Browse
Submit Data
Databases
API
Help

Dataset Information

235 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mitotic post-translational modifications of histones promote chromatin compaction in vitro

ABSTRACT: As histones undergo major changes in their post-translational modifications during mitotic entry, we speculated that the spectrum of cell cycle-specific histone modifications might contribute to chromosome compaction during mitosis. To test this hypothesis, we isolated core histones from interphase and mitotic cells and reconstituted chromatin with them. We used mass spectrometry to show that key post-translational modifications remained intact during our isolation procedure.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Gallus Gallus (chicken)

TISSUE(S): Cell Culture

SUBMITTER: Juan Jose Bonfiglio

LAB HEAD: William Earnshaw

PROVIDER: PXD007116 | Pride | 2018-10-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Mitotic post-translational modifications of histones promote chromatin compaction <i>in vitro</i>.

Zhiteneva Alisa A Bonfiglio Juan Jose JJ Makarov Alexandr A Colby Thomas T Vagnarelli Paola P Schirmer Eric C EC Matic Ivan I Earnshaw William C WC

Open biology 20170901 9

How eukaryotic chromosomes are compacted during mitosis has been a leading question in cell biology since the nineteenth century. Non-histone proteins such as condensin complexes contribute to chromosome shaping, but appear not to be necessary for mitotic chromatin compaction. Histone modifications are known to affect chromatin structure. As histones undergo major changes in their post-translational modifications during mitotic entry, we speculated that the spectrum of cell-cycle-specific histon ...[more]

PMID: 28903997

Similar Datasets

Genome-wide analysis of condensin binding sites in vertebrate genome

Project description:The condensin complex is well known to be essential for correct packaging and segregation of chromosomes during mitosis and meiosis in all eukaryotes. To date, the genome wide location and the nature of condensin binding sites has remained elusive in vertebrate systems. A detailed knowledge of condensin binding sites is essential to understand the as-yet enigmatic function of this complex and to define its greater role in chromosome architecture. To address this, we have used next generation sequencing to map condensin I in chicken DT40 cells. Unexpectedly, we found condensin I binds predominately to promoter sequences in mitotic cells. We also found a striking enrichment at both centromeres and telomeres, highlighting the importance of the complex in chromosome segregation. Taken together, the results show condensin I is largely absent from heterochromatic regions. These results reveal for the first time the condensin I binding sites in the vertebrate genome, and demonstrate the importance of the complex in genome segregation and suggest a novel function in gene regulation. Condensin associated DNA from chicken DT40 cells were affinity purified using streptavidin and deep sequenced by Illumina Hiseq2000

2013-10-03 | E-GEOD-45552 | biostudies-arrayexpress

Chromatin transaction map during vertebrate mitotic entry

Project description:We have used a combination of chemical genetics, chromatin proteomics and imaging to map the earliest chromatin transactions during vertebrate cell entry into mitosis. Chicken DT40 Cdk1as cells undergo synchronous mitotic entry within 15 minutes following release from a 1NM-PP1-induced arrest in late G2. In addition to changes in chromatin association with nuclear pores and the nuclear envelope, earliest prophase is dominated by changes in the association of ribonucleoproteins with chromatin, particularly in the nucleolus, where pre-rRNA processing factors leave chromatin significantly before RNA polymerase I. Nuclear envelope barrier function is lost early in prophase and cytoplasmic proteins begin to accumulate on the chromatin. As a result, outer kinetochore assembly appears complete by nuclear envelope breakdown (NEBD). Most interphase chromatin proteins remain associated with chromatin until NEBD, after which their levels drop sharply.

2022-01-31 | PXD026385 | Pride

RNA-seq of H3.3 knockout and wild type chicken DT40 cells

Project description:RNA-seq was performed for transcriptional analysis of wild-type DT40 cells (Gallus gallus, B-cell line) and a H3.3 knockout line (h3.3a-/-, h3.3b-/-). H3.3 is a H3 histone variant encoded on two genes (H3.3A and H3.3B) in chickens.

