Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-chip of H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, H3K9Me2, H3K27Me3, CTCF and HP1a in MCF7 breast cancer cells

ABSTRACT: We report the high-throughput profiling of histone modifications, CTCF and HP1a binding sites in MCF7 breast cancer cells. ChIP-chip experiments were performed using the Agilent Human Genome CGH Microarray 1x1M. Regulatory markers H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, CTCF are known to be positively correlated with gene expression, and H3K9Me2, H3K27Me3 and HP1a are negative markers. Together with MCF7 methylation data, we showed hypomethylated promoters are significantly enriched with positive regulatory elements, and lacks repressive markers.

ORGANISM(S): Homo sapiens

SUBMITTER: Ming-Ta Hsu

PROVIDER: E-MTAB-1935 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes.

Lin I-Hsuan IH Chen Dow-Tien DT Chang Yi-Feng YF Lee Yu-Ling YL Su Chia-Hsin CH Cheng Ching C Tsai Yi-Chien YC Ng Swee-Chuan SC Chen Hsiao-Tan HT Lee Mei-Chen MC Chen Hong-Wei HW Suen Shih-Hui SH Chen Yu-Cheng YC Liu Tze-Tze TT Chang Chuan-Hsiung CH Hsu Ming-Ta MT

PloS one 20150223 2

Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation ...[more]

PMID: 25706888

Similar Datasets

Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells

Project description:Heterochromatin protein 1a (HP1a) is a well-known component of pericentromeric and telomeric heterochromatin in Drosophila. However, its role and the mechanisms of its binding in the chromosome arms (ChAs) remain largely unclear. Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamIDseq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. Although HP1a domains cover only 13% of ChAs, they non-randomly associate with 42% of TE insertions. Furthermore, HP1a propagates from TE insertions at distances up to 10-kb. These data confirm the role of TEs in formation of HP1a islands in ChAs. However, only 18% of HP1a domains have adjacent TEs, indicating the existence of other mechanisms of HP1a domain formation besides spreading from TEs. In particular, many TE-independent HP1a domains correspond to the regions attached to the nuclear pore complexes (NPCs), or contain active gene promoters. Surprisingly, HP1a occupancy on the promoters of these genes does not lead to their repression. However, the steady-state transcript level of many genes located outside of HP1a domains was altered upon HP1a knockdown in the somatic cells of ovaries, thus pointing to the strong indirect effect of HP1a depletion. Collectively, our results support an existence of at least three different mechanisms of HP1a domain emergence in ChAs: spreading from TE insertions, interaction with the chromatin located near NPCs and targeting to the promoters of moderately expressed genes.

2020-05-26 | GSE132756 | GEO

HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster

Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites.

2012-12-21 | GSE38366 | GEO

Drosophila HP1a IP-MS - The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic

Project description:Heterochromatin is enriched for characteristic epigenetic factors, including Heterochromatin Protein 1a (HP1a) and is essential for many organismal functions. However, how this nuclear domain is organized and functions is unclear. We extensively investigated heterochromatin protein compostion by biochemically purifying Drosophila melanogaster HP1a interactors.

2016-08-18 | PXD003780 | Pride

Gene expression signatures in Tif1b, Hp1a or Hp1g knockdown hematopoietic progenitors

Project description:Gene expression analyses of Tif1b, Hp1a or Hp1g knockdown hematopoietic progenitors. Growth of hematopoietic stem cells (HSCs) are significantly impaired upon knockdown of Hp1a and Hp1g. Results provide insight into the role of these factors in hematopoiesis.

2014-08-01 | GSE48897 | GEO

RNA expression in Drosophila melanogaster mutants lacking HP1a

Project description:mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes].

2012-09-01 | GSE39083 | GEO

Next Generation Sequencing of HM1, HP1a-/-, and HP1b-/- ESC transcriptomes

Project description:HM1, HP1a-/-, and HP1b-/- ESC transcriptomes were generated to determine whether depletion of these HP1 proteins influences gene and/or retroelement expression

2013-05-25 | GSE47370 | GEO

RNA-seq of S2 cells after GFP (control), dKDM4A, or HP1a RNAi

Project description:Analysis of transcriptional changes from genes and repetitive elements after dKDM4A and HP1a RNAi of S2 cells

2018-02-15 | GSE99023 | GEO

RNA expression in Drosophila melanogaster mutants lacking HP1a

Project description:mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes]. RNA samples from wildtype (OR) and HP1a mutant third instar larvae were examined, using duplicate biological samples and Illumina NGS.

2012-09-01 | E-GEOD-39083 | biostudies-arrayexpress

The large fraction of heterochromatin in Drosophila neurons is simultaneously bound by B-type lamin and HP1a

Project description:In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin as observed by both microscopy observations and DamID mapping of lamina-associated domains (LADs), enriched in dimethylated Lys9 of histone H3 (H3K9me2). In Drosophila Kc167 cell culture, where LADs were only mapped to the moment, they are neither H3K9me2-enriched, nor overlap with the domains of Heterochromatin Protein 1a (HP1a). Here, using a cell type-specific DamID approach we mapped genome-wide LADs, HP1a and Pc domains from the central brain, Repo-positive glia, Elav-positive neurons and the fat body of Drosophila third instar larvae. Silent or weakly-expressed genes occupy LADs, HP1a and Pc domains, with genes residing in the HP1a-bound LADs expressed at the lowest level. However, a fraction of HP1a domains contain actively expressed genes. The inter-LAD regions that are shared by all cell types are populated by ubiquitously expressed genes, whereas the conserved LADs are less abundant than in mammals. Importantly, in the central brain and in neurons we found strong overlap of HP1a domains with LADs both in the chromosome arms and in pericentromeric regions. In the glia and fat bodies, this overlap was less frequent. Consistent with these results, centromeres appear to reside closer to nuclear lamina in neurons than in Kc167 cells. The discovery of Drosophila peripheral chromatin bound by both HP1a and B-type lamin implies that mechanisms of heterochromatin compaction and attachment to nuclear lamina may be similar in Drosophila and mammals.

2018-10-31 | GSE109495 | GEO

HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster

Project description:Heterochromatin protein 1a (HP1a) is a chromatin associated protein that has been well studied in many model organisms, such as Drosophila, where it is a determining factor for classical heterochromatin. HP1a is associated with the two histone methyltransferases SETDB1 and Su(var)3-9, which mediate H3K9 methylation marks and participate in the establishment and spreading of HP1a enriched chromatin. While HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4 specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggested that HP1a has a repressing function on chromosome 4, where it preferentially targets non-ubiquitously expressed genes (NUEGs), and a stimulating function in pericentromeric regions. Further, we showed that the effects of SETDB1 and Su(var)3-9 are similar to HP1a, and on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In contrast, transposons are repressed by HP1a and Su(var)3-9 but are un-affected by SETDB1 and POF. In addition, we found that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment.

2013-04-05 | GSE43478 | 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