ArticlePLoS computational biology2019
Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
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- Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation.Communications biology · 2024Article
- Prediction and analysis of cis-regulatory elements in Dorsal and Ventral patterning genes of Tribolium castaneum and its comparison with Drosophila melanogaster.Molecular and cellular biochemistry · 2024Article
- A Novel Repetition Frequency-Based DNA Encoding Scheme to Predict Human and Mouse DNA Enhancers with Deep Learning.Biomimetics (Basel, Switzerland) · 2023Article
- Computational approaches to understand transcription regulation in development.Biochemical Society transactions · 2023Review
- A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.Nature communications · 2023Article
- Using epigenomics to understand cellular responses to environmental influences in diseases.PLoS genetics · 2023Review
- ZNF146/OZF and ZNF507 target LINE-1 sequences.G3 (Bethesda, Md.) · 2022Article
- Interactions between lineage-associated transcription factors govern haematopoietic progenitor states.The EMBO journal · 2020Article
- Data integration for inferring context-specific gene regulatory networks.Current opinion in systems biology · 2020Article
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 1 country.
Funding
Abstract
Gene expression governs cell fate, and is regulated via a complex interplay of transcription factors and molecules that change chromatin structure. Advances in sequencing-based assays have enabled investigation of these processes genome-wide, leading to large datasets that combine information on the dynamics of gene expression, transcription factor binding and chromatin structure as cells differentiate. While numerous studies focus on the effects of these features on broader gene regulation, less work has been done on the mechanisms of gene-specific transcriptional control. In this study, we have focussed on the latter by integrating gene expression data for the in vitro differentiation of murine ES cells to macrophages and cardiomyocytes, with dynamic data on chromatin structure, epigenetics and transcription factor binding. Combining a novel strategy to identify communities of related control elements with a penalized regression approach, we developed individual models to identify the potential control elements predictive of the expression of each gene. Our models were compared to an existing method and evaluated using the existing literature and new experimental data from embryonic stem cell differentiation reporter assays. Our method is able to identify transcriptional control elements in a gene specific manner that reflect known regulatory relationships and to generate useful hypotheses for further testing.
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Registered trials
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