Searching journal content for articles similar to Adai et al. 15 (1): 78.

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  1. Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
    • Juncheng Lin,
    • Fu-Yu Hung,
    • Congting Ye,
    • Liwei Hong,
    • Yuan-Hsin Shih,
    • Keqiang Wu,
    • and Qingshun Q. Li
    Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
    ....ResultsHDA6 affects mRNA 3′ end processingPAT-seq, which uniquely sequences the 3′ end of mRNA, was applied for Col-0 and HDA6 mutants to uncover the effect of HDA6 on polyadenylation of Arabidopsis. An overview of the experimental and computational analysis scheme is summarized in Supplemental Figure S1...
  2. Resource: High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis
    • Natalie W. Breakfield,
    • David L. Corcoran,
    • Jalean J. Petricka,
    • Jeffrey Shen,
    • Juthamas Sae-Seaw,
    • Ignacio Rubio-Somoza,
    • Detlef Weigel,
    • Uwe Ohler,
    • and Philip N. Benfey
    Genome Res. January 2012 22: 163-176; Published in Advance September 22, 2011, doi:10.1101/gr.123547.111
    ...High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis Natalie W. Breakfield 1 , 2 , 5 , 7 , David L. Corcoran 2 , 7 , Jalean J. Petricka 1 , 2 , Jeffrey Shen 2 , Juthamas Sae...
  3. Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
    • Seung Cho Lee,
    • Evan Ernst,
    • Benjamin Berube,
    • Filipe Borges,
    • Jean-Sebastien Parent,
    • Paul Ledon,
    • Andrea Schorn,
    • and Robert A. Martienssen
    Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
    ...(Creasey et al. 2014), and SISYPHUS LTRs were targeted by a single miRNA in the R region of the LTR. Consistent with this miRNA acting as a trigger, easiRNA accumulated along the length of the mRNA between the LTRs (Fig. 6B; Supplemental Table S4). In the case of EVADE, four miRNA were predicted to target...
  4. Research: Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
    • Hai-Xi Sun,
    • Yan Li,
    • Qi-Wen Niu,
    • and Nam-Hai Chua
    Genome Res. August 2017 27: 1427-1436; Published in Advance May 18, 2017, doi:10.1101/gr.218669.116
    ...that proliferating cells tend to express mRNAs with shortened 3′ UTRs and fewer miRNA target sites leading to increased protein production by these mRNAs (Sandberg et al. 2008). Therefore, we asked whether the extended 3′ UTRs havemoremiRNA target sites, and accordingly we predicted miRNA target sites (Wu et al...
  5. Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
    • Georg Zeller,
    • Richard M. Clark,
    • Korbinian Schneeberger,
    • Anja Bohlen,
    • Detlef Weigel,
    • and Gunnar Rätsch
    Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
    .... As our PR predictions have high specificity and sensitivity in noncoding regions, we also used PR content to assess sequence variation within and among micro-RNA (miRNA) genes, where comparatively little is known about within-species polymorphism. Among A. thaliana miRNAs with homologs in other species...
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  6. Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
    • Wei-Jen Chung,
    • Phaedra Agius,
    • Jakub O. Westholm,
    • Michael Chen,
    • Katsutomo Okamura,
    • Nicolas Robine,
    • Christina S. Leslie,
    • and Eric C. Lai
    Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
    .... Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a <8-kb region in C. elegans harboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent...
    OPEN ACCESS ARTICLE
  7. LETTER: Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana
    • Manpreet S. Katari,
    • Vivekanand Balija,
    • Richard K. Wilson,
    • Robert A. Martienssen,
    • and W. Richard McCombie
    Genome Res. April 2005 15: 496-504; doi:10.1101/gr.3239105
    ...). To accomplish this task, we need a complete set of genes and their correct gene structure. The current annotation of the Arabidopsis thaliana is composed of predictions from gene-finding programs, alignment of expressed sequences; ESTs (Expressed Sequenced Tags), and full-length cDNA clones ( Haas et al. 2002...
  8. Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
    ..., and Arabidopsis thaliana. It can further map annotation effectively across species pairs as far apart as mouse and rat or Drosophila melanogaster and Drosophila erecta.Recent advancements in sequencing technologies have resulted in an exponential increase in available assemblies. Long-read sequencing technology...
  9. Resource: The Proteome Folding Project: Proteome-scale prediction of structure and function
    • Kevin Drew,
    • Patrick Winters,
    • Glenn L. Butterfoss,
    • Viktors Berstis,
    • Keith Uplinger,
    • Jonathan Armstrong,
    • Michael Riffle,
    • Erik Schweighofer,
    • Bill Bovermann,
    • David R. Goodlett,
    • Trisha N. Davis,
    • Dennis Shasha,
    • Lars Malmström,
    • and Richard Bonneau
    Genome Res. November 2011 21: 1981-1994; Published in Advance August 8, 2011, doi:10.1101/gr.121475.111
    ...function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 s (including human, Arabidopsis...
    OPEN ACCESS ARTICLE
  10. LETTER: Evolution of Arabidopsis microRNA families through duplication events
    • Christopher Maher,
    • Lincoln Stein,
    • and Doreen Ware
    Genome Res. April 2006 16: 510-519; Published in Advance March 6, 2006, doi:10.1101/gr.4680506
    .... , Smith D. , Carrington J.C. , Kasschau K.D. ( 2005 ) ASRP: The Arabidopsis Small RNA Project Database. Nucleic Acids Res. 33 : D637 – D640 . ↵ Jones-Rhoades M.W. , Bartel D.P. ( 2004 ) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 : 787...
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