Searching journal content for articles similar to Brooks et al. 25 (11): 1771.

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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
    ..., and translation efficiency. In contrast, ALE-APA results from multiple PASs located in alternative terminal exons, which could lead to the production of truncated protein isoforms (Mariella et al. 2019; Goering et al. 2021). These alternatively polyadenylated mRNAs greatly expand the diversity of transcripts...
  2. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...), and similar results were reported for the mouse(Kiyosawa et al. 2003), Drosophila(Misra et al. 2002), Arabidopsis(Meyers et al. 2004; Wang et al. 2014), and rice s(Osato et al. 2003). In addition, many long intergenic non-coding RNAs (lincRNAs) have been identified as antisense transcripts, further...
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  3. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ....The radiation of cactophilic Drosophila species across different hosts is an evolutionary outcome that gave rise to specific adaptations (Rane et al. 2019). They can be summarized into three steps: localization, acceptance, and host usage (Markow 2019). In the localization step, odorant-binding proteins (OBPs...
  4. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    .... The data shown in Figure 3 allow us to start looking at the sequence level at these mysterious regions of the Drosophila Y Chromosome in which protein-coding exons are embedded in huge blocks of intronic satellite DNA (Kurek et al. 2000; Reugels et al. 2000) and yet are properly transcribed and spliced...
  5. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...), recoding is overrepresented in twomajor clades, coleoids (Cephalopoda) (Alon et al. 2015; Liscovitch-Brauer et al. 2017) and Drosophila (Insecta) (Yu et al. 2016; Yablonovitch et al. 2017a; Duan et al. 2024a). The temporospatial regulation of RNA editing circumvents the pleiotropic effects caused by DNA...
  6. Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
    • José Carlos Montañés,
    • Marta Huertas,
    • Simone G. Moro,
    • William R. Blevins,
    • Mercè Carmona,
    • José Ayté,
    • Elena Hidalgo,
    • and M. Mar Albà
    Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
    ...2020). The reference transcript is composed of five exons and encodes a protein that is 95 aa long. The dRNA reads provided direct evidence of an alternative isoform arising from a downstream alternative splice site in intron 3 and skipping of exon 4. The alternative isoform had a frequency of 27% (161...
  7. 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
    ...interrogating distinct pre-mRNA maturation steps. Indeed, long-read sequencing studies have shown direct coupling between AS and APA in Drosophila and humans (Hardwick et al. 2022; Alfonso-Gonzalez et al. 2023; Zhang et al. 2023). Furthermore, long reads are particularly advantageous for allele...
  8. Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
    • Alice S. Naftaly,
    • Shana Pau,
    • and Michael A. White
    Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
    ...that did not fall into these three regions. These uncategorized ncRNAs did not overlap with known ncRNAs but did overlap with other annotations.Many isoforms have sex-specific alternative splicingAlternative splicing plays a key role in increasing protein diversity using a limited number of genes. Isoforms...
  9. Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
    • Aditi Singh,
    • Lilia Häußermann,
    • Christiane Emmerich,
    • Emily Nischwitz,
    • Brandon K.B. Seah,
    • Falk Butter,
    • Mariusz Nowacki,
    • and Estienne C. Swart
    Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
    ...necessitating additional molecules for their removal.Paramecium germline-limited sequences are thought to be targeted by two small noncoding RNA classes: scnRNAs and iesRNAs. scnRNAs are produced by Dicer-like proteins Dcl2 and Dcl3 in the MICs and loaded on Piwi proteins Ptiwi01/09 and transported to the old...
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  10. Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
    • Heidi Dvinge,
    • Jamie Guenthoer,
    • Peggy L. Porter,
    • and Robert K. Bradley
    Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
    ...@wisc.edu, rbradley@fredhutch.orgAbstractAlternative splicing of pre-mRNAs plays a pivotal role during the establishment and maintenance of human cell types. Characterizing the trans-acting regulatory proteins that control alternative splicing has therefore been the focus of much research. Recent work has established...
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