ArticleNucleic acids research2009
Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- GATA1: A key biomarker for predicting the prognosis of patients with diffuse large B-cell lymphoma.Open medicine (Warsaw, Poland) · 2025Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- Targeting GATA1 and p2x7r Locus Binding in Spinal Astrocytes Suppresses Chronic Visceral Pain by Promoting DNA Demethylation.Neuroscience bulletin · 2022Article
- An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding.Genome biology · 2021Article
- Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility.Nature communications · 2018Article
- Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution.Molecular and cellular biology · 2016Article
- GATA1 Activity Governed by Configurations ofFrontiers in oncology · 2016Review
- Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility.Epigenetics & chromatin · 2015Article
- Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.Genome research · 2014Article
- Epigenetic and genetic mechanisms in red cell biology.Current opinion in hematology · 2014Review
- Evolution of hemoglobin and its genes.Cold Spring Harbor perspectives in medicine · 2012Article
- Article
- Genomic approaches towards finding cis-regulatory modules in animals.Nature reviews. Genetics · 2012Review
- Article
- Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.Genome research · 2011Article
- Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Role of helix-loop-helix proteins during differentiation of erythroid cells.Molecular and cellular biology · 2011Review
- A varying threshold method for ChIP peak-calling using multiple sources of information.Bioinformatics (Oxford, England) · 2010Article
- Genome-wide identification of TAL1's functional targets: insights into its mechanisms of action in primary erythroid cells.Genome research · 2010Article
- Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.Genome research · 2009Article
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Authors and funding
8 authors.
Funding
Abstract
DNA sequence motifs and epigenetic modifications contribute to specific binding by a transcription factor, but the extent to which each feature determines occupancy in vivo is poorly understood. We addressed this question in erythroid cells by identifying DNA segments occupied by GATA1 and measuring the level of trimethylation of histone H3 lysine 27 (H3K27me3) and monomethylation of H3 lysine 4 (H3K4me1) along a 66 Mb region of mouse chromosome 7. While 91% of the GATA1-occupied segments contain the consensus binding-site motif WGATAR, only approximately 0.7% of DNA segments with such a motif are occupied. Using a discriminative motif enumeration method, we identified additional motifs predictive of occupancy given the presence of WGATAR. The specific motif variant AGATAA and occurrence of multiple WGATAR motifs are both strong discriminators. Combining motifs to pair a WGATAR motif with a binding site motif for GATA1, EKLF or SP1 improves discriminative power. Epigenetic modifications are also strong determinants, with the factor-bound segments highly enriched for H3K4me1 and depleted of H3K27me3. Combining primary sequence and epigenetic determinants captures 52% of the GATA1-occupied DNA segments and substantially increases the specificity, to one out of seven segments with the required motif combination and epigenetic signals being bound.
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