Methylation-sensitive SMiLE-seq sequencing data (illumina) of human transcription factors profiled in the Codebook/GRECO-BiT collaboration
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): synthetic construct
SUBMITTER: Antoni Gralak
PROVIDER: E-MTAB-14597 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We assayed 284 human transcription factors (TFs) for DNA binding using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). These experiments were part of the Codebook/GRECO-BiT collaboration aiming to identify the DNA binding sites of yet-uncharacterized TFs. All data has already been demultiplexed and associated with the corresponding TFs.
2024-11-11 | E-MTAB-14598 | biostudies-arrayexpress
Project description:A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide mRNA expression profiling to identify genes that are activated or repressed by the muscle HD TFs Slouch (Slou) and Muscle segment homeobox (Msh). Next, we used protein binding microarrays to define the sequences that are bound by Slou, Msh and other HD TFs having mesodermal expression. These studies revealed that a large class of HDs, including Slou and Msh, predominantly recognize TAAT core sequences but that each HD also binds to unique sites that deviate from this canonical motif. To better understand the regulatory specificity of an individual FC identity HD, we evaluated the functions of atypical binding sites that are preferentially bound by Slou relative to other HDs within muscle enhancers that are either activated or repressed by this TF. These studies showed that Slou regulates the activities of particular myoblast enhancers through Slou-preferred sequences, whereas swapping these sequences for sites that are capable of binding to multiple HD family members does not support the normal regulatory functions of Slou. Moreover, atypical Slou binding sites are overrepresented in putative enhancers associated with additional Slou-responsive FC genes. Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity. 10 Protein binding microarray (PBM) experiments of Drosophila transcription factors were performed. Briefly, the PBMs involved binding GST-tagged fly transcription factors to double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006 (PMID: 16998473). A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. Individual de Bruijn sequences have different properties, including representation of gapped patterns. The array probe sequences on the custom array design used in this study were reported previously in Berger et al., Cell 2008 (PMID: 18585359) and are available via an academic research use license. Here we provide the data transformed into median signal intensities (after normalization and detrending of the original array data) for all 32,896 8-base sequences, Z-scores for these intensities, and E-scores. E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots. 'Keep fraction' (kf) parameter setting of 0.9 was used to calculate E-scores. In general the E-scores are slightly more reproducible than Z-scores, but contain less information about relative binding affinity. Additional experimental details are found in Berger et al., Nature Biotechnology 2006 (PMID: 16998473), and the accompanying Supplementary information.
2012-01-28 | E-GEOD-35380 | biostudies-arrayexpress
Project description:Background: DNA methylation is a fundamental epigenetic modification which is involved in many biological systems such as differentiation and disease. We and other groups recently discovered that a part of transcription factors (TFs) plays a role for site-specificity determination of DNA demethylation in a binding site-directed manner, although number of reports for such TFs are limited. Results: Here, we develop a screening system to identify TFs which induce the binding site-directed DNA methylation changes. The system consists of ectopic expression of target TFs in model cells and the DNA methylome analysis followed by overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. Our system successfully identifies binding site-directed demethylation of SPI1 which is known to promote DNA demethylation in a binding-site directed manner. We extend our screening system to 15 master TFs which are involved in cellular differentiations, and identified 8 (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA and TBX5) novel binding site-directed DNA demethylation inducing TFs. Gene ontology and specifically expressing tissue enrichment analysis revealed that those 8 TFs demethylate genome regions which are associated with corresponding biological roles, supporting performance of our system. We also describe characteristics of the binding site-directed DNA demethylation induced by those TFs; targeting highly methylated CpGs, local DNA demethylation, and overlap of demethylated regions between same family TFs. Conclusion: Thus, our results emphasize usefulness of the developed screening system for identification of TFs which induce DNA demethylation in a site-directed manner.
