Inactive or moderately active human promoters are enriched for inter-individual epialleles
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Thomas Down
PROVIDER: E-GEOD-46220 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing. H2A.z ChIP-seq, RNA-seq, and DNA methylation data (submitted separately) were collected for five normal individuals. T21/T22 and T31/T32 are monozygotic twins.
2013-04-22 | E-GEOD-46217 | biostudies-arrayexpress
Project description: Not available
| S-EPMC4053860 | biostudies-other
Project description:We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing. DNA Methylation, H2A.z ChIP-seq, RNA-seq (submitted) separately were collected for five normal individuals (samples with "T" prefixes). T21/T22 and T31/T32 are monozygotic twins. Further DNA methylation data was collected from and additional two pairs of MZ twins with technical replication (samples with "C" prefixes - the three digits are pair number, individual number, and replicate number). Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2013-04-22 | E-GEOD-46168 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2013-04-22 | GSE46220 | GEO
Project description:We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing.
2013-04-22 | GSE46217 | GEO
Project description:We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing.
2013-04-22 | GSE46168 | GEO
Project description:Here we report a novel role for H2A.Z.2 (H2AFV) as a mediator of cell proliferation and sensitivity to targeted therapies in malignant melanoma. While both H2A.Z.1 and H2A.Z.2 are highly expressed in metastatic melanoma and correlate with decreased patient survival, only H2A.Z.2 deficiency results in impaired cellular proliferation of melanoma cells, which occurs via a G1/S arrest. Integrated gene expression and ChIP-seq analyses revealed that H2A.Z.2 positively regulates E2F target genes, and that such genes acquire a distinct H2A.Z occupancy signature over the promoter and gene body in metastatic melanoma cells. We further identified the BET family member BRD2 as an H2A.Z-interacting protein in melanoma cells, and demonstrate that H2A.Z.2 silencing cooperates with BET inhibition to induce cell death. Mononucleosomes from SK-mel147 (wt and stably expressing eGFP-H2A. eGFP-H2A.Z.1 and eGFP-H2A.Z.2) and melanocytes were isolated for ChIP with H2A.Z antibody or GFP trap beads (Chromotek).
2015-07-01 | E-GEOD-68222 | biostudies-arrayexpress
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2015-08-01 | E-GEOD-56665 | biostudies-arrayexpress
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:Light spectrum quality is an important signal for plant growth and development. We aimed to analyze the effects of different light spectra on in vitro shoot development and proteomic and polyamine (PA) profiles in shoots of Cedrela fissilis. Cotyledonary and apical nodal segments were grown under different light emitting diode (LED) lamps and a fluorescent lamp. Shoots from cotyledonary nodal segments cultured with 6-benzyladenine (BA) grown under WmBdR LED increased their length, fresh and dry matter compared to shoots grown under fluorescent light. A non-redundant protein databank generated by transcriptome sequencing and de novo assembly of C. fissilis improved, and almost doubled, protein identification compared to a Citrus sinensis databank. Using the C. fissilis protein databank, a total of 616 proteins were identified, with 23 up- and 103 downaccumulated in shoots under WmBdR LED compared to fluorescent lamp. Differential accumulation of argininosuccinate synthase protein was associated with an increase in free-Put contents and, consequently, with higher shoot elongation under WmBdR LED. Furthermore, the proteins S-adenosylmethionine synthase, which is related to PA and ethylene biosynthesis, and 1-aminocyclopropane-1-carboxylate oxidase, related to ethylene biosynthesis, were unique in shoots grown under fluorescent lamp, showing lower elongation of shoots, possibly due to ethylene production. The downaccumulation of calreticulin, heat shock proteins, plastid-lipid-associated protein, ubiquitin-conjugating enzymes, and ultraviolet-B receptor UVR8 isoform X1 could be related to better shoot length under LED. This work provides important data related to the effects of light spectrum quality on in vitro morphogenesis via modulation of specific proteins and free-Put biosynthesis.
2020-09-04 | PXD018020 | Pride