ArticleGenome research2007
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed.
- An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder.Molecular psychiatry · 2019Article
- Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2019Article
- OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs.Nature communications · 2017Article
- The complexity of TRIM28 contribution to cancer.Journal of biomedical science · 2017Review
- Dysregulated IER3 Expression is Associated with Enhanced Apoptosis in Titin-Based Dilated Cardiomyopathy.International journal of molecular sciences · 2017Article
- TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability.Scientific reports · 2015Article
- FOXM1 binds directly to non-consensus sequences in the human genome.Genome biology · 2015Article
- KAPtain in charge of multiple missions: Emerging roles of KAP1.World journal of biological chemistry · 2014Review
- Predicting expression: the complementary power of histone modification and transcription factor binding data.Epigenetics & chromatin · 2014Article
- Comparative SRY incorporation on the regulatory regions of pluripotency/differentiation genes in human embryonic carcinoma cells after retinoic acid induction.Molecular and cellular biochemistry · 2013Article
- Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.Genome biology · 2012Article
- Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction.Scientifica · 2012Review
- Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments.Methods in molecular biology (Clifton, N.J.) · 2012Article
- KAP1 protein: an enigmatic master regulator of the genome.The Journal of biological chemistry · 2011Review
- Functional analysis of KAP1 genomic recruitment.Molecular and cellular biology · 2011Article
- Dual roles of Oct4 in the maintenance of mouse P19 embryonal carcinoma cells: as negative regulator of Wnt/β-catenin signaling and competence provider for Brachyury induction.Stem cells and development · 2011Article
- Transcription factor effector domains.Sub-cellular biochemistry · 2011Article
- Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data.BMC systems biology · 2010Article
- Article
- Review of the Y chromosome, Sry and hypertension.Steroids · 2010Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
ChIP-chip studies have revealed that many in vivo binding sites have a weak match to the consensus sequence for the transcription factor being analyzed. Possible explanations for these observations include (1) the in vitro-derived consensus site does not represent the in vivo binding site and/or (2) the factor is recruited to a weak binding site via interaction with another protein. To address these possibilities, we developed an approach (ChIPMotifs) that incorporates a bootstrap resampling method to statistically infer the optimal cutoff threshold for a position weight matrix (PWM) of a motif identified from ChIP-chip data by ab initio motif discovery programs. Using OCT4 ChIP-chip data and the ChIPMotifs approach, we first developed a refined OCT4 PWM. We then used the refined PWM and a ChIPModules approach to identify transcription factors colocalizing with OCT4 in Ntera2 testicular embryonal carcinoma cells. We found that the consensus binding site for SRY, a transcription factor critical for testis development, colocalizes with the OCT4 PWM. To further characterize the relationship between OCT4 and SRY, we performed ChIP-chip experiments with human promoter microarrays, and found that 49% of the top approximately 1000 OCT4 target promoters were also bound by SRY. This analysis represents the first identification of SRY target promoters. Interestingly, we determined that promoters bound by OCT4 and SRY, but not those bound by SRY alone, were also bound by the transcriptional repressor KAP1. Our studies not only validate the ChIPMotifs and ChIPModules combinatorial approach but also identify a possible new regulatory partner of OCT4.
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Registered trials
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