ArticleBMC genomics2019
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 15 citations in OpenAlex.
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- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer.Nature communications · 2023Article
- Novel CSF biomarkers for diagnosis and integrated analysis of neuropsychiatric systemic lupus erythematosus: based on antibody profiling.Arthritis research & therapy · 2023Article
- Transcription factors organize into functional groups on the linear genome and in 3D chromatin.Heliyon · 2023Article
- Glandular trichome specificity of menthol biosynthesis pathway gene promoters from Mentha × piperita.Planta · 2022Article
- Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin.iScience · 2021Article
- Predict long-range enhancer regulation based on protein-protein interactions between transcription factors.Nucleic acids research · 2021Article
- Analysis of the genes controlling three quantitative traits in three diverse plant species reveals the molecular basis of quantitative traits.Scientific reports · 2020Article
- Computer genomics research at the bioinformatics conference series in Novosibirsk.BMC genomics · 2019Article
- Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk.BMC genomics · 2019Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and promoters in linear DNA (1D). Enhancers and promoters are fundamental non-coding elements enriched with transcription factors (TFs) to form chromatin loops. However, the specific cooperation of TFs involved in forming chromatin loops is not fully understood.
resultsHere, we proposed a method for investigating the cooperation of TFs in four cell lines by the integrative analysis of DNA sequences, ChIP-Seq and ChIA-PET data. Results demonstrate that the interaction of enhancers and promoters is a hierarchical and dynamic complex process with cooperative interactions of different TFs synergistically regulating gene expression and chromatin structure. The TF cooperation involved in maintaining and regulating the chromatin loop of cells can be regulated by epigenetic factors, such as other TFs and DNA methylation.
conclusionsSuch cooperation among TFs provides the potential features that can affect chromatin's 3D architecture in cells. The regulation of chromatin 3D organization and gene expression is a complex process associated with the hierarchical and dynamic prosperities of TFs.
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