Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (MNase-seq)

ABSTRACT: To analyse nucleosome positioning and occupancy we performed micrococcal nuclease digestion of Arabidopsis wild type (Col-0) chromatin and gel purified the resulting ~150 bp mononucleosomal DNA band. This DNA was used to generate a library and paired-end sequencing performed (MNase-seq). To further examine influence of SWR1 chromatin remodelling complex and DNA methylation on nucleosome occupancy, we repeated MNase-seq in Aarabidopsis arp6 and met1 mutant.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Xiaohui Zhao

PROVIDER: E-MTAB-5042 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (H3K4m3 ChIP-seq)

Project description:To investigate the relationship between meiotic recombination initiation and H3K4m3 in Arabidopsis, we generated and sequenced H3K4m3 ChIP libraries from meiotic stage floral buds in wild type, arp6 and met1. To produce high-resolution of H3K4m3 mapping, we used micrococcal nuclease (MNase) to digest chromatins that were cross-linked by formaldehyde for ChIP. This experiment provides for H3K4m3 maps with the resolution of mononucleosomal DNA level (~150 bp).

2017-06-05 | E-MTAB-5048 | biostudies-arrayexpress

Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (SPO11-1-oligonucleotides-seq)

Project description:To determine meiotic recombination initiation sites in Arabidopsis thaliana genome we purified and sequenced oligonucleotides (35-45 nt) bound to SPO11-1, meiosis specific transesterase that induces meiotic DSB formation. This reveals that SPO11-1-oligonucleotide hotspots occur at nucleosome depleted regions of gene promoters, introns, terminators and specific families of DNA transposons (recomposons). To investigate the influence of chromatin structure and epigenetic factors on meiotic DSB formation we performed sequencing of SPO11-1-oligonucleotides in arp6, met1 and suvh4 suvh5 suvh6.

2017-06-05 | E-MTAB-5041 | biostudies-arrayexpress

MNase-Seq for nucleosome occupancy

Project description:MNase-Seq for nucleosome occupancy

| PRJNA649224 | ENA

Quantitative MNase-seq accurately maps nucleosome occupancy levels

Project description:Chromatin mapping using micrococcal nuclease (MNase) has been the standard tool for mapping nucleosomes for >40 years. When coupled with DNA sequencing, MNase-seq can provide base-pair-resolution nucleosome maps. However, determining nucleosome occupancy using MNase-seq has been hampered by its aggressive endo-/exo-nuclease activities, whereby cleavages within linker regions produce oligo- and mono-nucleosomes whereas cleavages within nucleosomes destroy them. Here we introduce a theoretical framework for predicting nucleosome occupancies and an experimental protocol with appropriate spike-in normalization that confirms our theory and provides accurate occupancy levels over an MNase digestion time-course. As expected, DNaseI hypersensitive sites and transcription units are digested by MNase at elevated rates, and the apparent deficiency of nucleosomes at 3’ ends of Drosophila genes is an artifact of MNase preference for AT-rich DNA. Surprisingly, we observed no overall differences between Drosophila euchromatin and heterochromatin, which implies that heterochromatin compaction does not render nucleosomal DNA less accessible than euchromatin.

2019-08-27 | GSE128689 | GEO

Nucleosome-depleted DNA transposons act as enhancers of meiotic recombination at Arabidopsis genes (RNA-seq)

Project description:To investigate the influence of heterochromatin on transposon transcription, we performed sequencing of RNA in wild type plant and met1 mutant which is defective in maintenance of CG context DNA methylation. The met1 mutant showed de-repression of centromeric transposons including Gypsy and EnSpm, which is coincident with increased meiotic DSBs and decreased nucleosome occupancy.

2017-06-05 | E-MTAB-5417 | biostudies-arrayexpress

Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

Project description:We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.

2017-02-26 | GSE70122 | GEO

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

Project description:Chromatin accessibility plays a fundamental role in gene regulation. One mechanism to regulate accessibility is nucleosome placement, which is often measured by quantifying protection of DNA from enzymatic digestion. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC, quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both location of nucleosomes and accessibility to MNase in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares behavior of nucleosomes to that of non-histone proteins. We find that enhancers, promoters and other regulatory regions have changes in accessibility that do not correlate with changes in nucleosome occupancy. Moreover, we show that high nucleosome occupancy does not necessarily preclude high accessibility, revealing novel principles of chromatin regulation.

2016-04-18 | GSE78984 | GEO

High-resolution analysis of chromatin structure by Mnase-SSP

Project description:Proof-of-concept for Mnase-SSP: a variant of Mnase-seq. Mnase-SSP dramatically increases the representation of short fragments of nucleolytically-digested DNA, enabling simultaneous analysis of transcription factor binding and nucleosome occupancy using the same assay. We used MNase-SSP to demarcate chromatin architecture at murine promoters and at transcription factor binding sites in murine embryonic stem cells. Are results reveal heterogeneity in the binding mode of C2H2 zinc fingers like Ctcf and Rest, demonstrating that Mnase-SSP, and SSP in general, as a flexible platform for profiling nucleolytically digested DNA for MNase-seq, MNase-ChIP, or CUT&RUN with reduced bias.

2019-02-12 | GSE125053 | GEO

In vivo nucleosome occupancy in yeast (MNase-seq)

Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. Thus, nucleosome remodelling and modification should be intimately coupled with open chromatin formation and regulation. However, our knowledge of nucleosome regulation is largely limited to promoter regions, which comprise only a subset of all regulatory loci in the genome. In order to examine nucleosome patterns in open chromatin regions, we performed micrococcal nuclease (MNase) sequencing for a laboratory strain of yeast. Nucleosome occupancy profiled by Micrococcal nuclease (MNase) digestion

2013-01-06 | E-GEOD-34923 | biostudies-arrayexpress

Project description:The SWR1 chromatin remodeling complex, which contains Arp6 and Swr1 as components, exchanges H2A in nucleosomes with its variant H2AZ. We have investigated the chromosome-wide dynamic distribution of Arp6 and Swr1 in budding yeast cells by chromatin immunoprecipitation analysis using a high-density genome tiling array. We found that the majority of Arp6 colocalizes with Swr1 on chromosomes and is enriched in the promoters of divergently promoters. This shows that Arp6 binds chromatin as a component of the SWR1 complex and is involved in transcriptional regulation in these regions. On the other hand, in some chromosomal regions, including telomere, centromere and ribosomal protein genes, the binding of Arp6 did not coincide with that of Swr1, and was remained in the absence of Swr1. This shows that a portion of Arp6 binds to chromosomes in Swr1-independent manner. These observations suggest that Arp6 has Swr1-dependent and –independent functions on chromosomes. Keywords: ChIP-chip

2010-05-11 | GSE9213 | 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