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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Role of BACH1 in HEK 293T cells

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE28050: Expression data from knockdown of BACH1 in HEK 293T cells GSE28051: Genome-wide map of BACH1 binding in HEK293T cells Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Hans-JM-CM-6rg Warnatz

PROVIDER: E-GEOD-28053 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.

Warnatz Hans-Jörg HJ Schmidt Dominic D Manke Thomas T Piccini Ilaria I Sultan Marc M Borodina Tatiana T Balzereit Daniela D Wruck Wasco W Soldatov Alexey A Vingron Martin M Lehrach Hans H Yaspo Marie-Laure ML

The Journal of biological chemistry 20110509 26

The regulation of gene expression in response to environmental signals and metabolic imbalances is a key step in maintaining cellular homeostasis. BTB and CNC homology 1 (BACH1) is a heme-binding transcription factor repressing the transcription from a subset of MAF recognition elements at low intracellular heme levels. Upon heme binding, BACH1 is released from the MAF recognition elements, resulting in increased expression of antioxidant response genes. To systematically address the gene regula ...[more]

PMID: 21555518

Similar Datasets

Genome-wide map of BACH1 binding in HEK 293T cells

Project description:BTB and CNC homology 1 (BACH1) is a heme-binding transcription factor repressing the transcription from a subset of MAF recognition elements (MAREs) at low intracellular heme levels. Upon heme binding, BACH1 is released from the MAREs, resulting in increased expression of antioxidant response genes. To systematically address the gene regulatory networks involving BACH1, we combined chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of BACH1 target genes in HEK 293 cells with knock-down of BACH1 using three independent types of small interfering RNAs followed by transcriptome profiling using microarrays. The 59 BACH1 target genes identified by ChIP-seq were found highly enriched in genes showing expression changes after BACH1 knock-down, demonstrating the impact of BACH1 repression on transcription. In addition to known and new BACH1 targets involved in heme degradation (HMOX1, FTL, FTH1, ME1, SLC48A1) and redox regulation (GCLC, GCLM, SLC7A11), we also discovered BACH1 target genes effecting cell cycle and apoptosis pathways (ITPR2, CALM1, SQSTM1, TFE3, EWSR1, CDK6, BCL2L11, MAFG) as well as subcellular transport processes (CLSTN1, PSAP, MAPT, vault RNA). The newly identified impact of BACH1 on genes involved in neurodegenerative processes and proliferation provides an interesting basis for future dissection of BACH1-mediated gene repression in neurodegeneration and virus-induced cancerogenesis. Examination of BACH1 binding in HEK 293T cells by chromatin immunoprecipitation-sequencing (CHIP-seq) with input DNA as control.

2011-05-13 | E-GEOD-28051 | biostudies-arrayexpress

Epstein-Barr virus maintains lymphomas via its miRNAs

Project description:EpsteinM-bM-^@M-^PBarr virus (EBV) has evolved exquisite controls over its host cells, human B lymphocytes, not only directing these cells during latency to proliferate and thereby expand the pool of infected cells, but also to survive and thereby persist for the lifetime of the infected individual. Although these activities ensure the virus is successful, they also make the virus oncogenic, particularly when infected people are immunosuppressed. Here we show, strikingly, that one set of EBVM-bM-^@M-^Ys miRNAs both sustain BL (BurkittM-bM-^@M-^Ys lymphoma) cells in the absence of other viral oncogenes and promote the transformation of primary B lymphocytes. BurkittM-bM-^@M-^Ys Lymphoma cells were engineered to lose EBV and found to die by apoptosis and could be rescued by constitutively expressing viral miRNAs in them. Two of these EBV miRNAs were found to target Caspase 3 to inhibit apoptosis at physiological concentrations. Examination of RISC associated transcripts under 4 conditions in Sav S1-1 cells

2013-04-30 | E-GEOD-44769 | biostudies-arrayexpress

Comparing proteomics and RISC immunoprecipitations to identify targets of Epstein-Barr viral miRNAs [RISC-IP-seq]

Project description:Epstein-Barr virus is a gamma-herpes virus that is causally associated with several lymphomas and carcinomas. This virus encodes at least 25 pre-miRNAs, which are expressed in infected cells to yield more than 50 detected mature miRNAs. miRNAs are small, non-coding RNAs that inhibit gene expression by promoting the inhibition of translation or of degradation of mRNAs. Currently, the function of these viral miRNAs and the contribution they provide to EBV's life-cycle remain largely unknown, due to difficulties in identifying cellular and viral genes regulated by these miRNAs. We have compared and contrasted two methods to identify targets of viral miRNAs in order to identify the advantages and limitations of each method to aid in uncovering the functions of EBV's miRNAs. Examination of RISC (RNA Induced Silencing Complexes) associated transcripts under 2 conditions in BJAB cells

