Literature DB >> 29361313

Big Strides in Cellular MicroRNA Expression.

Marc K Halushka1, Bastian Fromm2, Kevin J Peterson3, Matthew N McCall4.   

Abstract

A lack of knowledge of the cellular origin of miRNAs has greatly confounded functional and biomarkers studies. Recently, three studies characterized miRNA expression patterns across >78 human cell types. These combined data expand our knowledge of miRNA expression localization and confirm that many miRNAs show cell type-specific expression patterns.
Copyright © 2017 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  RNA-seq; cell expression; microRNA

Mesh：

Substances：

Year:  2018        PMID： 29361313      PMCID： PMC5834366          DOI： 10.1016/j.tig.2017.12.015

Source DB:  PubMed          Journal:  Trends Genet        ISSN： 0168-9525            Impact factor:   11.639


  13 in total

Review 1.  A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome.

Authors:  Bastian Fromm; Tyler Billipp; Liam E Peck; Morten Johansen; James E Tarver; Benjamin L King; James M Newcomb; Lorenzo F Sempere; Kjersti Flatmark; Eivind Hovig; Kevin J Peterson
Journal:  Annu Rev Genet       Date:  2015-10-14       Impact factor: 16.830

2.  Deep characterization of blood cell miRNomes by NGS.

Authors:  Eva C Schwarz; Christina Backes; Arne Knörck; Nicole Ludwig; Petra Leidinger; Cora Hoxha; Gertrud Schwär; Thomas Grossmann; Sabine C Müller; Martin Hart; Jan Haas; Valentina Galata; Isabelle Müller; Tobias Fehlmann; Hermann Eichler; Andre Franke; Benjamin Meder; Eckart Meese; Markus Hoth; Andreas Keller
Journal:  Cell Mol Life Sci       Date:  2016-02-13       Impact factor: 9.261

3.  Distribution of miRNA expression across human tissues.

Authors:  Nicole Ludwig; Petra Leidinger; Kurt Becker; Christina Backes; Tobias Fehlmann; Christian Pallasch; Steffi Rheinheimer; Benjamin Meder; Cord Stähler; Eckart Meese; Andreas Keller
Journal:  Nucleic Acids Res       Date:  2016-02-25       Impact factor: 16.971

Review 4.  Toward the promise of microRNAs - Enhancing reproducibility and rigor in microRNA research.

Authors:  Kenneth W Witwer; Marc K Halushka
Journal:  RNA Biol       Date:  2016-09-19       Impact factor: 4.652

5.  An integrated expression atlas of miRNAs and their promoters in human and mouse.

Authors:  Derek de Rie; Imad Abugessaisa; Tanvir Alam; Erik Arner; Peter Arner; Haitham Ashoor; Gaby Åström; Magda Babina; Nicolas Bertin; A Maxwell Burroughs; Ailsa J Carlisle; Carsten O Daub; Michael Detmar; Ruslan Deviatiiarov; Alexandre Fort; Claudia Gebhard; Daniel Goldowitz; Sven Guhl; Thomas J Ha; Jayson Harshbarger; Akira Hasegawa; Kosuke Hashimoto; Meenhard Herlyn; Peter Heutink; Kelly J Hitchens; Chung Chau Hon; Edward Huang; Yuri Ishizu; Chieko Kai; Takeya Kasukawa; Peter Klinken; Timo Lassmann; Charles-Henri Lecellier; Weonju Lee; Marina Lizio; Vsevolod Makeev; Anthony Mathelier; Yulia A Medvedeva; Niklas Mejhert; Christopher J Mungall; Shohei Noma; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Helena Persson; Patrizia Rizzu; Filip Roudnicky; Pål Sætrom; Hiroki Sato; Jessica Severin; Jay W Shin; Rolf K Swoboda; Hiroshi Tarui; Hiroo Toyoda; Kristoffer Vitting-Seerup; Louise Winteringham; Yoko Yamaguchi; Kayoko Yasuzawa; Misako Yoneda; Noriko Yumoto; Susan Zabierowski; Peter G Zhang; Christine A Wells; Kim M Summers; Hideya Kawaji; Albin Sandelin; Michael Rehli; Yoshihide Hayashizaki; Piero Carninci; Alistair R R Forrest; Michiel J L de Hoon
Journal:  Nat Biotechnol       Date:  2017-08-21       Impact factor: 54.908

Review 6.  MicroRNA profiling: approaches and considerations.

