ArticleScientific reports2018
Global dynamics of stage-specific transcription factor binding during thymocyte development.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 17 citations in OpenAlex.
- Transcriptional network dynamics in early T cell development.The Journal of experimental medicine · 2024Review
- RORγt up-regulates RAG gene expression in DP thymocytes to expand theScience immunology · 2024Article
- PTCL, NOS: An update on classification, risk-stratification, and treatment.Frontiers in oncology · 2023Review
- A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs.Evolutionary applications · 2022Article
- Transcriptional Regulation of Early T-Lymphocyte Development in Thymus.Frontiers in immunology · 2022Review
- Shifting gears: Id3 enables recruitment of E proteins to new targets during T cell development and differentiation.Frontiers in immunology · 2022Review
- AProceedings of the National Academy of Sciences of the United States of America · 2021Article
- How transcription factors drive choice of the T cell fate.Nature reviews. Immunology · 2021Review
- The transcription factor BCL-6 controls early development of innate-like T cells.Nature immunology · 2020Article
- ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation.Epigenetics & chromatin · 2020Article
- Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia.Genome research · 2020Article
- From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.Genome biology · 2020Review
- Applications of ENCODE data to Systematic Analyses via Data Integration.Current opinion in systems biology · 2018Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) to execute developmental expression changes. ChIP experiments are often used to identify where TFs bind to regulatory elements in the genome, but the requirement of TF-specific antibodies hampers analyses of tens of TFs at multiple loci. Here we tested whether TF binding predictions using ATAC-seq can be used to infer the identity of TFs that bind to functionally validated enhancers of the Cd4, Cd8, and Gata3 genes in thymocytes. We performed ATAC-seq at four distinct stages of development in mouse thymus, probing the chromatin accessibility landscape in double negative (DN), double positive (DP), CD4 single positive (SP4) and CD8 SP (SP8) thymocytes. Integration of chromatin accessibility with TF motifs genome-wide allowed us to infer stage-specific occupied TF binding sites within known and potentially novel regulatory elements. Our results provide genome-wide stage-specific T cell open chromatin profiles, and allow the identification of candidate TFs that drive thymocyte differentiation at each developmental stage.
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Registered trials
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.