Literature DB >> 25665566

Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends.

Irina O Vvedenskaya1, Seth R Goldman, Bryce E Nickels.   

Abstract

We provide a detailed protocol for preparing cDNA libraries suitable for high-throughput sequencing that are derived specifically from the 5' ends of RNA (5' specific RNA-seq). The protocol describes how cDNA libraries for 5' specific RNA-seq can be tailored to analyze specific classes of RNAs based upon the phosphorylation status of the 5' end. Thus, the analysis of cDNA libraries generated by these methods provides information regarding both the sequence and phosphorylation status of the 5' ends of RNAs. 5' specific RNA-seq can be used to analyze transcription initiation and posttranscriptional processing of RNAs with single base pair resolution on a genome-wide level.

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Year:  2015        PMID： 25665566      PMCID： PMC4349364          DOI： 10.1007/978-1-4939-2392-2_12

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  10 in total

1.  NanoRNAs prime transcription initiation in vivo.

Authors:  Seth R Goldman; Josh S Sharp; Irina O Vvedenskaya; Jonathan Livny; Simon L Dove; Bryce E Nickels
Journal:  Mol Cell       Date:  2011-06-24       Impact factor: 17.970

Review 2.  Regulation of gene expression by reiterative transcription.

Authors:  Charles L Turnbough
Journal:  Curr Opin Microbiol       Date:  2011-02-19       Impact factor: 7.934

3.  An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.

Authors:  Jan Mitschke; Jens Georg; Ingeborg Scholz; Cynthia M Sharma; Dennis Dienst; Jens Bantscheff; Björn Voss; Claudia Steglich; Annegret Wilde; Jörg Vogel; Wolfgang R Hess
Journal:  Proc Natl Acad Sci U S A       Date:  2011-01-18       Impact factor: 11.205

4.  Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs.

Authors:  Irina O Vvedenskaya; Josh S Sharp; Seth R Goldman; Pinal N Kanabar; Jonathan Livny; Simon L Dove; Bryce E Nickels
Journal:  Genes Dev       Date:  2012-07-01       Impact factor: 11.361

5.  The primary transcriptome of the major human pathogen Helicobacter pylori.

Authors:  Cynthia M Sharma; Steve Hoffmann; Fabien Darfeuille; Jérémy Reignier; Sven Findeiss; Alexandra Sittka; Sandrine Chabas; Kristin Reiche; Jörg Hackermüller; Richard Reinhardt; Peter F Stadler; Jörg Vogel
Journal:  Nature       Date:  2010-02-17       Impact factor: 49.962

6.  The transcription unit architecture of the Escherichia coli genome.

Authors:  Byung-Kwan Cho; Karsten Zengler; Yu Qiu; Young Seoub Park; Eric M Knight; Christian L Barrett; Yuan Gao; Bernhard Ø Palsson
Journal:  Nat Biotechnol       Date:  2009-11-01       Impact factor: 54.908

7.  A new method for stranded whole transcriptome RNA-seq.

Authors:  David F B Miller; Pearlly S Yan; Aaron Buechlein; Benjamin A Rodriguez; Ayse S Yilmaz; Shokhi Goel; Hai Lin; Bridgette Collins-Burow; Lyndsay V Rhodes; Chris Braun; Sunila Pradeep; Rajesha Rupaimoole; Mehmet Dalkilic; Anil K Sood; Matthew E Burow; Haixu Tang; Tim H Huang; Yunlong Liu; Douglas B Rusch; Kenneth P Nephew
Journal:  Methods       Date:  2013-04-01       Impact factor: 3.608

8.  Widespread antisense transcription in Escherichia coli.

Authors:  James E Dornenburg; Anne M Devita; Michael J Palumbo; Joseph T Wade
Journal:  MBio       Date:  2010-05-18       Impact factor: 7.867

