Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Direct histone proteoform profiling of the unannotated, endangered coral Acropora cervicornis

ABSTRACT: Epigenetic modifications directly regulate the patterns of gene expression by altering DNA accessibility and chromatin structure. A knowledge gap is presented by the need to directly measure these modifications, especially for unannotated organisms with unknown primary histone sequences. In the present work, we developed and applied a novel workflow for identifying and annotating histone proteoforms directly from mass spectrometry-based measurements for the endangered Caribbean coral Acropora cervicornis. Combining high accuracy de novo top-down and bottom-up analysis based on tandem liquid chromatography, trapped ion mobility spectrometry, non-ergodic electron-based fragmentation, and high-resolution mass spectrometry, near complete primary sequence (up to 99%) and over 86 post-translational modification annotations were obtained from pull-down histone fractions. In the absence of reliable genome annotations, H2A, H2B and H4 histone sequences and the annotation of the post-translational modifications of the stressed A. cervicornis coral allow for a better understanding of chromatin remodeling and new strategies for target intervention and restoration of endangered reef corals.

INSTRUMENT(S): maXis II, timsTOF Pro 2

ORGANISM(S): Acropora Cervicornis (ncbitaxon:6130)

SUBMITTER: Francisco A Fernandez-Lima

PROVIDER: MSV000096788 | MassIVE | Tue Jan 07 06:06:00 GMT 2025

SECONDARY ACCESSION(S): PXD059506

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Project description:The magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this question in a systematic manner, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated with different subsets of ENCODE annotations. The results of chromosomally-based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson's R2 of 0.347 for predicting the results of chromosomally integrated reporter assays. This is substantially better than with either chromatin annotations or sequence information alone and also outperforms predictive models of episomal assays. Our results have broad implications for how cis-regulatory elements are identified, prioritized and functionally validated.

2016-10-01 | GSE83894 | GEO

The BAF complex enhances transcription through interaction with H3K56ac in the histone globular domain

Project description:Histone post-translational modifications play pivotal roles in eukaryotic gene expression. To date, most studies have focused on modifications in unstructured histone N-terminal tail domains and their binding proteins. However, transcriptional regulation by chromatin-effector proteins that directly recognize modifications in histone globular domains has yet to be clearly demonstrated, despite the richness of their multiple modifications. Here, we show that the ATP-dependent chromatin-remodeling BAF complex stimulates p53-dependent transcription through direct interaction with H3K56ac located on the lateral surface of the histone globular domain. Mechanistically, the BAF complex recognizes nucleosomal H3K56ac via the DPF domain in the DPF2 subunit and exhibits enhanced nucleosome-remodeling activity in the presence of H3K56ac. We further demonstrate that a defect in H3K56ac–BAF complex interaction leads to impaired p53-dependent gene expression and DNA damage responses. Our study provides direct evidence that histone globular domain modifications participate in the regulation of gene expression.

2024-09-30 | PXD051883 | JPOST Repository

Genome-wide maps of chromatin state in neural stem/progenitor cells (NSC) from mouse neonatal forebrain [ChIP-seq]

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in NSC. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of NSC. We compared histone modifications between wild type and Sox2-deleted NSC.

2019-03-07 | GSE90558 | GEO

Project description:Plasmodium falciparum histone post-translational modifications

| PRJNA386433 | ENA

Defining the chromatin compaction state of all histone post-translational modifications

Project description:Defining the chromatin compaction state of all histone post-translational modifications

| PRJNA516172 | ENA

Histone H3.1 is a chromatin embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multi-drug resistance [ChIP-Seq]

Project description:Chromatin structure is regulated through histone post-translational modifications as well as histone variants. Although highly homologous, histone variants display unique amino acid sequences associated with specialized functions in gene transcription regulation. Abnormal incorporation of histone variants into chromatin contributes to cancer initiation, progression, metastasis, as well as, therapy resistance. The current study reports a novel epigenetic function of histone H3.1 as a redox sensor embedded in heterochromatin. We found that this new function depends on oxidation by nuclear ROS and lead to changes in the transcriptional profile of MCF10A cells.

2024-02-20 | GSE255615 | GEO

Histone H3.1 is a chromatin embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multi-drug resistance [RNA-Seq]

2024-02-20 | GSE255598 | GEO

Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [Mnase-seq]

Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination. Two samples, one WT MNase-seq and one MNase-seq from yeast with a lysine->arginine mutation at H4K44, no replicates Two replicates each of MNase-seq in WT and H4K44->R mutant yeast grown in YPD or YPA.

2015-12-07 | E-GEOD-59004 | biostudies-arrayexpress

The ULK3 kinase is a key determinant of keratinocyte self-renewal and tumorigenesis targeting the arginine methylome

Project description:Epigenetic mechanisms oversee epidermal homeostasis and oncogenesis. The identification of kinases controlling these processes has direct therapeutic implications. We show that ULK3 is a nuclear kinase with elevated expression levels in squamous cell carcinomas (SCCs) arising in multiple body sites, including skin and Head/Neck. ULK3 loss by gene silencing or deletion reduces proliferation and clonogenicity of human keratinocytes and SCC-derived cells and affects transcription impinging on stem cell-related and metabolism programs. Mechanistically, ULK3 directly binds and regulates the activity of two histone arginine methyltransferases, PRMT1 and PRMT5 (PRMT1/5), with ULK3 loss compromising PRMT1/5 chromatin association to specific genes and overall methylation of histone H4, a shared target of these enzymes. These findings are of translational significance, as downmodulating ULK3 by RNA interference or locked antisense nucleic acids (LNAs) blunts the proliferation and tumorigenic potential of SCC cells and promotes differentiation in two orthotopic models of skin cancer.

2022-11-14 | MTBLS5155 | MetaboLights

Effects of temperature on gene expression in coral larvae of Montastraea faveolata

Project description:Background Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in embryos of the coral Montastraea faveolata. Embryos were exposed to 27.5C, 29.0C, and 31.5C directly after fertilization. Differences in gene expression were measured after 12 and 48 hours. Results Analysis of differentially expressed genes indicated that increased temperatures may lead to oxidative stress, apoptosis, and a structural reconfiguration of the cytoskeletal network. Metabolic processes were downregulated, and the action of histones and zinc finger-containing proteins may have played a role in the long-term regulation upon heat stress. Conclusions Embryos responded differently depending on exposure time and temperature level. Embryos showed expression of stress-related genes already at a temperature of 29.0C, but seemed to be able to counteract the initial response over time. By contrast, embryos at 31.5C displayed continuous expression of stress genes. The genes that played a role in the response to elevated temperatures consisted of both highly conserved and coral-specific genes. These genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change. The experimental setup followed a reference design, i.e. all samples were hybridized against the same pool made up of equal amounts of RNA from all samples. We used three technical replicates for each temperature. Common reference samples were labeled with Cy3, temperature samples with Cy5. Microarrays for M. faveolata contained 1,314 coding sequences, of which 43% had functional annotations as determined by homology to known genes.

2010-05-06 | E-GEOD-15088 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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