Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq of human HeLa cell lines at different cell fractionation stages

ABSTRACT: We investigated RNAs involved in the maintenance of spatial chromatin organization during interphase. Various RNA fractions from HeLa cells were prepared, tested in in vivo experiments and sequenced in order to identify and characterize the RNA fraction presenting the higher activity.

ORGANISM(S): Homo sapiens

SUBMITTER: Maiwen Caudron-Herger

PROVIDER: E-MTAB-582 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Coding RNAs with a non-coding function: maintenance of open chromatin structure.

Caudron-Herger Maïwen M Müller-Ott Katharina K Mallm Jan-Philipp JP Marth Caroline C Schmidt Ute U Fejes-Tóth Katalin K Rippe Karsten K

Nucleus (Austin, Tex.) 20110901 5

The multi-layered organization of the genome in a large nucleoprotein complex termed chromatin regulates nuclear functions by establishing subcompartments with distinct DNA-associated activities. Here, we demonstrate that RNA plays an important role in maintaining a decondensed and biologically active interphase chromatin conformation in human and mouse cell lines. As shown by RNase A microinjection and fluorescence microscopy imaging, digestion of single-stranded RNAs induced a distinct microme ...[more]

PMID: 21983088

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Project description:Mycoplasma hominis is a facultative human pathogen primarily associated with bacterial vaginosis and pelvic inflammatory disease, but it is also able to spread to other sites, leading to arthritis or, in neonates, meningitis. With a minimal set of 537 annotated genes, M. hominis is the second smallest self-replicating mycoplasma and thus an ideal model organism for studying the effects of an infectious agent on its host more closely. M. hominis adherence, colonisation and invasion of HeLa cells were characterised in a time-course study using scanning electron microscopy, confocal microscopy and microarray-based analysis of the HeLa cell transcriptome. At 4 h post infection, cytoadherence of M. hominis to the HeLa cell surface was accompanied by differential regulation of 723 host genes (>2 fold change in expression). Genes associated with immune responses and signal transduction pathways were mainly affected and components involved in cell-cycle regulation, growth and death were highly upregulated. At 48 h post infection, when mycoplasma invasion started, 1588 host genes were differentially expressed and expression of genes for lysosome-specific proteins associated with bacterial lysis was detected. In a chronically infected HeLa cell line (2 weeks), the proportion of intracellular mycoplasmas reached a maximum of 10% and M. hominis-filled protrusions of the host cell membrane were seen by confocal microscopy, suggesting exocytotic dissemination. Of the 1972 regulated host genes, components of the ECM-receptor interaction pathway and phagosome-related integrins were markedly increased. The immune response was quite different to that at the beginning of infection, with a prominent induction of IL1B gene expression, affecting pathways of MAPK signalling, and genes connected with cytokine-cytokine interactions and apoptosis. These data show for the first time the complex, time-dependent reaction of the host directed at mycoplasmal clearance and the counter measures of this pestering pathogen.

Dataset Information

RNA-Seq of human HeLa cell lines at different cell fractionation stages

Publications

Coding RNAs with a non-coding function: maintenance of open chromatin structure.

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