Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq

Weiqiang Zhou, Zhicheng Ji, Weixiang Fang, Hongkai Ji

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Conventional high-throughput genomic technologies formapping regulatory element activities in bulk samples such as ChIP-seq, DNase-seq and FAIREseq cannot analyze samples with small numbers of cells. The recently developed low-input and singlecell regulome mapping technologies such as ATACseq 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 smallcell- 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.

Original languageEnglish (US)
Pages (from-to)E121
JournalNucleic acids research
Issue number19
StatePublished - Nov 4 2019

ASJC Scopus subject areas

  • Genetics


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