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Towards the human cellular microRNAome

Matthew N. McCall, Min-Sik Kim, Mohammed Adil, Arun H. Patil, Yin Lu, Christopher J. Mitchell, Pamela Leal-Rojas, Jinchong Xu, Manoj Kumar, Valina L. Dawson, Ted M. Dawson, Alexander S. Baras, Avi Z. Rosenberg, Dan E. Arking, Kathleen H. Burns, Akhilesh Pandey, Marc K. Halushka
doi: https://doi.org/10.1101/120394
Matthew N. McCall
1Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
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Min-Sik Kim
2Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, South Korea 3
3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Mohammed Adil
4Department School of Life Sciences, B.S. Abdur Rahman University, Chennai, 600048, India
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Arun H. Patil
3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
5School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
6Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
7YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.
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Yin Lu
8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD, USA
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Christopher J. Mitchell
9Ginkgo Bioworks, Boston, MA, USA
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Pamela Leal-Rojas
10Center of Excellence in Translational Medicine (CEMT) & Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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Jinchong Xu
11Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
12Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Manoj Kumar
11Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
12Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Valina L. Dawson
11Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
12Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
13Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine
14Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD.
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Ted M. Dawson
11Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
12Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
13Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine
15Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine
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Alexander S. Baras
8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD, USA
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Avi Z. Rosenberg
8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD, USA
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Dan E. Arking
3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Kathleen H. Burns
3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD, USA
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Akhilesh Pandey
3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Marc K. Halushka
8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD, USA
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Abstract

microRNAs are short RNAs that serve as master 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 has caused considerable confusion and comprehensive cell-level data does 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 super-enhancer activity. Analysis of unaligned RNA reads uncovered 207 unknown minor strand (passenger) microRNAs of known microRNA loci and 2,632 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 Dicer-dependent microRNA processing variability. Cell-specific patterns of microRNA expression were used to deconvolute variable cellular composition of adipose tissue samples highlighting one use of this 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 24, 2017.
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Towards the human cellular microRNAome
Matthew N. McCall, Min-Sik Kim, Mohammed Adil, Arun H. Patil, Yin Lu, Christopher J. Mitchell, Pamela Leal-Rojas, Jinchong Xu, Manoj Kumar, Valina L. Dawson, Ted M. Dawson, Alexander S. Baras, Avi Z. Rosenberg, Dan E. Arking, Kathleen H. Burns, Akhilesh Pandey, Marc K. Halushka
bioRxiv 120394; doi: https://doi.org/10.1101/120394
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Towards the human cellular microRNAome
Matthew N. McCall, Min-Sik Kim, Mohammed Adil, Arun H. Patil, Yin Lu, Christopher J. Mitchell, Pamela Leal-Rojas, Jinchong Xu, Manoj Kumar, Valina L. Dawson, Ted M. Dawson, Alexander S. Baras, Avi Z. Rosenberg, Dan E. Arking, Kathleen H. Burns, Akhilesh Pandey, Marc K. Halushka
bioRxiv 120394; doi: https://doi.org/10.1101/120394

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