9.  Structural bias in T4 RNA ligase-mediated 3'-adapter ligation.

Authors:  Fanglei Zhuang; Ryan T Fuchs; Zhiyi Sun; Yu Zheng; G Brett Robb
Journal:  Nucleic Acids Res       Date:  2012-01-12       Impact factor: 16.971

10.  Comparative analysis of RNA sequencing methods for degraded or low-input samples.

Authors:  Xian Adiconis; Diego Borges-Rivera; Rahul Satija; David S DeLuca; Michele A Busby; Aaron M Berlin; Andrey Sivachenko; Dawn Anne Thompson; Alec Wysoker; Timothy Fennell; Andreas Gnirke; Nathalie Pochet; Aviv Regev; Joshua Z Levin
Journal:  Nat Methods       Date:  2013-05-19       Impact factor: 28.547
  10 in total
  9 in total

1.  Perivascular signals alter global gene expression profile of glioblastoma and response to temozolomide in a gelatin hydrogel.

Authors:  Mai T Ngo; Brendan A C Harley
Journal:  Biomaterials       Date:  2018-06-13       Impact factor: 12.479

2.  Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.

Authors:  Irina O Vvedenskaya; Hanif Vahedian-Movahed; Yuanchao Zhang; Deanne M Taylor; Richard H Ebright; Bryce E Nickels
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-09       Impact factor: 11.205

3.  Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.

Authors:  Irina O Vvedenskaya; Yuanchao Zhang; Seth R Goldman; Anna Valenti; Valeria Visone; Deanne M Taylor; Richard H Ebright; Bryce E Nickels
Journal:  Mol Cell       Date:  2015-11-25       Impact factor: 17.970

4.  Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae.

Authors:  Tingting Zhao; Irina O Vvedenskaya; William Km Lai; Shrabani Basu; B Franklin Pugh; Bryce E Nickels; Craig D Kaplan
Journal:  Elife       Date:  2021-10-15       Impact factor: 8.140

5.  Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase.

Authors:  Jonathan W Cruz; Jared D Sharp; Eric D Hoffer; Tatsuya Maehigashi; Irina O Vvedenskaya; Arvind Konkimalla; Robert N Husson; Bryce E Nickels; Christine M Dunham; Nancy A Woychik
Journal:  Nat Commun       Date:  2015-07-09       Impact factor: 14.919

6.  A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

Authors:  Sergey Y Druzhinin; Ngat T Tran; Kyle S Skalenko; Seth R Goldman; Jared G Knoblauch; Simon L Dove; Bryce E Nickels
Journal:  PLoS Genet       Date:  2015-07-01       Impact factor: 5.917

7.  Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma.

Authors:  Maria D Giraldez; Ryan M Spengler; Alton Etheridge; Annika J Goicochea; Missy Tuck; Sung Won Choi; David J Galas; Muneesh Tewari
Journal:  EMBO J       Date:  2019-05-03       Impact factor: 11.598

8.  Detection of spacer precursors formed in vivo during primed CRISPR adaptation.

Authors:  Anna A Shiriaeva; Ekaterina Savitskaya; Kirill A Datsenko; Irina O Vvedenskaya; Iana Fedorova; Natalia Morozova; Anastasia Metlitskaya; Anton Sabantsev; Bryce E Nickels; Konstantin Severinov; Ekaterina Semenova
Journal:  Nat Commun       Date:  2019-10-10       Impact factor: 14.919

9.  Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.

Authors:  Chenxi Qiu; Huiyan Jin; Irina Vvedenskaya; Jordi Abante Llenas; Tingting Zhao; Indranil Malik; Alex M Visbisky; Scott L Schwartz; Ping Cui; Pavel Čabart; Kang Hoo Han; William K M Lai; Richard P Metz; Charles D Johnson; Sing-Hoi Sze; B Franklin Pugh; Bryce E Nickels; Craig D Kaplan
Journal:  Genome Biol       Date:  2020-06-02       Impact factor: 13.583
  9 in total

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