Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds.

作者: Aldema Sas-Chen , Schraga Schwartz

DOI: 10.1016/J.YMETH.2018.10.011

关键词:

摘要: Abstract Post-transcriptional modification on mRNA has become a field of intense interest in recent years, and next-generation sequencing based technologies are constantly emerging to detect an increasing number modifications at transcriptome-wide level. Some these approaches identification misincorporation events induced by reverse transcriptase modified sites. Although conceptually trivial, sensitive specific such is challenge prone surprising artifacts, which can lead substantially inflated estimates the abundance diverse modifications. Here we discuss sources some artifacts delineate overcome them.

参考文章(77)
Junjie U Guo, Vikram Agarwal, Huili Guo, David P Bartel, Expanded identification and characterization of mammalian circular RNAs Genome Biology. ,vol. 15, pp. 409- 409 ,(2014) , 10.1186/S13059-014-0409-Z
Daniel R. Schrider, Jean-Francois Gout, Matthew W. Hahn, Very Few RNA and DNA Sequence Differences in the Human Transcriptome PLoS ONE. ,vol. 6, pp. e25842- ,(2011) , 10.1371/JOURNAL.PONE.0025842
S. Mohr, E. Ghanem, W. Smith, D. Sheeter, Y. Qin, O. King, D. Polioudakis, V. R. Iyer, S. Hunicke-Smith, S. Swamy, S. Kuersten, A. M. Lambowitz, Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. RNA. ,vol. 19, pp. 958- 970 ,(2013) , 10.1261/RNA.039743.113
André E Minoche, Juliane C Dohm, Heinz Himmelbauer, Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems Genome Biology. ,vol. 12, pp. 1- 15 ,(2011) , 10.1186/GB-2011-12-11-R112
S. Granneman, G. Kudla, E. Petfalski, D. Tollervey, Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs Proceedings of the National Academy of Sciences of the United States of America. ,vol. 106, pp. 9613- 9618 ,(2009) , 10.1073/PNAS.0901997106
Richard Redon, Shumpei Ishikawa, Karen R. Fitch, Lars Feuk, George H. Perry, T. Daniel Andrews, Heike Fiegler, Michael H. Shapero, Andrew R. Carson, Wenwei Chen, Eun Kyung Cho, Stephanie Dallaire, Jennifer L. Freeman, Juan R. González, Mònica Gratacòs, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R. MacDonald, Christian R. Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J. Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F. Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P. Carter, Hiroyuki Aburatani, Charles Lee, Keith W. Jones, Stephen W. Scherer, Matthew E. Hurles, Global variation in copy number in the human genome Nature. ,vol. 444, pp. 444- 454 ,(2006) , 10.1038/NATURE05329
Natalia Volfovsky, Brian J Haas, Steven L Salzberg, Computational discovery of internal micro-exons. Genome Research. ,vol. 13, pp. 1216- 1221 ,(2003) , 10.1101/GR.677503
Thomas M. Carlile, Maria F. Rojas-Duran, Boris Zinshteyn, Hakyung Shin, Kristen M. Bartoli, Wendy V. Gilbert, Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells Nature. ,vol. 515, pp. 143- 146 ,(2014) , 10.1038/NATURE13802
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna, Aaron McKenna, Tim J Fennell, Andrew M Kernytsky, Andrey Y Sivachenko, Kristian Cibulskis, Stacey B Gabriel, David Altshuler, Mark J Daly, A framework for variation discovery and genotyping using next-generation DNA sequencing data Nature Genetics. ,vol. 43, pp. 491- 498 ,(2011) , 10.1038/NG.806
Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras, STAR: ultrafast universal RNA-seq aligner Bioinformatics. ,vol. 29, pp. 15- 21 ,(2013) , 10.1093/BIOINFORMATICS/BTS635