2017-11-29 | GSE102822 | GEO
Project description:We have developed a high throughput, next-generation DNA sequencing assay for rapid transcription factor binding site (TFBS) discovery in a genomic context. DNA affinity purification sequencing (DAP-seq), which uses affinity-purified transcription factors (TFs) to capture genomic DNA fragments, was applied to all 1,725 Arabidopsis thaliana TFs. High confidence TFBS motifs for 529 TFs and genome-wide enrichment maps for 349 factors were identified. In total,~ 2.7 million TFBS were identified which predict thousands of TF target genes enriched for known and novel functions.. Comparison of TF-binding using cytosine-methylated and -unmethylated genomic DNA revealed a 2-50 fold inhibition at methylated motifs for ~82% (264) of factors tested while 4.6% (15) showed stronger binding to methylated motifs. Finally, we describe how binding of Arabidopsis and maize Auxin Response Factors (ARFs) at phased motif repeats is highly enriched at ARF target gene promoters and how this architecture may allow for stabilization of dimers/multimers.
2016-05-25 | GSE60141 | GEO
Project description:Access of mammalian transcription factors (TFs) to regulatory regions, an essential event for transcription regulation, is hindered by chromatin compaction involving nucleosome wrapping, repressive histone modifications and DNA methylation. Moreover, methylation of TF binding sites (TBSs) affects TF binding affinity to these sites. Remarkably, a special class of TFs called pioneer transcription factors (PFs) can access nucleosomal DNA, leading to nucleosome remodelling and chromatin opening. However, whether PFs can bind to methylated sites and induce DNA demethylation is largely unknown. Here, we set up a highly parallelized approach to investigate PF ability to bind methylated DNA and induce demethylation. Our results indicate that the interdependence between DNA methylation and TF binding is more complex than previously thought, even within a select group of TFs that have a strong pioneering activity; while most PFs do not induce changes in DNA methylation at their binding sites, we identified PFs that can protect DNA from methylation and PFs that can induce DNA demethylation at methylated binding sites. We called the latter “super pioneer transcription factors” (SPFs), as they are seemingly able to overcome several types of repressive epigenetic marks. Importantly, while most SPFs induce TET-dependent active DNA demethylation, SOX2 binding leads to passive demethylation by inhibition of the maintenance methyltransferase DNMT1 during replication. This important finding suggests a novel mechanism allowing TFs to interfere with the epigenetic memory during DNA replication.
2021-03-18 | GSE144524 | GEO
Project description:To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. mRNA-seq of primary female mouse dermal fibroblasts with and without thapsigargin identified differentially expressed genes. Genes that are commonly bound by CEBPB and ATF4 to TGAT|GCAA (the best-bound 8-mer in the array) at the promoters were highly expressed and up-regulated or remained unchanged in the thapsigargin treated primary female mouse dermal fibroblasts. RNA-Seq: Examination of whole genome transcriptome profiles (RNA-seq) of primary mouse dermal fibroblasts with and without Thapsigargin treatment ChIP-Seq: Examination of transcription factor binding in dermal fibroblasts with and without Thapsigargin teratment BS-Seq: Determination of whole genome DNA methylation profiles (BS-seq) of primary mouse dermal fibroblasts
2013-03-08 | E-GEOD-44942 | biostudies-arrayexpress
Project description:To identify transcription factor (TF) genes exhibiting preferential expression during SE, expression profiles of 1,880 TFs were compared in two genotypes with largely different capacities for SE induction in IZE culture on auxin medium, namely the highly embryonic Col-0 accession and the tanmei mutant unable to form somatic embryos. Our study revealed 729 TFs whose expression changes during the 10-day incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. This study provides comprehensive data focused on the expression of TF genes during SE and provides guidelines for further research on functional genomics of SE. The experiment was designed to monitor the expression of 1,880 TF genes at three distinctive stages of IZE-derived embryogenic culture, which refer to: (i) freshly isolated explants competent to undergo embryogenic transition (0 d), (ii) explant tissue subjected to SE induction (5 d), and (iii) the advanced phase of embryogenesis related to somatic embryo formation (10 d).
