The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing
Open accessAbstract
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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Cites
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Alternative isoform regulation in human tissue transcriptomes
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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Mechanisms and Consequences of Alternative Polyadenylation
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Self-citation
Cited by
Alternative polyadenylation of mRNA precursors
Tian, B., & Manley, J. L. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.116 · Cited by 1,179
Self-citationMayr, C. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a034728 · Cited by 519
TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications
Chang, H., Lim, J., Ha, M., & Kim, V. N. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.007 · Cited by 454
Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
de Klerk, E., & ‘t Hoen, P. A. C. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.01.001 · Cited by 350
Context-specific regulation and function of mRNA alternative polyadenylation
Mitschka, S., & Mayr, C. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00507-5 · Cited by 336
Metadata
- Authors
- Hoque, M., Ji, Z., Zheng, D., Luo, W., Li, W., You, B., Park, J. Y., Yehia, G., & Tian, B.
- Venue
- Nature Methods
- Published
- 2012-12-16
- Volume
- 10
- Issue
- 2
- Pages
- 133-139
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2108264419
- Cited by
- 440
- References
- 9
- FWCI
- 8.71
- Type
- journal article
- Language
- en
- Open access
- green
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