ArticleGenome research2016
A synergistic DNA logic predicts genome-wide chromatin accessibility.
Article in Genome research, 2016. 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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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
13 citing papers in PubMed, 21 citations in OpenAlex.
- DMRU: generative deep learning to unravel condition-specific cytosine methylation in plants.Briefings in bioinformatics · 2025Article
- Quantifying the tissue-specific regulatory information within enhancer DNA sequences.NAR genomics and bioinformatics · 2021Article
- Computing Leapfrog Regularization Paths with Applications to Large-Scale K-mer Logistic Regression.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay.Genome research · 2020Article
- A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding.Cell systems · 2020Article
- Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species.American journal of human genetics · 2019Article
- coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.PLoS computational biology · 2018Article
- Sequential regulatory activity prediction across chromosomes with convolutional neural networks.Genome research · 2018Article
- Impact of regulatory variation across human iPSCs and differentiated cells.Genome research · 2018Article
- Functional interrogation of non-coding DNA through CRISPR genome editing.Methods (San Diego, Calif.) · 2017Review
- Inference of cell type specific regulatory networks on mammalian lineages.Current opinion in systems biology · 2017Article
- Non-coding genetic variation in cancer.Current opinion in systems biology · 2017Article
- A CRISPR view of gene regulation.Current opinion in systems biology · 2017Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that log-additive cis-acting DNA sequence features can predict chromatin accessibility at high spatial resolution. We develop a new type of high-dimensional machine learning model, the Synergistic Chromatin Model (SCM), which when trained with DNase-seq data for a cell type is capable of predicting expected read counts of genome-wide chromatin accessibility at every base from DNA sequence alone, with the highest accuracy at hypersensitive sites shared across cell types. We confirm that a SCM accurately predicts chromatin accessibility for thousands of synthetic DNA sequences using a novel CRISPR-based method of highly efficient site-specific DNA library integration. SCMs are directly interpretable and reveal that a logic based on local, nonspecific synergistic effects, largely among pioneer TFs, is sufficient to predict a large fraction of cellular chromatin accessibility in a wide variety of cell types.
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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.