2013-07-31 | E-GEOD-45697 | biostudies-arrayexpress
Project description:DNA methylation (mC) on CpG sites is the most common epigenetic modification. Recently methylation on non-CpG context was found to widely occur on genomic DNA. However, how non-CpG methylation influences DNA/protein interaction and regulates transcription is unknown. Using single-molecule assays, we studied the interactions of transcription factors (TFs) GR, ER and BMAL1-CLOCK with methylated or unmethylated cognate DNA binding sequences. The results demonstrated that these TFs interact with methylated DNA discriminatively. We then performed BisChIP-seq with GR and BMAL1-CLOCK in HEK-293T cells and showed that they can recognize and bind to the methylated sites within chromatin. The effects of non-CpG methylation on transcriptional regulation were validated by in vitro transcription assays with correlated RNA level, and further studied mechanistically by crystallographic analyses and molecular dynamics simulations. We conclude that the non-CpG methylation of DNA provides another general mechanism for regulating gene expression through affecting TFs binding affinity.
2016-06-22 | GSE64171 | GEO
Project description:Multiple gene expression studies have demonstrated that breast cancer biological diversity is associated with distinct transcriptional programs. Transcription factors, because of their unique ability to coordinate the expression of multiple genes, are speculated to play a role in generating phenotypic plasticity associated with cancer progression including acquired drug resistance. Combinatorial libraries of artificial zinc-finger transcription factors (ZF-TFs) provide a robust means for inducing and understanding various functional components of the cancer phenotype. Herein, we utilized combinatorial ZF-TF library technology to better understand how breast cancer cells acquire resistance to a fulvestrant, a clinically important anti-endocrine therapeutic agent. We isolated six ZF-TF library members capable of inducing stable, long-term anti-endocrine drug-resistance in two independent estrogen receptor positive breast cancer cell lines. Comparative gene expression profile analysis of the ZF-TF-transduced breast cancer cell lines revealed a 72-gene cluster that constituted a common signature for the fulvestrant-resistance phenotype. Pathway enrichment-analysis of gene expression data revealed that the ZF-TF-induced fulvestrant resistance is associated with an estrogen receptor negative-like gene set and four unique myb-regulated gene sets. Furthermore, we identified a set of genes strongly expressed in the ZF-TF-induced fulvestrant-resistant cells that was correlated with a lower probability of distant metastasis-free or death-from-relapse-free survival of breast cancer patients. MCF7-R73 cells, a monoclonal MCF7 subline that is highly sensitive to fulvestrant-induced cytocidal activity, underwent retroviral transduction with the zinc finger transcription factor (ZF-TF) activator library or with a control plasmid encoding only the NF-kB p65 activation domain. Both populations of cells were enriched for transduced cells by selecting for growth in puromycin and for fulvestrant-resistant cells by selecting with 100 nM fulvestrant. After 6 weeks of continuous treatment with fulvestrant, hundreds of drug-resistant colonies emerged from the population of cells infected with the ZF-TF activator library. By contrast, as expected, the control MCF7cell line transduced by NF-kB p65-only underwent massive cell death resulting in the complete absence of resistant colonies. DNA encoding the zinc-finger arrays was rescued by PCR from genomic DNA of pooled fulvestrant-resistant cells. The sequences of the ZF-TFs were determined and 46 unique ZF-TF clones identified. These 46 unique ZF-TFs were re-cloned into the retroviral vector and converted into clonal virus stocks that were used to transduce MCF7-R73 cells. These 46 retrovirally transduced cell populations were then challenged with fulvestrant. As compared with the control MCF-238 cells, MCF7-R73 cells transduced with six unique ZF-TFs demonstrated survival and growth in the presence of 100nM fulvestrant.
2011-07-17 | E-GEOD-27444 | biostudies-arrayexpress
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.
2013-09-25 | E-GEOD-51142 | biostudies-arrayexpress