miRNA Biogenesis

238 Pages·2018·8.87 MB·English

by  Ulf Andersson Vang Ørom

Methods in
Molecular Biology 1823
Ulf Andersson Vang Ørom Editor
miRNA
Biogenesis
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:
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miRNA Biogenesis
Methods and Protocols
Edited by
Ulf Andersson Vang Ørom
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
Editor
Ulf Andersson Vang Ørom
Department of Molecular Biology and Genetics
Aarhus University
Aarhus, Denmark
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-8623-1 ISBN 978-1-4939-8624-8 (eBook)
https://doi.org/10.1007/978-1-4939-8624-8
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Preface
miRNAs are well-studied regulatory small RNAs affecting the translation and stability of
numerous mRNAs. miRNAs are emerging through a complex biogenesis pathway going
from primary transcripts that can be as long as 30 kb to mature miRNA of approximately
21 nts. miRNA biogenesis is a sophisticated series of events assuring a finely tuned regula-
tion of miRNA expression and activity. Understanding miRNA biogenesis better could
expand our knowledge of molecular events, contribute to extended molecular networks in
gene regulation, and lead to development of new therapeutic interventions.
It is my hope that this protocol series will contribute to the further development of knowl-
edge and application of miRNA biogenesis, both in the basic research lab and in the clinic.
Aarhus, Denmark Ulf Andersson Vang Ørom
v
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 High-Throughput Characterization of Primary microRNA Transcripts . . . . . . . . 1
Tsung-Cheng Chang and Joshua T. Mendell
2 Identifying Pri-miRNA Transcription Start Sites . . . . . . . . . . . . . . . . . . . . . . . . . 11
Georgios Georgakilas, Nikos Perdikopanis, and Artemis G. Hatzigeorgiou
3 Metabolic Pulse-Chase RNA Labeling for pri-miRNA Processing Dynamics . . . . 33
Annita Louloupi and Ulf Andersson Vang Ørom
4 In Vitro System for Coupling RNAP II Transcription to Primary
microRNA Processing and a Three-Way System for RNAP II
Transcription/Splicing/microRNA Processing . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Shanye Yin, Alexander Iocolano, Yong Yu, Jaya Gangopadhyay,
and Robin Reed
5 Purification of Microprocessor-Associated Factors . . . . . . . . . . . . . . . . . . . . . . . 51
Ross A. Cordiner and Sara Macias
6 Inhibiting Pri-miRNA Processing with Target Site Blockers . . . . . . . . . . . . . . . . 63
Annita Louloupi and Ulf Andersson Vang Ørom
7 MicroRNA Analysis Using the Quantitative Real-Time PCR Reaction . . . . . . . . 69
Marta Kotlarek, Anna Kubiak, Krystian Jażdżewski, and Anna Wójcicka
8 MicroRNA Analysis Using Next-Generation Sequencing . . . . . . . . . . . . . . . . . . 87
Monika Kolanowska, Anna Kubiak, Krystian Jażdżewski, and Anna Wójcicka
9 Identification of microRNA Precursor-Associated Proteins . . . . . . . . . . . . . . . . . 103
Thomas Treiber, Nora Treiber, and Gunter Meister
10 Analysis of 3′ End Modifications in microRNAs by High-T hroughput
Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Madalena M. Reimão-Pinto, Angela M. Rodrigues-Viana,
and Stefan L. Ameres
11 Uncovering the Stability of Mature miRNAs by 4-Thio-U ridine
Metabolic Labeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Matteo J. Marzi and Francesco Nicassio
12 Detection of microRNA-Target Interactions by Chimera PCR (ChimP) . . . . . . . 153
James P. Broughton and Amy E. Pasquinelli
13 High-Quality Overlapping Paired-End Reads for the Detection
of A-to-I Editing on Small RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Josephine Galipon, Rintaro Ishii, Soh Ishiguro, Yutaka Suzuki,
Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita,
and Kumiko Ui-Tei
vii
viii Contents
14 Targeting miRNA for Therapeutics Using a Micronome Based
Method for Identification of miRNA- mRNA Pairs and Validation
of Key Regulator miRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Parveen Bansal, Ashish Kumar, Sudhir Chandna, Malika Arora,
and Renu Bansal
15 Method for Detection of miRNAs in Non-Model Organisms
with Unreported Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Parveen Bansal, Ashish Kumar, Sudhir Chandna, Malika Arora,
and Renu Bansal
16 Detection and Verification of Mammalian Mirtrons by Northern Blotting . . . . . 209
Mohammad Farid Zia and Alex S. Flynt
17 Detecting Agotrons in Ago CLIPseq Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Thomas B. Hansen
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Contributors
Stefan L. amereS • IMBA—Institute of Molecular Biotechnology, Vienna Biocenter,
Vienna, Austria
maLika arora • Multidisciplinary Research Unit, Indian Council of Medical Research,
GGSMCH, Faridkot, Punjab, India
Parveen BanSaL • University Centre of Excellence in Research, Baba Farid University of
Health Sciences, Faridkot, Punjab, India
renu BanSaL • Department of Microbiology, GGSMCH, Faridkot, Punjab, India
JameS P. Broughton • Department of Dermatology, Stanford University School of
Medicine, Stanford, CA, USA
Sudhir Chandna • Division of Natural Radiation Response Mechanisms, Institute of
Nuclear Medicine and Allied Sciences, Timarpur, Delhi, India
tSung-Cheng Chang • Department of Molecular Biology, University of Texas
Southwestern Medical Center, Dallas, TX, USA
roSS a. Cordiner • Centre for mRNP Biogenesis and Metabolism, Department of
Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
