RT Journal
A1 McCall, Matthew N.
A1 Kim, Min-Sik
A1 Adil, Mohammed
A1 Patil, Arun H.
A1 Lu, Yin
A1 Mitchell, Christopher J.
A1 Leal-Rojas, Pamela
A1 Xu, Jinchong
A1 Kumar, Manoj
A1 Dawson, Valina L.
A1 Dawson, Ted M.
A1 Baras, Alexander S.
A1 Rosenberg, Avi Z.
A1 Arking, Dan E.
A1 Burns, Kathleen H.
A1 Pandey, Akhilesh
A1 Halushka, Marc K.
T1 Toward the human cellular microRNAome
JF Genome Research 
JO Genome Research 
YR 2017 
FD October 01 
VO 27 
IS 10 
SP 1769 
OP 1781 
DO 10.1101/gr.222067.117 
UL http://genome.cshlp.org/content/27/10/1769.abstract 
AB MicroRNAs are short RNAs that serve as regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell-autonomously, and thus their localization to specific cell types is needed to guide our understanding of microRNA activity. Current tissue-level data have caused considerable confusion, and comprehensive cell-level data do not yet exist. Here, we establish the landscape of human cell-specific microRNA expression. This project evaluated 8 billion small RNA-seq reads from 46 primary cell types, 42 cancer or immortalized cell lines, and 26 tissues. It identified both specific and ubiquitous patterns of expression that strongly correlate with adjacent superenhancer activity. Analysis of unaligned RNA reads uncovered 207 unknown minor strand (passenger) microRNAs of known microRNA loci and 495 novel putative microRNA loci. Although cancer cell lines generally recapitulated the expression patterns of matched primary cells, their isomiR sequence families exhibited increased disorder, suggesting DROSHA- and DICER1-dependent microRNA processing variability. Cell-specific patterns of microRNA expression were used to de-convolute variable cellular composition of colon and adipose tissue samples, highlighting one use of these cell-specific microRNA expression data. Characterization of cellular microRNA expression across a wide variety of cell types provides a new understanding of this critical regulatory RNA species.