2014-08-31 | E-MTAB-2754 | biostudies-arrayexpress

Condensin plays a role in both interphase nuclei and premature chromosome condensation

Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase. Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.

2017-05-03 | E-GEOD-74892 | biostudies-arrayexpress

histone post-translational modification during Plasmodium falciparum gametocyte development

Project description:Histone post-translational modifications (PTMs) play an essential role in epigenetic gene regulation. The Plasmodium falciparum genome encodes canonical and variant histones and a collection of conserved enzymes for histone PTMs and chromatin remodeling. Herein, we characterized the P. falciparum histone PTMs during the development of gametocytes, the obligatory for parasite transmission, we extracted histones from the early (day 4), middle (day 8), and late (day 12) stages of gametocytes, and analyzed them by advanced mass spectrometry.

2022-09-14 | PXD031817 | Pride

Mitotic chromatin proteomics - Proteomics analysis with a nano Random Forest approach reveals novel functional interactions regulated by SMC complexes on mitotic chromosomes

Project description:we used stable isotope labeling with amino acids in cell culture (SILAC) to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes.

2016-05-31 | PXD003427 | Pride

Quantification of histone H3 and H4 modifications by mass spectrometry in wildtype and MCM2-2A mutants of mice ESCs

Project description:During DNA replication modified parental histones H3-H4 are segregated almost symmetrically to the two daughter DNA strands enabling mitotic inheritance of histone PTMs. Whether heritable histone modifications confer epigenetic regulation by maintaining chromatin states and gene expression is unclear. Using MCM2 histone-binding mutant embryonic stem cells (ESCs) and mass spectrometry, we show that asymmetric segregation of parental histones to the leading strand causes imbalanced inheritance of histone H3K27 methylations to daughter cells.

2023-08-30 | PXD020326 | Pride

Histone ADP Ribosylation - Serine is a new target residue for endogenous ADP-ribosylation on histones

Project description:ADPr sites on histones obtained from cells were directly identified. We have identified 12 unique ADPr sites in human osteosarcoma cells and report serine ADPr as a new type of histone mark that responds to DNA damage.

2016-12-22 | PXD005462 | Pride

Two distinct modes for propagation of histone PTMs across the cell cycle

Project description:Epigenetic states defined by chromatin can be maintained through mitotic cell division. However, it remains unknown how histone-based information is transmitted. Here we combine nascent chromatin capture (NCC) and triple-SILAC labelling to track histone modifications and histone variants during DNA replication and across the cell cycle. We show that post-translational modifications (PTMs) are transmitted with parental histones to newly replicated DNA. Di- and tri-methylation marks are diluted two-fold upon DNA replication, as a consequence of new histone deposition. Importantly, within one cell cycle all PTMs are restored. In general, new histones are modified to mirror the parental histones. However, H3K9me3 and H3K27me3 are propagated by continuous modification of parental and new histones, because the establishment of these marks extends over several cell generations. Together, our results reveal how histone marks propagate and demonstrate that chromatin states oscillate within the cell cycle.

2015-03-30 | PXD001980 | Pride

Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity

Project description:Modified parental histones are segregated symmetrically to daughter DNA strands during replication and inherited through mitosis. How this may sustain the epigenome and cell identity remains unknown. Here, we show that transmission of histone-based information during replication maintains epigenome fidelity and embryonic stem cell plasticity. Asymmetric segregation of parental histones H3-H4 in MCM2-2A mutants compromised mitotic inheritance of histone modifications and globally altered the epigenome. This included widespread spurious deposition of repressive modifications, suggesting elevated epigenetic noise. Moreover, H3K9me3 loss at repeats caused de-repression and H3K27me3 redistribution across bivalent promoters correlated with misexpression of developmental genes. MCM2-2A mutation challenged dynamic transitions in cellular states across the cell cycle, enhancing naïve pluripotency and reducing lineage priming in G1. Further, developmental competence was diminished, correlating with impaired exit from pluripotency. Collectively, this argues that epigenetic inheritance of histone modifications maintains a correctly balanced and dynamic chromatin landscape able to support mammalian differentiation.

2023-06-15 | GSE154391 | 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