Searching journal content for articles similar to Fu et al. 26 (12): 1753.

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  1. 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
    ..., the poly(A) signal is an AAUAAA hexamer, but we recently found that the deeply branching eukaryote Giardia lamblia uses a distinct hexamer (AGURAA) and lacks any known auxiliary elements. Our discovery prompted us to explore the evolutionary dynamics of poly(A) signals and auxiliary elements...
  2. Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
    • Chenxin Li,
    • Hengping Xu,
    • Fang-Fang Fu,
    • Scott D. Russell,
    • Venkatesan Sundaresan,
    • and Jonathan I. Gent
    Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
    ...the proportion of differentially methylated regions (DMRs) in the CHH context between mature WT and drm2 embryo across 24-nt siRNA loci categories (Fig. 3E). Genome-wide, 39% of eligible loci (loci that had sufficient coverage to be included in DMR analysis) were hypomethylated for mCHH in the drm2 embryo...
  3. Research: Resetting of the 24-nt siRNA landscape in rice zygotes
    • Chenxin Li,
    • Jonathan I. Gent,
    • Hengping Xu,
    • Hong Fu,
    • Scott D. Russell,
    • and Venkatesan Sundaresan
    Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
    ...are relatively low (Anderson et al. 2017; Chen et al. 2017; Zhao et al. 2019).Along with dynamic changes in gene expression, epigenomic reprogramming has been observed during flowering plant reproduction. In rice and maize, the egg cell is ∼10 times larger than sperm in diameter and thus ∼1000 times larger than...
  4. Research: Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
    • Xiaochuan Liu,
    • Mainul Hoque,
    • Marc Larochelle,
    • Jean-François Lemay,
    • Nathan Yurko,
    • James L. Manley,
    • François Bachand,
    • and Bin Tian
    Genome Res. October 2017 27: 1685-1695; Published in Advance September 15, 2017, doi:10.1101/gr.222331.117
    ..., Greenberg ME. 2008. Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60: 1022–1038. Geisberg JV, Moqtaderi Z, Fan X, Ozsolak F, Struhl K. 2014. Global analysis of mRNA isoform half-lives reveals...
  5. 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 the different layers of the Circos plot and are ordered from outwards to inwards. 1, intron retention (IR); 2, multi-IR (MIR); 3, skipped exon (SKIP); 4, multiexon SKIP (MSKIP); 5, alternative exon 5′ (AE5′); 6, alternative exon 3′ (AE3′); 7, alternative transcription start (ATS); 8, alternative polyadenylation...
  6. Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
    • Tsung-Cheng Chang,
    • Mihaela Pertea,
    • Sungyul Lee,
    • Steven L. Salzberg,
    • and Joshua T. Mendell
    Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
    ...Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms Tsung-Cheng Chang 1 , Mihaela Pertea 2 , Sungyul Lee 1 , Steven L. Salzberg 2 , 3 and Joshua T. Mendell 1 , 4 , 5 1...
  7. 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
    ...al. 2007). Additional long-read sequencing of transcriptomes will help clarify how extensive alternative transcripts are among taxa.Sex chromosomes evolve sex-biased gene content owing to different selection pressures in males and females (Rice 1984). The X Chromosome is transmitted two...
  8. Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
    • Huan Wang,
    • Pil Joong Chung,
    • Jun Liu,
    • In-Cheol Jang,
    • Michelle J. Kean,
    • Jun Xu,
    • and Nam-Hai Chua
    Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
    ...Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis Huan Wang 1 , 4 , Pil Joong Chung 1 , 2 , 4 , Jun Liu 1 , In-Cheol Jang 1 , 3 , Michelle J. Kean 1 , Jun Xu...
  9. 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
    ...protein synthesis. Studies have uncovered a number of alternative translation initiation sites (TISs) in mammalian mRNAs and showed their roles in reshaping the proteome. However, the extent to which alternative TISs affect gene expression across plants remains largely unclear. Here, by profiling...
  10. Resource: Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
    • Nicolas J. Tourasse,
    • Jonathan R.M. Millet,
    • and Denis Dupuy
    Genome Res. December 2017 27: 2120-2128; Published in Advance October 31, 2017, doi:10.1101/gr.224626.117
    ...-splicing is strongly preferred when the closest exon is located either ∼50 or ∼100 nucleotides (nt) upstream of the acceptor site, thus confirming and refining the previously reported observations (Allen et al. 2011).Genome-wide quantitative visualization of differential exon usageFor each C. elegans gene, we...
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