Searching journal content for articles similar to Vainberg Slutskin et al. 29 (10): 1635.

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  1. 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
    ...), which are known to promote cell proliferation and inhibit apoptosis (Kota et al. 2021; Yang et al. 2021; Lachiondo-Ortega et al. 2022).Cell type–specific APA spectrum in skeletal muscleGiven the crucial role of the muscle differentiation in determining pork quantity and quality, we further investigated...
  2. Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    • Karine Choquet,
    • Louis-Philippe Chaumont,
    • Simon Bache,
    • Autum R. Baxter-Koenigs,
    • and L. Stirling Churchman
    Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
    ...splicing enhancers or silencers, which are bound by RNA-binding proteins (RBPs) that regulate AS (Fairbrother and Chasin 2000; Zhang and Chasin 2004; Barash et al. 2010; Blencowe 2012). As such, the order in which introns are removed may determine how long splicing regulatory elements remain within...
  3. 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
    ...how the poly(A) sites are determined across yeast species, although experiments showed that 3′ UTRs are modular entities that can determine the cleavage and polyadenylation profiles independent of the coding sequences (Lui et al. 2022).A challenge to characterizing yeast poly(A) signals...
  4. 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
    ...Gaussian mixture models to separate overlapping peaks (Fig. 1B), (2) determining the interval of peak-to-PA distance using single-PA–single-peak genes (Supplemental Fig. S1A), (3) using integrated PA references (Wang et al. 2018; Herrmann et al. 2020; Agarwal et al. 2021) to annotate the identified peaks...
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  5. Research: Transposable elements drive the evolution of metazoan zinc finger genes
    • Jonathan N. Wells,
    • Ni-Chen Chang,
    • John McCormick,
    • Caitlyn Coleman,
    • Nathalie Ramos,
    • Bozhou Jin,
    • and Cédric Feschotte
    Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
    ...determined. Searching for each of 236 experimentally determined KZNF binding sites in the set of predicted binding motifs, we found that 11 (5%) produced significant matches to their predicted counterpart (Q-value < 0.05), compared with zero matches after shuffling the predicted motifs. Similar results have...
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  6. 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
    ...driver in colorectal cancer modulated by a promoter-enhancer interaction. Am J Hum Genet 105: 29–47. doi:10.1016/j.ajhg.2019.05.004 ↵Vainberg Slutskin I, Weinberger A, Segal E. 2019. Sequence determinants of polyadenylation-mediated regulation. Genome Res 29: 1635–1647. doi:10.1101/gr.247312.118 ↵Wang RJ...
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  7. 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
    ...in PDAC are enriched in promoters of cancer-associated genes and pathways (Feigin et al. 2017). However, our understanding of the mechanisms driving dysregulated gene expression in cancer remains incomplete. Determining the regulatory mechanisms driving dysregulated gene expression is critical...
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  8. Research: Widespread context dependency of microRNA-mediated regulation
    • Florian Erhard,
    • Jürgen Haas,
    • Diana Lieber,
    • Georg Malterer,
    • Lukasz Jaskiewicz,
    • Mihaela Zavolan,
    • Lars Dölken,
    • and Ralf Zimmer
    Genome Res. June 2014 24: 906-919; Published in Advance March 25, 2014, doi:10.1101/gr.166702.113
    ...Harbor Laboratory Press; ISSN 1088-9051/14; www..org bind at a certain binding site. This is an example of individual context, since an RBP is able to affect individual target sites of a microRNA. In contrast, dynamic microRNA expression determines a global context, i.e., if a microRNA is differentially...
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