Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

78 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

5â-tag sequencing analysis of mouse mitotic chromosome RNA

ABSTRACT: As one of the most commonly recognized sub-cellular structures, mitotic chromosome structure and assembly is still lacking. Except the identified proteins and well known genomic composition, the identified mitotic chromosome RNA species is limited. We used a targeted protocol based on 5â-tag sequencing to profile mouse 3T3 cell mitotic chromosome associated RNA composition.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Yicong Meng

PROVIDER: E-MTAB-3810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

phosphoproteome in mitotic chromosomes

Project description:Identification and characterization of mitosis-specific phosphorylation in mitotic chromosome-associated proteins

2016-09-27 | PXD003877 | Pride

Loss of H3K9 tri-methylation alters mitotic chromosome compaction and transcription factor retention during mitosis

Project description:Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases (DNMTs) and Polycomb Repressor Complexes (PRCs), bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a, GLP are also retained by mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes that are associated with increased H3S10ph and H3K27me3 levels. Chromosome size and centromere compaction in these mutants was rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1,2 double null ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

2022-10-12 | PXD030771 | Pride

5â-tag sequencing analysis of mouse mitotic chromosome RNA

Project description:5â-tag sequencing analysis of mouse mitotic chromosome RNA

| PRJEB10240 | ENA

Loss of H3K9 tri-methylation alters chromosome compaction and transcription factor retention during mitosis

Project description:Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and Polycomb Repressor Complexes, bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Here we show that enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes associated with increased H3S10ph and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1/Suv39h2 double-null mouse ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

2023-01-25 | PXD039521 | 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

SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

Project description:In the associated paper, SERBP1 is shown to form granules in mitotic cells in a PKCɛ-dependent manner (M-bodies). We performed SERBP1 iCLIP in DLD1 cells that were either asynchronous or enriched for mitotic cells and after treatment with 2 hours of 500nM Blu577 or equivalent DMSO. We found that SERBP1 alters its positioning on rRNA in mitosis in a Blu577-dependent manner, identifying an alternative binding position that coincides with the formation of M-bodies. Mitotic enrichment was performed by single thymidine block, release in to G2 block with RO3306, and release and mitotic shake-off. The fastq files provided are demultiplexed, with adapters and barcodes trimmed and UMI sequences are found in the fastq headers.

2021-10-05 | E-MTAB-10830 | biostudies-arrayexpress

Analysis of barley chromosomal proteome: a multiapproach exploration of flow cytometry-sorted mitotic chromosomes

Project description:Proteins contribute to the structure of chromatin and regulate its functions. The basic building block of chromatin in eukaryotes is the nucleosome containing histones. Structural maintenance of chromosomes complexes perform the assembly of genomic DNA into the higher organizational structures of interphase chromatin as well as the compact arrangement of dividing chromosomes. Here, proteins were extracted from flow cytometry-sorted barley mitotic chromosomes after a nuclease treatment to remove DNA. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system prior to liquid chromatography coupled to tandem mass spectrometry. Nuclear and chromosomal proteins (almost 900 identifications) were then classified based on a combination of software prediction results, available database localization information, sequence homology, and domain representation. The degree of enrichment of the chromosome samples by chromosomal proteins was evaluated by comparing the results with controls (depleted flow cytometric fraction and initial cell lyzate). A biological context evaluation indicated the presence of several groups of abundant proteins including histone variants, topoisomerase 2, PARP2, Condensin complex subunits, and many proteins with chromatin-related functions. Interestingly, nucleolar proteins were found as wells as proteins documenting processes related to replication, transcription and DNA repair in barley mitotic chromosomes.

2021-07-21 | PXD024689 | Pride

FoxA1 binding in asynchronous and mitotic HUH7 cells

Project description:During mitosis, RNA polymerase and most transcription factors are excluded from the chromosomes and transcription ceases. The transcriptional re-activation of the genome, following mitosis, requires the re-setting of cell-type specific programs that were initially established during development. However, only about one-fifth of transcription factors are retained on chromosomes throughout mitosis and a subset of these have been shown to facilitate target gene reactivation during mitotic exit. How such M-bM-^@M-^\bookmarkingM-bM-^@M-^] factors bind to chromatin in mitosis and re-activate transcription is central to the stability of transcriptional programs across multiple cell cycles. We compared a diverse set of transcription factors involved in liver differentiation and found different modes of mitotic chromosome binding. The pioneer transcription factor FoxA1, which is among the first to bind liver genes in development, exhibits virtually complete mitotic chromosome binding, whereas other liver factors bind with a range of efficiencies. Yet genome-wide analysis shows that only about 15% of the FoxA1 interphase target sites are bound in mitosis; the latter include sites at genes for maintaining cell differentiation. FoxA1 mutants that perturb specific and nonspecific DNA binding reveal a significant contribution of nonspecific binding events in mitotic chromatin. Such nonspecific binding appears to spread from interphase FoxA1 targets and may serve as storage sites. The hierarchy of specific binding, nonspecific binding, partial chromatin binding, and failure to bind mitotic chromosomes reflects the temporal sequence of the factorsM-bM-^@M-^Y developmental roles in gene activation. Three replicate chIP-seq data sets each are included for mitotic and asynchronously cycling cells; a single input lane from each condition is also included.

2013-03-31 | E-GEOD-39241 | biostudies-arrayexpress

Analysis of factors bound to native metaphase ESC chromosomes following purification by flow cytometry

Project description:Stem cells are able to self-renew and also generate differentiated progeny. How gene expression patterns are transmitted through mitosis remains unresolved. Conventional studies have relied upon rigorous cell-cycle-stage synchronisation to find factors in mitotic lysates that could ‘bookmark’ the genome. Here we use an alternative approach, purifying native-unfixed mitotic chromosomes from different cell types using flow cytometry and directly identifying chromosome-bound proteins by LC-MS/MS. This revealed a rich profile of pluripotency- and lineage-specific transcription factors that remained bound to mitotic chromosomes in pluripotent ESCs and lymphocytes, as well as factors implicated in chromosome condensation, architecture and gene silencing. Removal of DNA methylation, PRC2 activity, or in situ cleavage of cohesin, each resulted in the reduced compaction of mitotic chromosomes. These data provide a comprehensive catalogue of bookmarking factors in pluripotent versus lineage-restricted cells and demonstrate an expected duality of function by candidates in regulating both gene expression and mitotic chromosome structure.

2020-06-15 | PXD015251 | Pride

RNAseq of isolated mitotic HeLa cells treated with Actinomycin D

Project description:The goal of this experiment was to assess whether transcription happens during mitosis. For this, we isolated mitotic HeLa cells and treated them with a transcription inhibitor, ActD.

2018-08-28 | E-MTAB-6661 | biostudies-arrayexpress