Dataset Information

Mass spectrometry analysis following chromatin fractionation in growing and senescent cells

ABSTRACT: This project contains the raw and result files for a mass spectrometry analysis comparing the abundance of proteins following chromatin fractionation in growing cells and in senescent cells for the WI-38hTERT/GFP-RAF1-ER cell line. Two replicas were analysed for each cell condition. The data are used to support a study on using polymer modelling to investigate the roles of heterochromatin and lamina interactions on chromosome reorganisation in senescence.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Diploid Cell, Fibroblast

SUBMITTER: Michael Chiang

LAB HEAD: Hisham Mohammed

PROVIDER: PXD014929 | Pride | 2019-09-25

REPOSITORIES: Pride

ACCESS DATA

Publications

Polymer Modeling Predicts Chromosome Reorganization in Senescence.

Chiang Michael M Michieletto Davide D Brackley Chris A CA Rattanavirotkul Nattaphong N Mohammed Hisham H Marenduzzo Davide D Chandra Tamir T

Cell reports 20190901 12

Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy, and mass spectrometry to dissect the roles played by heterochromatin- and lamina-mediated interactions in nuclear organization. Our model explains the conventional organization of heterochromatin and euchromatin in growing cells and the pathological organization found in oncogene-induced sene ...[more]

PMID: 31533042

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Project description:RNA polymerase (RNA Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of RNA Pol III and its associated transcription factors on the genome of mouse embryonic stem (ES) cell using a highly specific tandem ChIP-Seq method. Only a subset of the annotated class-III genes was bound and thus transcribed. A few hundred SINEs were associated with the RNA Pol III transcription machinery. We observed that RNA Pol III and its transcription factors were present at thirty unannotated sites on the mouse genome, only one of which was conserved in human. An RNA was associated with more than 80% of these regions. More than 2200 regions bound by TFIIIC transcription factor were devoid of RNA Pol III. These sites are correlated with association of CTCF and the cohesin. Cohesin has been shown to occupy sites bound by CTCF and to contribute to DNA loop formation associated with gene repression or activation. This observation suggests that TFIIIC may play a role in chromosome organization in mouse. We also investigated the genome-wide distribution of the ubiquitous TFIIS variant, TCEA1. We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a RNA Pol III transcription factor in mammals. We performed ChIP-seq experiment on mouse ES cells, in order to analyse the distribution of the RNA Pol III, with two of its subunits, RPC1 and RPC4, of the two distinct forms of the transcription factor TFIIIB, with BRF1 and BRF2, respectively subunit of TFIIIB-beta, and TFIIIB-alpha form, and three subunits of the transcription factor TFIIIC, TFIIIC90, TFIIIC110, TFIIIC220. We also analysed the distribution of the RNA Pol II elongation factor TCEA1. We used tagged proteins, in order to develop a highly specific and generic ChIP-seq protocol. A sequence encoding a 6 histidine-Flag-HA tag was inserted just after the last codon of the gene encoding proteins of the RNA Pol III machinery subunits, or just after the start codon for TCEA1, using the recombineering technology. Untagged ES cell line was used as negative control for data processing. Our dataset comprises of ten ChIP-seq samples, eight from tagged proteins, two from untagged cell line.

Dataset Information

Mass spectrometry analysis following chromatin fractionation in growing and senescent cells

Publications

Polymer Modeling Predicts Chromosome Reorganization in Senescence.

Similar Datasets

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