Literature DB >> 24590790

Global and quantitative profiling of polyadenylated RNAs using PAS-seq.

Chengguo Yao1, Yongsheng Shi.   

Abstract

mRNA alternative polyadenylation (APA) has been increasingly recognized as a widespread and evolutionarily conserved mechanism for eukaryotic gene regulation. Here we describe a method called poly(A) site sequencing that can not only map RNA polyadenylation sites on a transcriptome level but also provide quantitative information on the relative abundance of polyadenylated RNAs. This method has been successfully used for both global APA analysis and digital gene expression profiling.

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Year:  2014        PMID: 24590790      PMCID: PMC4412162          DOI: 10.1007/978-1-62703-971-0_16

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


  14 in total

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Authors:  Rickard Sandberg; Joel R Neilson; Arup Sarma; Phillip A Sharp; Christopher B Burge
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5.  Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction.

Authors:  Y Y Zhu; E M Machleder; A Chenchik; R Li; P D Siebert
Journal:  Biotechniques       Date:  2001-04       Impact factor: 1.993

Review 6.  Alternative polyadenylation: new insights from global analyses.

Authors:  Yongsheng Shi
Journal:  RNA       Date:  2012-10-24       Impact factor: 4.942

7.  Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq.

Authors:  Peter J Shepard; Eun-A Choi; Jente Lu; Lisa A Flanagan; Klemens J Hertel; Yongsheng Shi
Journal:  RNA       Date:  2011-02-22       Impact factor: 4.942

8.  Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation.

Authors:  Fatih Ozsolak; Philipp Kapranov; Sylvain Foissac; Sang Woo Kim; Elane Fishilevich; A Paula Monaghan; Bino John; Patrice M Milos
Journal:  Cell       Date:  2010-12-10       Impact factor: 41.582

9.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

10.  Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

Authors:  Steven W Flavell; Tae-Kyung Kim; Jesse M Gray; David A Harmin; Martin Hemberg; Elizabeth J Hong; Eirene Markenscoff-Papadimitriou; Daniel M Bear; Michael E Greenberg
Journal:  Neuron       Date:  2008-12-26       Impact factor: 17.173

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  6 in total

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Review 2.  Whole transcriptome analysis with sequencing: methods, challenges and potential solutions.

Authors:  Zhihua Jiang; Xiang Zhou; Rui Li; Jennifer J Michal; Shuwen Zhang; Michael V Dodson; Zhiwu Zhang; Richard M Harland
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3.  Quantifying alternative polyadenylation in RNAseq data with LABRAT.

Authors:  Austin E Gillen; Raeann Goering; J Matthew Taliaferro
Journal:  Methods Enzymol       Date:  2021-04-23       Impact factor: 1.682

4.  EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates.

Authors:  Joshua D Welch; Michael K Slevin; Deirdre C Tatomer; Robert J Duronio; Jan F Prins; William F Marzluff
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5.  Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq).

Authors:  Xiang Zhou; Rui Li; Jennifer J Michal; Xiao-Lin Wu; Zhongzhen Liu; Hui Zhao; Yin Xia; Weiwei Du; Mark R Wildung; Derek J Pouchnik; Richard M Harland; Zhihua Jiang
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6.  Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver.

Authors:  Kerry L Gendreau; Benjamin A Unruh; Chuanli Zhou; Shihoko Kojima
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  6 in total

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