aLex S. fLynt • Department of Biological Sciences, University of Southern Mississippi,
Hattiesburg, MS, USA
JoSePhine gaLiPon • Institute for Advanced Biosciences, Keio University, Tsuruoka,
Yamagata, Japan; Systems Biology Program, Graduate School of Media and Governance,
Keio University, Fujisawa, Kanagawa, Japan; Department of Biological Sciences,
Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
Jaya gangoPadhyay • Department of Cell Biology, Harvard Medical School, Boston, MA,
USA
georgioS georgakiLaS • Department of Genetics, University of Pennsylvania,
Philadelphia, PA, USA; Institute for Immunology, University of Pennsylvania,
Philadelphia, PA, USA; Epigenetics Institute at Perelman School of Medicine, University
of Pennsylvania, Philadelphia, PA, USA
thomaS B. hanSen • Department of Molecular Biology and Genetics (MBG) and
Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
artemiS g. hatzigeorgiou • DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece;
Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece
aLexander ioCoLano • Department of Cell Biology, Harvard Medical School, Boston,
MA, USA
Soh iShiguro • Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata,
Japan; Systems Biology Program, Graduate School of Media and Governance, Keio
University, Fujisawa, Kanagawa, Japan; Department of Biological Sciences, Graduate
School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
rintaro iShii • Department of Computational Biology, Graduate School of Frontier
Sciences, The University of Tokyo, Kashiwa-shi, Chiba-ken, Japan
ix
x Contributors
kryStian JażdżewSki • Warsaw Genomics INC, Warsaw, Poland; Genomic Medicine,
Medical University of Warsaw, Warsaw, Poland; Centre of New Technologies,
University of Warsaw, Warsaw, Poland
monika koLanowSka • Warsaw Genomics INC, Warsaw, Poland; Genomic Medicine,
Medical University of Warsaw, Warsaw, Poland; Centre of New Technologies,
University of Warsaw, Warsaw, Poland
ShinJi kondo • Inter-University Research Institute Corporation, Research Organization
of Information and Systems, Tachikawa, Tokyo, Japan
marta kotLarek • Warsaw Genomics INC, Warsaw, Poland; Genomic Medicine,
Medical University of Warsaw, Warsaw, Poland
anna kuBiak • Warsaw Genomics INC, Warsaw, Poland; Genomic Medicine,
Medical University of Warsaw, Warsaw, Poland; Centre of New Technologies,
University of Warsaw, Warsaw, Poland
aShiSh kumar • Texas Biomedical Research Institute, San Antonio, TX, USA
annita LouLouPi • Max Planck Institute for Molecular Genetics, Berlin, Germany;
Free University of Berlin, Berlin, Germany
Sara maCiaS • Institute of Immunology and Infection Research, School of Biological
Sciences, University of Edinburgh, Edinburgh, UK
matteo J. marzi • Center for Genomic Science of IIT@SEMM, Istituto Italiano di
Tecnologia (IIT), Milan, Italy
gunter meiSter • Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR),
University of Regensburg, Regensburg, Germany
JoShua t. mendeLL • Department of Molecular Biology, University of Texas Southwestern
Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and
Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons
Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas,
TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical
Center, Dallas, TX, USA
franCeSCo niCaSSio • Center for Genomic Science of IIT@SEMM, Istituto Italiano di
Tecnologia (IIT), Milan, Italy
mariko okada-hatakeyama • Laboratory for Integrated Cellular Systems,
RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan;
Laboratory of Cell Systems, Institute for Protein Research, Osaka University, Suita-shi,
Osaka-fu, Japan
uLf anderSSon vang Ørom • Department of Molecular Biology and Genetics,
Aarhus University, Aarhus, Denmark
amy e. PaSquineLLi • Division of Biology, University of California, San Diego, La Jolla,
CA, USA
nikoS PerdikoPaniS • DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece;
Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece
roBin reed • Department of Cell Biology, Harvard Medical School, Boston, MA, USA
madaLena m. reimão-Pinto • IMBA—Institute of Molecular Biotechnology, Vienna
Biocenter, Vienna, Austria
angeLa m. rodrigueS-viana • IMBA—Institute of Molecular Biotechnology, Vienna
Biocenter, Vienna, Austria
Contributors xi
yutaka Suzuki • Department of Computational Biology, Graduate School of Frontier
Sciences, The University of Tokyo, Kashiwa-shi, Chiba-ken, Japan
maSaru tomita • Institute for Advanced Biosciences, Keio University, Tsuruoka,
Yamagata, Japan; Systems Biology Program, Graduate School of Media and Governance,
Keio University, Fujisawa, Kanagawa, Japan
nora treiBer • Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR),
University of Regensburg, Regensburg, Germany
thomaS treiBer • Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR),
University of Regensburg, Regensburg, Germany
kumiko ui-tei • Department of Biological Sciences, Graduate School of Science, The
University of Tokyo, Bunkyo-ku, Tokyo, Japan; Department of Computational Biology,
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba-ken,
Japan
anna wóJCiCka • Warsaw Genomics INC, Warsaw, Poland; Genomic Medicine, Medical
University of Warsaw, Warsaw, Poland
Shanye yin • Department of Cell Biology, Harvard Medical School, Boston, MA, USA
yong yu • Department of Cell Biology, Harvard Medical School, Boston, MA, USA
mohammad farid zia • Department of Biological Sciences, University of Southern
Mississippi, Hattiesburg, MS, USA