Expanding the annotation of zebrafish microRNAs based on small RNA sequencing
作者： Thomas Desvignes , Michael J. Beam , Peter Batzel , Jason Sydes , John H. Postlethwait
DOI: 10.1016/J.GENE.2014.05.036
关键词:
摘要: MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range biological processes. Because their role in expression, miRs essential players development by acting on cell fate determination and progression towards differentiation increasingly relevant human health disease. Although zebrafish Danio rerio is major model for studies development, genetics, physiology, evolution, biology, annotation miR-producing genes remains limited. In present work, we report deep sequencing data small from brain, heart, testis, ovary. Results provide evidence 56 un-annotated mir 248 mature strands, increasing number over those already deposited miRBase 16% sequences 63%. We also describe existence three pairs mirror-mir two mirtron genes, genetic features previously undescribed non-mammalian vertebrates. This provides information substantially increases our knowledge miRNome will benefit entire miR community.
sci-hub.se 参考文章(38)
Monte Westerfield, The zebrafish book : a guide for the laboratory use of zebrafish (Danio rerio) M. Westerfield. ,(1995)
Xinjun He, Yi-Lin Yan, April DeLaurier, John H. Postlethwait, Observation of miRNA Gene Expression in Zebrafish Embryos by In Situ Hybridization to MicroRNA Primary Transcripts Zebrafish. ,vol. 8, pp. 1- 8 ,(2011) , 10.1089/ZEB.2010.0680
Helen Scott, Joanna Howarth, Youn Bok Lee, Liang-Fong Wong, Ioannis Bantounas, Leonidas Phylactou, Paul Verkade, James. B. Uney, MiR-3120 Is a Mirror MicroRNA That Targets Heat Shock Cognate Protein 70 and Auxilin Messenger RNAs and Regulates Clathrin Vesicle Uncoating Journal of Biological Chemistry. ,vol. 287, pp. 14726- 14733 ,(2012) , 10.1074/JBC.M111.326041
Erno Wienholds, Wigard P Kloosterman, Eric Miska, Ezequiel Alvarez-Saavedra, Eugene Berezikov, Ewart De Bruijn, H Robert Horvitz, Sakari Kauppinen, Ronald HA Plasterk, MicroRNA Expression in Zebrafish Embryonic Development Science. ,vol. 309, pp. 310- 311 ,(2005) , 10.1126/SCIENCE.1114519
Kerstin Howe, Matthew D Clark, Carlos F Torroja, James Torrance, Camille Berthelot, Matthieu Muffato, John E Collins, Sean Humphray, Karen McLaren, Lucy Matthews, Stuart McLaren, Ian Sealy, Mario Caccamo, Carol Churcher, Carol Scott, Jeffrey C Barrett, Romke Koch, Gerd-Jörg Rauch, Simon White, William Chow, Britt Kilian, Leonor T Quintais, José A Guerra-Assunção, Yi Zhou, Yong Gu, Jennifer Yen, Jan-Hinnerk Vogel, Tina Eyre, Seth Redmond, Ruby Banerjee, Jianxiang Chi, Beiyuan Fu, Elizabeth Langley, Sean F Maguire, Gavin K Laird, David Lloyd, Emma Kenyon, Sarah Donaldson, Harminder Sehra, Jeff Almeida-King, Jane Loveland, Stephen Trevanion, Matt Jones, Mike Quail, Dave Willey, Adrienne Hunt, John Burton, Sarah Sims, Kirsten McLay, Bob Plumb, Joy Davis, Chris Clee, Karen Oliver, Richard Clark, Clare Riddle, David Elliott, Glen Threadgold, Glenn Harden, Darren Ware, Sharmin Begum, Beverley Mortimore, Giselle Kerry, Paul Heath, Benjamin Phillimore, Alan Tracey, Nicole Corby, Matthew Dunn, Christopher Johnson, Jonathan Wood, Susan Clark, Sarah Pelan, Guy Griffiths, Michelle Smith, Rebecca Glithero, Philip Howden, Nicholas Barker, Christine Lloyd, Christopher Stevens, Joanna Harley, Karen Holt, Georgios Panagiotidis, Jamieson Lovell, Helen Beasley, Carl Henderson, Daria Gordon, Katherine Auger, Deborah Wright, Joanna Collins, Claire Raisen, Lauren Dyer, Kenric Leung, Lauren Robertson, Kirsty Ambridge, Daniel Leongamornlert, Sarah McGuire, Ruth Gilderthorp, Coline Griffiths, Deepa Manthravadi, Sarah Nichol, Gary Barker, Siobhan Whitehead, Michael Kay, Jacqueline Brown, Clare Murnane, Emma Gray, Matthew Humphries, Neil Sycamore, Darren Barker, David Saunders, Justene Wallis, Anne Babbage, Sian Hammond, Maryam Mashreghi-Mohammadi, Lucy Barr, Sancha Martin, Paul Wray, Andrew Ellington, Nicholas Matthews, Matthew Ellwood, Rebecca Woodmansey, Graham Clark, James D Cooper, Anthony Tromans, Darren Grafham, Carl Skuce, Richard Pandian, Robert Andrews, Elliot Harrison, Andrew Kimberley, Jane Garnett, Nigel Fosker, Rebekah Hall, Patrick Garner, Daniel Kelly, Christine Bird, Sophie Palmer, Ines Gehring, Andrea Berger, Christopher M Dooley, Zübeyde Ersan-Ürün, Cigdem Eser, Horst Geiger, Maria Geisler, Lena Karotki, Anette Kirn, Judith Konantz, Martina Konantz, Martina Oberländer, Silke Rudolph-Geiger, Mathias Teucke, None, The zebrafish reference genome sequence and its relationship to the human genome. Nature. ,vol. 496, pp. 498- 503 ,(2013) , 10.1038/NATURE12111
Luke Pase, Judith E. Layton, Wigard P. Kloosterman, Duncan Carradice, Peter M. Waterhouse, Graham J. Lieschke, miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2 Blood. ,vol. 113, pp. 1794- 1804 ,(2009) , 10.1182/BLOOD-2008-05-155812
Anja P. M. Verhagen, Ger J. M. Pruijn, Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity BioEssays. ,vol. 33, pp. 674- 682 ,(2011) , 10.1002/BIES.201100048
Xinjun He, Yi-Lin Yan, Johann K. Eberhart, Amaury Herpin, Toni U. Wagner, Manfred Schartl, John H. Postlethwait, miR-196 regulates axial patterning and pectoral appendage initiation. Developmental Biology. ,vol. 357, pp. 463- 477 ,(2011) , 10.1016/J.YDBIO.2011.07.014
Zhiqiang Xu, Jiaping Chen, Xuguang Li, Jiachun Ge, Jianlin Pan, Xiaofeng Xu, Identification and Characterization of MicroRNAs in Channel Catfish (Ictalurus punctatus) by Using Solexa Sequencing Technology PLoS ONE. ,vol. 8, pp. e54174- ,(2013) , 10.1371/JOURNAL.PONE.0054174
Victor Ambros, The functions of animal microRNAs Nature. ,vol. 431, pp. 350- 355 ,(2004) , 10.1038/NATURE02871