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  1. Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
    • Fu-Yuan Zhu,
    • Xin Chen,
    • Yu-Chen Song,
    • Lydia Pui Ying Lam,
    • Yuki Tobimatsu,
    • Bei Gao,
    • Mo-Xian Chen,
    • and Fu-Liang Cao
    Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
    ...to other plants, is needed.In the transcriptomic landscape, alternative splicing (AS) is regarded as an important mechanism for increasing the coding capacity of s (James et al. 2012; Rühl et al. 2012). Its identification and characterization in plants are widely considered a milestone to understanding...
  2. Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
    • Mattia Furlan,
    • Eugenia Galeota,
    • Nunzio Del Gaudio,
    • Erik Dassi,
    • Michele Caselle,
    • Stefano de Pretis,
    • and Mattia Pelizzola
    Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
    ...steady-state RNA dynamics. SnapShot-Seq enables the inference of splicing kinetics by the differential coverage that introns have in their 5′ and 3′ ends, whereas this is not amenable for gene-level analyses (Gray et al. 2014). Alternatively, by assuming invariant splicing kinetics SnapShot-Seq allows...
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  3. 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
    ...(fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here...
  4. 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
    ...accurately detect all isoforms. To detect all splice junctions among alternative isoforms, there must be sufficient read depth at alternative exon–exon boundaries (Bryant et al. 2012; Steijger et al. 2013). For experiments with insufficient read coverage, lowly expressed isoforms are challenging to recover...
  5. Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
    • Ya-Ru Li and
    • Ming-Jung Liu
    Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
    ...start sites in plants and mammals, suggesting biased utilization of specific near-cognate codons as TIS codons.Characteristics of near-cognate start sitesWe showed that alternative TISs occurred in both 5′ UTR and CDS regions for several individual genes (Fig. 2C). In addition, global analyses...
  6. Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Sergei A. Filichkin,
    • Henry D. Priest,
    • Scott A. Givan,
    • Rongkun Shen,
    • Douglas W. Bryant,
    • Samuel E. Fox,
    • Weng-Keen Wong,
    • and Todd C. Mockler
    Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
    ...Genome-wide mapping of alternative splicing in Arabidopsis thaliana Sergei A. Filichkin 1 , Henry D. Priest 1 , Scott A. Givan 1 , Rongkun Shen 1 , 3 , Douglas W. Bryant 1 , 2 , Samuel E. Fox 1 , Weng-Keen Wong 2...
  7. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...Accurate typing of short tandem repeats from genome-wide sequencing data and its applications Arkarachai Fungtammasan 1 , 2 , 3 , 4 , 8 , Guruprasad Ananda 1 , 3 , 4 , 5 , 8 , 9 , Suzanne E. Hile 3 , 6 , Marcia Shu-Wei Su 2 , 3...
  8. Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
    • Xin Li,
    • San-Gang He,
    • Wen-Rong Li,
    • Ling-Yun Luo,
    • Ze Yan,
    • Dong-Xin Mo,
    • Xing Wan,
    • Feng-Hua Lv,
    • Ji Yang,
    • Ya-Xi Xu,
    • Juan Deng,
    • Qiang-Hui Zhu,
    • Xing-Long Xie,
    • Song-Song Xu,
    • Chen-Xi Liu,
    • Xin-Rong Peng,
    • Bin Han,
    • Zhong-Hui Li,
    • Lei Chen,
    • Jian-Lin Han,
    • Xue-Zhi Ding,
    • Renqing Dingkao,
    • Yue-Feng Chu,
    • Jin-Yan Wu,
    • Li-Min Wang,
    • Ping Zhou,
    • Ming-Jun Liu,
    • and Meng-Hua Li
    Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
    ...-copy orthologous genes. Numbers in green to the right of nodes are the divergence times and their 95% confidence intervals (95% CIs). Values next to the branches represent the numbers of gene family expansions/contractions. (MYA) Million years ago. (G) Genome-wide syntenic relationship among goat (C. hircus...
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  9. Resource: Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
    • Angela N. Brooks,
    • Michael O. Duff,
    • Gemma May,
    • Li Yang,
    • Mohan Bolisetty,
    • Jane Landolin,
    • Ken Wan,
    • Jeremy Sandler,
    • Benjamin W. Booth,
    • Susan E. Celniker,
    • Brenton R. Graveley,
    • and Steven E. Brenner
    Genome Res. November 2015 25: 1771-1780; Published in Advance August 20, 2015, doi:10.1101/gr.192518.115
    .... 2005. Global analysis of positive and negative pre-mRNA splicing regulators inDrosophila.Genes Dev 19: 1306–1314. BlanchetteM,Green RE,MacArthur S, Brooks AN, Brenner SE, EisenMB, Rio DC. 2009. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of theDrosophila hn...
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  10. Research: Genome-wide analysis of long noncoding RNA stability
    • Michael B. Clark,
    • Rebecca L. Johnston,
    • Mario Inostroza-Ponta,
    • Archa H. Fox,
    • Ellen Fortini,
    • Pablo Moscato,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. May 2012 22: 885-898; Published in Advance March 9, 2012, doi:10.1101/gr.131037.111
    ...loci. This is useful as such loci can contain numerous overlapping transcripts with alternative splice sites and varying start and end positions, which can be very challenging to distinguish. We searched the four most populous super-clusters (0, 1, 3, and 5, containing 94% of clustered probes...
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