PT  - JOURNAL ARTICLE
AU  - Weiqiang Zhou
AU  - Zhicheng Ji
AU  - Hongkai Ji
TI  - Global Prediction of Chromatin Accessibility Using RNA-seq from Small Number of Cells
AID  - 10.1101/035816
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 035816
4099  - http://biorxiv.org/content/early/2016/01/01/035816.short
4100  - http://biorxiv.org/content/early/2016/01/01/035816.full
AB  - Conventional high-throughput technologies for mapping regulatory element activities such as ChIP-seq, DNase-seq and FAIRE-seq cannot analyze samples with small number of cells. The recently developed ATAC-seq allows regulome mapping in small-cell-number samples, but its signal in single cell or samples with ≤500 cells remains discrete or noisy. Compared to these technologies, measuring transcriptome by RNA-seq in single-cell and small-cell-number samples is more mature. Here we show that one can globally predict chromatin accessibility and infer regulome using RNA-seq. Genome-wide chromatin accessibility predicted by RNA-seq from 30 cells is comparable with ATAC-seq from 500 cells. Predictions based on single-cell RNA-seq can more accurately reconstruct bulk chromatin accessibility than using single-cell ATAC-seq by pooling the same number of cells. Integrating ATAC-seq with predictions from RNA-seq increases power of both methods. Thus, transcriptome-based prediction can provide a new tool for decoding gene regulatory programs in small-cell-number samples.