Authors:  Colin C Pritchard; Heather H Cheng; Muneesh Tewari
Journal:  Nat Rev Genet       Date:  2012-04-18       Impact factor: 53.242

7.  MicroRNA profiling of diverse endothelial cell types.

Authors:  Matthew N McCall; Oliver A Kent; Jianshi Yu; Karen Fox-Talbot; Ari L Zaiman; Marc K Halushka
Journal:  BMC Med Genomics       Date:  2011-11-02       Impact factor: 3.063

8.  microRNA target prediction programs predict many false positives.

Authors:  Natalia Pinzón; Blaise Li; Laura Martinez; Anna Sergeeva; Jessy Presumey; Florence Apparailly; Hervé Seitz
Journal:  Genome Res       Date:  2016-11-15       Impact factor: 9.043

9.  A comprehensive, cell specific microRNA catalogue of human peripheral blood.

Authors:  Simonas Juzenas; Geetha Venkatesh; Matthias Hübenthal; Marc P Hoeppner; Zhipei Gracie Du; Maren Paulsen; Philip Rosenstiel; Philipp Senger; Martin Hofmann-Apitius; Andreas Keller; Limas Kupcinskas; Andre Franke; Georg Hemmrich-Stanisak
Journal:  Nucleic Acids Res       Date:  2017-09-19       Impact factor: 16.971

Review 10.  Lessons from miR-143/145: the importance of cell-type localization of miRNAs.

Authors:  Oliver A Kent; Matthew N McCall; Toby C Cornish; Marc K Halushka
Journal:  Nucleic Acids Res       Date:  2014-05-29       Impact factor: 16.971
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  14 in total

1.  In Silico Analysis of Micro-RNA Sequencing Data.

Authors:  Ernesto Aparicio-Puerta; Bastian Fromm; Michael Hackenberg; Marc K Halushka
Journal:  Methods Mol Biol       Date:  2021

Review 2.  Opportunities for microRNAs in the Crowded Field of Cardiovascular Biomarkers.

Authors:  Perry V Halushka; Andrew J Goodwin; Marc K Halushka
Journal:  Annu Rev Pathol       Date:  2018-10-17       Impact factor: 23.472

3.  xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells.

Authors:  Avi Z Rosenberg; Carrie Wright; Karen Fox-Talbot; Anandita Rajpurohit; Courtney Williams; Corey Porter; Olga Kovbasnjuk; Matthew N McCall; Joo Heon Shin; Marc K Halushka
Journal:  Sci Rep       Date:  2018-06-28       Impact factor: 4.379

4.  miRge 2.0 for comprehensive analysis of microRNA sequencing data.

Authors:  Yin Lu; Alexander S Baras; Marc K Halushka
Journal:  BMC Bioinformatics       Date:  2018-07-23       Impact factor: 3.169

5.  miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish.

Authors:  Thomas Desvignes; Peter Batzel; Jason Sydes; B Frank Eames; John H Postlethwait
Journal:  Sci Rep       Date:  2019-03-08       Impact factor: 4.379

6.  MirGeneDB 2.0: the metazoan microRNA complement.

Authors:  Bastian Fromm; Diana Domanska; Eirik Høye; Vladimir Ovchinnikov; Wenjing Kang; Ernesto Aparicio-Puerta; Morten Johansen; Kjersti Flatmark; Anthony Mathelier; Eivind Hovig; Michael Hackenberg; Marc R Friedländer; Kevin J Peterson
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

7.  A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks.

Authors:  Pedro G Nachtigall; Luiz A Bovolenta; James G Patton; Bastian Fromm; Ney Lemke; Danillo Pinhal
Journal:  BMC Genomics       Date:  2021-03-04       Impact factor: 3.969

8.  Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types.

Authors:  Suvi Linna-Kuosmanen; Minna U Kaikkonen; Pierre R Moreau; Vanesa Tomas Bosch; Maria Bouvy-Liivrand; Kadri Õunap; Tiit Örd; Heidi H Pulkkinen; Petri Pölönen; Merja Heinäniemi; Seppo Ylä-Herttuala; Johanna P Laakkonen
Journal:  Arterioscler Thromb Vasc Biol       Date:  2021-05-13       Impact factor: 8.311

9.  Evolution after Whole-Genome Duplication: Teleost MicroRNAs.

Authors:  Thomas Desvignes; Jason Sydes; Jerôme Montfort; Julien Bobe; John H Postlethwait
Journal:  Mol Biol Evol       Date:  2021-07-29       Impact factor: 16.240

10.  Expression of miR-200c corresponds with increased reactive oxygen species and hypoxia markers after transient focal ischemia in mice.

Authors:  Oiva Arvola; Brian Griffiths; Anand Rao; Lijun Xu; Iason-Alexander Pastroudis; Creed M Stary
Journal:  Neurochem Int       Date:  2021-07-31       Impact factor: 4.297
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