Searching journal content for articles similar to Byrne et al. 19 (7): 1233.

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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
...poly(A) tails to the 3′ end through the selection of different polyadenylation sites (PASs), generating diverse transcript isoforms with varying lengths of 3′ untranslated regions (3′ UTRs) (Reyes and Huber 2018). In general, the APA occurs in over 70% of protein-coding genes in mammals and manifests...
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Method: Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
- Bowei Kang,
- Yalan Yang,
- Kaining Hu,
- Xiangbin Ruan,
- Yi-Lin Liu,
- Pinky Lee,
- Jasper Lee,
- Jingshu Wang,
- and Xiaochang Zhang
Genome Res. October 2023 33: 1774-1787; Published in Advance October 31, 2023, doi:10.1101/gr.277864.123
..., Illinois 60637, USA; 2Department of Statistics, The University of Chicago, Chicago, Illinois 60637, USA; 3The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, USA Corresponding authors: xczhang@uchicago.edu, jingshuw@uchicago.eduAbstractDifferential polyadenylation sites (PAs...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...information is integrated (onto the available/annotated or new transcripts) while enabling tracking and assessing splice-site variability through unique yielded descriptors. The resulting annotation from the ENACT framework enables exon features to be tractable, facilitating a systematic analysis of isoform...
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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
...the transcription initiation and elongation have been well characterized using these model organisms, the regulation of cleavage and polyadenylation has been understudied. Only recently, studies used deep sequencing approaches to map -wide poly(A) sites and examine the functional roles of different 3′-end RNA...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...studies as well as new therapeutic angles to target eukaryotic pathogens.Cleavage and polyadenylation (CPA) are key steps in eukaryotic mRNA maturation, specifying the 3′ end of the transcript and the addition of the poly(A) tail. Required for the proper expression of nearly all mRNAs, the site of pre...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...and addition of the poly(A) tail (Proudfoot 2011; Elkon et al. 2013; Shi and Manley 2015). Because most transcripts contain multiple polyadenylation sites (PAS), the choice of where to cleave is a critical determinant of 3′-UTR length. In humans, a majority of genes (51%–79%) express alternative 3′ UTRs...
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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
....segal@weizmann.ac.ilAbstractThe cleavage and polyadenylation reaction is a crucial step in transcription termination and pre-mRNA maturation in human cells. Despite extensive research, the encoding of polyadenylation-mediated regulation of gene expression within the DNA sequence is not well understood. Here, we utilized a massively...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...meaning all sequenced transcripts are polyadenylated. Some read-through events were observed but we did not analyze them systematically as we were mindful of the relatively low percentage of full-length reads in our analyses of archival tissue. Despite using total RNA as input for PCS and DRS library...
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Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
- Meng Chen,
- Ran Wei,
- Gang Wei,
- Mingqing Xu,
- Zhixi Su,
- Chen Zhao,
- and Ting Ni
Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
...Var databases annotate this variant as pathogenic, with relative frequencies of 4.3% in Guadeloupe, 3.39% in Cuba, 1% in Morocco, 0.7% in Sri Lanka, and 0.4% in the UK. Northern blot and S1 nuclease mapping indicated a longer transcript that possibly escaped the polyadenylation site of HBB due to the PAS...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...transcripts) with fusion sites corresponding to the breakpoints of the mitochondrial “common deletion.” Paired long-read sequencing of the same samples demonstrated the presence of a single clonal deletion at this location (Supplemental Fig. 1).To test whether chimeric mtRNA transcripts exist in human...

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