ArticleNucleic acids research2019
Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- CUT&RUN as a Powerful Tool for Chromatin Profiling: A Focus on Neuropsychiatric Disorders.Biological psychiatry · 2026Review
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- The evolution and mutational robustness of chromatin accessibility in Drosophila.Genome biology · 2023Article
- DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence.Nucleic acids research · 2023Article
- Complex Analysis of Single-Cell RNA Sequencing Data.Biochemistry. Biokhimiia · 2023Review
- Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation.Nature communications · 2022Article
- Bibliometric review of ATAC-Seq and its application in gene expression.Briefings in bioinformatics · 2022Review
- Review
- Review
- BABEL enables cross-modality translation between multiomic profiles at single-cell resolution.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Profiling Chromatin Accessibility at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2021Review
- A systematic evaluation of single-cell RNA-sequencing imputation methods.Genome biology · 2020Article
- The intersectional genetics landscape for humans.GigaScience · 2020Article
- IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.Nucleic acids research · 2020Article
- Exploring Additional Valuable Information From Single-Cell RNA-Seq Data.Frontiers in cell and developmental biology · 2020Review
- Genome-wide prediction of DNase I hypersensitivity using gene expression.Nature communications · 2017Article
- Genome-wide Prediction of Chromatin Accessibility Based on Gene Expression.Wiley interdisciplinary reviews. Computational statisticsArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Conventional high-throughput genomic technologies for mapping regulatory element activities in bulk samples such as ChIP-seq, DNase-seq and FAIRE-seq cannot analyze samples with small numbers of cells. The recently developed low-input and single-cell regulome mapping technologies such as ATAC-seq and single-cell ATAC-seq (scATAC-seq) allow analyses of small-cell-number and single-cell samples, but their signals remain highly discrete or noisy. Compared to these regulome mapping technologies, transcriptome profiling by RNA-seq is more widely used. Transcriptome data in single-cell and small-cell-number samples are more continuous and often less noisy. Here, we show that one can globally predict chromatin accessibility and infer regulatory element activities using RNA-seq. Genome-wide chromatin accessibility predicted by RNA-seq from 30 cells can offer better accuracy than ATAC-seq from 500 cells. Predictions based on single-cell RNA-seq (scRNA-seq) can more accurately reconstruct bulk chromatin accessibility than using scATAC-seq. Integrating ATAC-seq with predictions from RNA-seq increases the power and value of both methods. Thus, transcriptome-based prediction provides a new tool for decoding gene regulatory circuitry in samples with limited cell numbers.
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Registered trials
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