Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic features shaping the landscape of meiotic double-strand break hotspots in maize [MNase-Seq]

ABSTRACT: We report the application of next generation sequencing techonology to study nucleosomal occupancy in flowers containing zygotene meiocytes. The results show DSB enrichment in nucleosome depleted regions associated with RAD51

ORGANISM(S): Zea mays

PROVIDER: GSE84368 | GEO | 2016/07/13

SECONDARY ACCESSION(S): PRJNA328990

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genomic features shaping the landscape of meiotic double-strand break hotspots in maize [ChIP-Seq]

Project description:To generate the double-strand break (DSB) hotspot map in maize, we used a chromatin immunoprecipitation (ChIP) approach, in which chromatin from flowers containing zygotene meiocytes was enriched in fragments associated with RAD51.

2016-07-08 | GSE55701 | GEO

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize.

Project description: Not available

| S-EPMC5699076 | biostudies-literature

Genomic features shaping the landscape of meiotic double-strand break hotspots in maize

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

2016-07-14 | GSE84369 | GEO

Project description:H3K4me3 ChIP-seq of Zea mays CML228 zygotene meiocytes, anthers and seedling control

| PRJNA451000 | ENA

Protein Determinants of Meiotic DNA Break Hotspots

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

2012-12-26 | GSE43122 | GEO

Arabidopsis thaliana

Project description:meiocytes-Transcriptomic of meiocytes.

| PRJNA110925 | ENA

Functional organization of protein determinants of meiotic DNA break hotspots.

Project description: Not available

| S-EPMC5431104 | biostudies-literature

RSC Defines MNase-sensitive Promoter Architecture in Yeast

Project description:The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently challenged by contradictory reports as to whether a distinct set of wider (≳150 bp) NDRs instead contain unusually unstable Micrococcal Nuclease-sensitive “fragile” particles, thought to be nucleosomal because of their size. To determine the composition of fragile particles we introduce CUT&RUN.ChIP, in which targeted nuclease cleavage and release is followed by chromatin immunoprecipitation. We find that fragile particles represent the occupancy and action of the RSC nucleosome remodeler acting on dynamically unwrapped nucleosomal intermediates. We also find that general regulatory factors (GRFs) bind to partially unwrapped nucleosomal intermediates at NDRs. We propose that RSC-engagement and its action cause nucleosomes to unravel, and subsequent binding of GRFs constitute a dynamic cycle of nucleosome deposition and clearance at the subset of wide Pol II promoter NDRs.

2018-12-22 | GSE116853 | GEO

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern. TIP-seq recovery of transposon insertion junctions in haploid and diploid yeast

2012-01-01 | E-GEOD-33986 | biostudies-arrayexpress

Unravelling the proteomic profile of rice meiocytes during early meiosis

Project description:Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodelling, nucleic acid binding, cell-cycle regulation and cytoskeleton. Moreover, the putative roles of sixteen proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins (such as SKP1 (OSK), a putative CDK2 like efector), a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs.

2014-08-13 | PXD001058 | Pride

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