Analysis of alterative cleavage and polyadenylation by 3′ region extraction and deep sequencing

1] Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, New Jersey, USA. [2].
Nature Methods (Impact Factor: 32.07). 12/2012; 10(2). DOI: 10.1038/nmeth.2288
Source: PubMed

ABSTRACT Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3' ends revealed over 5,000 previously overlooked pAs (∼8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. About 79% of mRNA genes and 66% of long noncoding RNA genes undergo APA, but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Quantitative analysis of APA isoforms by 3'READS indicated that promoter-distal pAs, regardless of intron or exon locations, become more abundant during embryonic development and cell differentiation and that upregulated isoforms have stronger pAs, suggesting global modulation of the 3' end-processing activity in development and differentiation.

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Available from: Bin Tian, Oct 25, 2014
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    • "Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T) 25 magnetic beads (New England Biolabs). A single-read cDNA library was prepared following the Illumina TrueSeq small RNA protocol for strand-specific RNA-seq with minor modifications (Hoque et al. 2013). Briefly, poly(A) + RNA was fragmented in an alkaline buffer (NaHCO 3 at pH 9.3) for 2 min at 94°C followed by dephosphorylation with recombinant shrimp alkaline phosphatase (New England Biolabs) and then phosphorylation with T4 polynucleotide kinase (New England Biolabs). "
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    • "Red dots indicate genes for which the longer 3 0 isoform was significantly upregulated in the population under investigation; yellow dots correspond to significant upregulation of the shorter 3 0 isoform. Significance was determined by Fisher's test (P < 0.05), see also Hoque et al (2013) "
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    • "Because PASs vary by a few nucleotides in a given isoform (at most 24 bp), we used the snow-ball method to define PASs (Hoque et al., 2013). We first aggregated the reads whose distances to the neighbors are less than 24 bp into one cluster. "
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