@article{2c0af182a09e4c0580e9fe7a48a31998,
title = "Toward the human cellular microRNAome",
abstract = "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.",
author = "McCall, {Matthew N.} and Kim, {Min Sik} and Mohammed Adil and Patil, {Arun H.} and Yin Lu and Mitchell, {Christopher J.} and Pamela Leal-Rojas and Jinchong Xu and Manoj Kumar and Dawson, {Valina L.} and Dawson, {Ted M.} and Baras, {Alexander S.} and Rosenberg, {Avi Z.} and Arking, {Dan E.} and Burns, {Kathleen H.} and Akhilesh Pandey and Halushka, {Marc K.}",
note = "Funding Information: The authors thank C. Porter and L. Blosser for their work in isolating colonic epithelium; Gourav Dey for illustrations; Srikanth Manda for cell culture and bioinformatics; both Josh Hertel and Tai C. Huang for RNA isolation; Bastian Fromm, Dongwon Lee, and Ashish Kapoor for helpful conversations; and Adriana Heguy and the NYUMC Genome Technology Center. M.K.H. was supported by the American Heart Association [13GRNT16420015]. The NYUMC Genome Technology Center is partially supported by the National Institutes of Health (NIH) Cancer Center Support Grant, P30CA016087, at the Laura and Isaac Perlmutter Cancer Center. A.P. was supported by NCI{\textquoteright}s Clinical Proteomic Tumor Analysis Consortium initiative (NIH Grants U24CA160036 and U24CA210985). P.L-R. was supported by the National Fund for Scientific and Technological Development, FONDECYT 1151008, Government of Chile. M.N.M. was supported by NIH Grants R00HG006853, R01GM083084, and UL1TR002001. This work was supported by grants from MSCRFII-0429 and MSCRFII-0125 to V.L.D., 2013-MSCRF-0054 to J.X., 2014-MSCRF-0665 to M.K., and NIH/NINDS NS67525, NS37388 to T.M.D. and V.L.D. T.M.D. is the Leonard and Madlyn Abramson Professor in Neurodegenerative Diseases. Publisher Copyright: {\textcopyright} 2017 McCall et al.",
year = "2017",
month = oct,
doi = "10.1101/gr.222067.117",
language = "English (US)",
volume = "27",
pages = "1769--1781",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "10",
}