2013-05-01 | E-GEOD-46514 | biostudies-arrayexpress

Expression data from knockdown of BACH1 in HEK 293T cells

Project description:BTB and CNC homology 1 (BACH1) is a heme-binding transcription factor repressing the transcription from a subset of MAF recognition elements (MAREs) at low intracellular heme levels. Upon heme binding, BACH1 is released from the MAREs, resulting in increased expression of antioxidant response genes. To systematically address the gene regulatory networks involving BACH1, we performed knock-down of BACH1 in HEK 293T cells using three independent types of small interfering RNAs followed by transcriptome profiling using microarrays. Knockdown of BACH1 in HEK 293T cells was carried out with three different types of siRNA molecules (esiRNA = e, siRNA1 SI00309876 from Qiagen = q and Stealth siRNA2 HSS100910 from Invitrogen = s), followed by RNA extraction after 24h and 72h of knockdown and hybridization on Affymetrix microarrays. For each siRNA type, we performed the experiments in triplicates, with four control replicates (mock transfections without siRNA) at 24h and three control replicates at 72h, resulting in nine samples and four controls at 24h and nine samples and three controls at 72h. Samples at 24h of knockdown: e_1_24, e_2_24, e_3_24, q_1_24, q_2_24, q_3_24, s_1_24, s_2_24, s_3_24. Controls at 24h: m_1_24, m_2_24, m_3_24, m_4_72. Samples at 72h of knockdown: e_1_72, e_2_72, e_3_72, q_1_72, q_2_72, q_3_72, s_1_72, s_2_72, s_3_72. Controls at 72h: m_1_72, m_2_72, m_3_72. REPEATS: biological replicate: BACH1_e_1_24, BACH1_e_2_24, BACH1_e_3_24 biological replicate: BACH1_q_1_24, BACH1_q_2_24, BACH1_q_3_24 biological replicate: BACH1_s_1_24, BACH1_s_2_24, BACH1_s_3_24 biological replicate: BACH1_m_1_24, BACH1_m_2_24, BACH1_m_3_24, BACH1_m_4_24 biological replicate: BACH1_e_1_72, BACH1_e_2_72, BACH1_e_3_72 biological replicate: BACH1_q_1_72, BACH1_q_2_72, BACH1_q_3_72 biological replicate: BACH1_s_1_72, BACH1_s_2_72, BACH1_s_3_72 biological replicate: BACH1_m_1_72, BACH1_m_2_72, BACH1_m_3_72

2011-05-13 | E-GEOD-28050 | biostudies-arrayexpress

Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL crosslinking and affinity purification

Project description:Short-read sequencing of DNA fractions of the BioTAP-XL pull-downs on human EZH2 and interacting proteins. ChIP-seq-like pulldown/input samples

2014-02-01 | E-GEOD-53495 | biostudies-arrayexpress

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites [GP5d/siRAD21 ChIP-Seq experiments]

Project description:During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M-phase. These results suggest that cohesin binding functions as a cellular memory that promotes re- stablishment of TF clusters after DNA replication and chromatin condensation. Examination of TF binding by ChIP-seq in a CRC cell-line treated with non-targeting siRNA, or siRNA specific to the cohesin subunit RAD21.

2013-09-28 | E-GEOD-51234 | biostudies-arrayexpress

Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChiP-seq) directly informs methylation status

Project description:Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation. Paired-end bisulphite sequencing of H3K27me3-ChIP DNA for LNCaP and PrEC cell lines

2012-01-18 | E-GEOD-30558 | biostudies-arrayexpress

Coordination of engineered factors with TET1/2 promotes early stage epigenetic modification during somatic cell reprogramming

Project description:Somatic cell reprogramming towards induced pluripotent stem cells (iPSCs) holds great promise in future regenerative medicine, however, the reprogramming process mediated by the traditional defined factors (OSNK) is slow and extremely inefficient. Here we show that a combination of modified reprogramming factors (OySyNyK), in which the transactivation domain of the Yes-associated protein is fused to OCT4, SOX2 and NANOG respectively, could be used to establish a highly efficient and rapid reprogramming system for iPSC generation. We show that the efficiency of OySyNyK-induced iPSCs was up to 100-fold higher than that of induction by traditional OSNK. Moreover we show that the reprogramming by OySyNyK is very rapid (initiated at 24 h versus 5 d by OSNK). Compared with OSNK, we found that OySyNyK factors significantly increased the expression of Tet1/2 at the early stage, which will interact with OSNK factors, and co-occupy pluripotency loci in the genome for somatic cell reprogramming. Our studies not only establish a rapid and highly efficient iPSC reprogramming system, but also uncover a novel mechanism by which OSNK factors coordinate with TET proteins to regulate 5hmC-mediated epigenetic control, thereby promoting somatic cell reprogramming. We examined DNA hydroxymethylation progression of reprogramming intermediates. To this end, we profiled the genome-wide 5hmC distribution in MEFs, the reprogramming intermediates at different stages induced by either the OSNK or OySyNyK methods, and iPSCs using the chemical capture approach

2013-08-08 | E-GEOD-46202 | biostudies-arrayexpress

G-Quadruplex structures are stable and detectable in human genomic DNA.

Project description:The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA. Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.

2013-05-08 | E-GEOD-45241 | biostudies-arrayexpress

Global expression analysis of BAP1 knockdown in transfected 92.1 cells

Project description:Analysis of the effect that reduced BAP1 levels have on global gene expression.The hypothesis tested was that reduction in BAP1 levels would produce changes in gene expression similar to changes observed in class 2 uveal melanomas. Data provided insight into genes that are disrupted with reduced BAP1 levels. Total RNA was isolated from 92.1 cells transfected with either control or BAP1 knockdown constructs for global expression analysis.

2011-01-06 | E-GEOD-24896 | biostudies-arrayexpress

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