ArticleEpigenetics & chromatin2013
Mapping genome-wide transcription factor binding sites in frozen tissues.
Article in Epigenetics & chromatin, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 35 citations in OpenAlex.
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- Transgenic mice for in vivo epigenome editing with CRISPR-based systems.Nature methods · 2021Article
- CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity.Nature cancer · 2021Article
- ETV4 Is Necessary for Estrogen Signaling and Growth in Endometrial Cancer Cells.Cancer research · 2020Article
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- Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver.American journal of human genetics · 2019Article
- Epigenetic targeting of bromodomain protein BRD4 counteracts cancer cachexia and prolongs survival.Nature communications · 2017Article
- A genome-wide interactome of DNA-associated proteins in the human liver.Genome research · 2017Article
- Vitamin D and VDR in cancer cachexia and muscle regeneration.Oncotarget · 2017Article
- Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome.Nature communications · 2017Article
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- Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.Seminars in cell & developmental biology · 2016Review
- Genome-wide epigenomic profiling for biomarker discovery.Clinical epigenetics · 2016Review
- Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites.Genome research · 2015Article
- CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins.Genome research · 2015Article
- NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells.Nature genetics · 2015Article
- Transcriptional (ChIP-Chip) Analysis of ELF1, ETS2, RUNX1 and STAT5 in Human Abdominal Aortic Aneurysm.International journal of molecular sciences · 2015Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide maps of transcription factor binding sites in primary tissues can expand our understanding of genome function, transcriptional regulation, and genetic alterations that contribute to disease risk. However, almost all genome-wide studies of transcription factors have been in cell lines, and performing these experiments in tissues has been technically challenging and limited in throughput.
resultsHere we outline a simple strategy for mapping transcription factor binding sites in frozen tissues that utilizes dry pulverization of samples and is scalable for high-throughput analyses. We show that the method leads to accurate and reproducible chromatin immunoprecipitation next-generation sequencing (ChIP-seq) data, and is highly sensitive, identifying high-quality transcription factor binding sites from chromatin corresponding to only 5 mg of liver tissue.
conclusionsThe enhanced reproducibility, robustness, and sensitivity of the dry pulverization method, in addition to the ease of implementation and scalability, makes ChIP-seq in primary tissues a widely accessible assay.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.