIDER: GSE140875 | GEO | 2022/04/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse (RNA-seq)

Project description:Chromatin remodeling is essential for the reprogramming process after fertilization. However, the detailed mechanism remains unclear to date. In this study, we reported the dynamic changes of nucleosome occupancy and positioning in pronuclear stages using low-input MNase-seq. We found distinct features of inheritance and reconstruction on nucleosome position can be observed in the male and female genome. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 hour after the injection of sperm. The nucleosome positioning pattern was further rebuilt continually to form nucleosome depletion regions (NDR) on promoter and transcription factor (TF) binding sites. The formation of promoter NDRs occurred faster on zygotic genome activation genes, which rely on the function of Brd4 but independent of transcription elongation or DNA replication. Importantly, we found the establishment of NDR on TF binding motifs might be associated with its potential pioneer function in zygotic genome activation (ZGA). Further verification suggested predicted factors Mlx and Rfx1 play important roles in minor and major ZGA, respectively. Our data do not only provided the first insight of nucleosome positioning dynamics in the very early stage of embryogenesis but also provided a way to identify key TF regulators in the developmental process.

2022-04-02 | GSE140876 | GEO

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

Project description:Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, most noncoding RNA (ncRNA) is rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, a SWI/SNF family nucleosome remodeling factor, suppresses transcription of ncRNAs from approximately 57,000 nucleosome-depleted regions (NDRs) throughout the genome of mouse embryonic stem cells (ESCs). We show that esBAF functions both to keep NDRs nucleosome-free and to promote elevated nucleosome occupancy adjacent to NDRs. Reduction of adjacent nucleosome occupancy upon esBAF depletion is strongly correlated with ncRNA expression, suggesting that flanking nucleosomes form a barrier to pervasive transcription. Upon forcing nucleosome occupancy near an NDR using a nucleosome-positioning sequence, we find that esBAF is no longer required to silence transcription. These data reveal a novel role for esBAF in suppressing pervasive transcription from open chromatin regions in ESCs. Examine nucleosome occupancy (MNase-Seq) and transcript production (CapSeq and RNA-Seq) in EGFP KD and Smarca4 KD ESCs

2015-02-12 | E-GEOD-57170 | biostudies-arrayexpress

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

2015-02-12 | GSE57170 | GEO

Asymmetric Reprogramming Capacity of Parental Pronuclei in Mouse Zygote

Project description:It has been demonstrated previously that the reprogramming factors are sequestered in the pronuclei of zygote after fertilization, as the enucleated zygotes at interphase cannot support the development of cloned embryos whereas the enucleated zygotes at M-phase can reprogram somatic cells to full pluripotency. However, it remains unknown whether the parental pronucleus, derived either from the sperm or oocyte, possesses the similar reprogramming ability. Here, we provide evidence demonstrating that the parental pronuclei are asymmetric in reprogramming and the reprogramming factors reside mainly in the male pronucleus. As a result, only the female pronucleus-depleted mouse zygotes enucleated at M-phase of mitosis can support the somatic cell reprogramming, the derivation of chromosome transfer embryonic stem (ctES) cells with full pluripotency and the full term development of cloned embryos. In striking contrast, the male pronucleus-depleted zygotes enucleated at M-phase of mitosis fail to support the pre-implantation development of somatic cell cloned embryos. Furthermore, we demonstrated that the distinct epigenetic reprogramming ability of the parental pronucleus might contribute directly to the developmental difference of somatic cloned embryos. Our study highlights the developmental asymmetry of parental pronuclei in reprogramming.

2014-12-30 | GSE49148 | GEO

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

2013-03-01 | GSE39431 | GEO

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

2013-03-01 | GSE39430 | GEO

Nucleosome profiles in strains with different inter-NDR distances at HML

Project description:Heterochromatin is a complex structure comprised of nucleosome arrays that are bound by silencing factors. This composition suggests that certain configurations of nucleosome arrays are permissible for heterochromatic silencing. We tested this idea in S. cerevisiae by systematically altering the distance between heterochromatic Nucleosome Depleted Regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, some inter-NDR distances led to poorly positioned nucleosome arrays within heterochromatin. Furthermore, these conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit a silenced transcriptional state. These findings strongly suggest that nucleosome positioning contributes to formation and maintenance of functional heterochromatin.

2020-02-06 | GSE144808 | GEO

S. pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from S. cerevisiae

Project description:Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome-wide. Using this resource we found surprising differences compared to the nucleosome organization in the distantly related yeast Saccharomyces cerevisiae [the cerevisiae data has been published by others (PMID: 17873876) and the raw data is deposited at ArrayExpress(E-MEXP-1172)]. DNA sequence guides nucleosome positioning differently, e.g., poly(dA:dT) elements are not enriched in S. pombe nucleosome-depleted regions (NDRs). Regular nucleosomal arrays emanate more asymmetrically, i.e., mainly co-directionally with transcription, from promoter NDRs, but promoters harbouring the histone variant H2A.Z show regular arrays also upstream. Regular nucleosome phasing in S. pombe has a very short repeat length of 154 base pairs, and requires a remodeler, Mit1, conserved in humans but not found in S. cerevisiae. Nucleosome positioning mechanisms are evidently not universal but evolutionarily plastic.

2010-02-01 | GSE16040 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data