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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...for mammalian genes. It remains unknown if the polyadenylation events occurring across a cleavage zone represent poly(A) site microheterogeneity or the utilization of separate alternative poly(A) sites. Both heterogeneous cleavage and alternative polyadenylation (APA) can generate mRNAs with different 3′ UTRs...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...polyadenylation (APA) plays a crucial role in gene regulation and phenotypic diversity. Whereas extensive studies have explored the global APA landscape using bulk RNA-seq data, in-depth analyses of APA events at the single-cell level remain limited—particularly in farm animals. In this study, we construct...
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Research: Sequence determinants of polyadenylation-mediated regulation
- Ilya Vainberg Slutskin,
- Adina Weinberger,
- and Eran Segal
Genome Res. October 2019 29: 1635-1647; Published in Advance September 17, 2019, doi:10.1101/gr.247312.118
...′ UTR and downstream sequences in the context of cleavage and polyadenylation efficiency may greatly advance our understanding of this crucial process.Some research efforts employed machine learning and deep learning approaches to prediction of alternative polyadenylation events and classification...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...(A) signals, which are precisely positioned 20–22 nt upstream of the pre-mRNA cleavage sites (indicated by the dashed, vertical line). Polyadenylation sites, signals, functional impact Genome Research 1147 www..org sets, see Supplemental Material) and the conserved poly(A) signals that we inferred...
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Resource: Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
...94158, USA. Abstract The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...of conserved differential splicing variation across mammalian tissues (Vaquero-Garcia et al. 2016). It is interesting to speculate how complex splicing events may arise during evolution. One likely model would involve complex events emerging from simpler ancestral splicing events. Comparisons of genomic...
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Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
- Kyu-Hyeon Yeom,
- Zhicheng Pan,
- Chia-Ho Lin,
- Han Young Lim,
- Wen Xiao,
- Yi Xing,
- and Douglas L. Black
Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
...samples and is also chromatin enriched. Whether this is a stable long isoform or nascent RNA is not clear. This longer RNA contributes a larger portion of the Neat1 transcripts in mNPCs and neurons, consistent with observations that Neat1 cleavage and polyadenylation may be modulated (Naganuma et al. 2012...
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Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
- Yulong Song,
- Lishi Li,
- Wenbing Yang,
- Qiang Fu,
- Wanying Chen,
- Zeng Fang,
- Wen Li,
- Nannan Gu,
- and Rui Zhang
Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
...RNAs. Through examining the unstranded targeted RNA-seq libraries covering all miRNA loci in 25 types of human tissues, we identified 7275 editing events located in 81% of the antisense strand of the miRNA loci, thus uncovering the previously unknown prevalent antisense transcription of the miRNAs. We found...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
..., studies of zygotic mRNA degradation have uncovered cell differentiation events that are influenced by mRNA decay. For example, timely decay of glial cells missing transcripts in the fly embryo is important for appropriate nervous system differentiation (Soustelle et al. 2008), and stabilization of muscle...
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Research: DDX54 regulates transcriptome dynamics during DNA damage response
- Miha Milek,
- Koshi Imami,
- Neelanjan Mukherjee,
- Francesca De Bortoli,
- Ulrike Zinnall,
- Orsalia Hazapis,
- Christian Trahan,
- Marlene Oeffinger,
- Florian Heyd,
- Uwe Ohler,
- Matthias Selbach,
- and Markus Landthaler
Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
...by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNAdamage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts...
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