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  1. Research: Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements
    • Joanne L. Harding,
    • Stuart Horswell,
    • Claire Heliot,
    • Javier Armisen,
    • Lyle B. Zimmerman,
    • Nicholas M. Luscombe,
    • Eric A. Miska,
    • and Caroline S. Hill
    Genome Res. January 2014 24: 96-106; Published in Advance September 24, 2013, doi:10.1101/gr.144469.112
    ...regulators of gene expression, both at the post-transcriptional and epigenetic level. Based on biogenesis criteria, there are three main classes of small RNAs: small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs), although small RNAs with novel functions continue...
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  2. Letter: Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis
    • Javier Armisen,
    • Michael J. Gilchrist,
    • Anna Wilczynska,
    • Nancy Standart,
    • and Eric A. Miska
    Genome Res. October 2009 19: 1766-1775; Published in Advance July 23, 2009, doi:10.1101/gr.093054.109
    ...of oogenesis. Small RNAs were size-selected and resolved on polyacrylamide gels (Supplemental Fig. S1). We observed a strikingly similar pattern of small RNAs in the different oogenic stages in X. tropicalis and X. laevis, where short ;22, ;24, and ;30 nt RNAs were most abundant. Given the known sizes of microRNAs...
  3. Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
    • Pauliina Paloviita,
    • Christel Hydén-Granskog,
    • Dawit A. Yohannes,
    • Priit Paluoja,
    • Juha Kere,
    • Juha S. Tapanainen,
    • Kaarel Krjutškov,
    • Timo Tuuri,
    • Urmo Võsa,
    • and Sanna Vuoristo
    Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
    ...RNAs in human oocytes and early embryos using an RNA-sequencing (RNA-seq) method suitable for low inputs of material. We show that OET in humans is temporally coupled with the transition from predominant expression of oocyte short piRNAs (os-piRNAs) in oocytes, to activation of microRNA (miRNA) expression...
  4. Resource: Extensive alternative polyadenylation during zebrafish development
    • Igor Ulitsky,
    • Alena Shkumatava,
    • Calvin H. Jan,
    • Alexander O. Subtelny,
    • David Koppstein,
    • George W. Bell,
    • Hazel Sive,
    • and David P. Bartel
    Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
    ..., such as targeting by microRNAs (miRNAs), has been hindered by incomplete 39UTR annotation. In version 66 of Ensembl zebrafish genes (Feb. 2012), only 64.4% of the transcriptmodels have any 39UTR annotation, and only 28.9% of the genes havemore than one annotated 39 end. By comparison, over 96% of the human genes...
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  5. Letter: Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard
    • Nicolas Di-Poï,
    • Juan I. Montoya-Burgos,
    • and Denis Duboule
    Genome Res. April 2009 19: 602-610; Published in Advance February 18, 2009, doi:10.1101/gr.087932.108
    .... ( 2006 ) A role for endogenous reverse transcriptase in tumorigenesis and as a target in differentiating cancer therapy . Genes Chromosomes Cancer 45 : 1 – 10 . ↵ Tanzer, A. , Amemiya, C.T. , Kim, C.B. , Stadler, P.F. ( 2005 ) Evolution of microRNAs located within Hox gene clusters . J. Exp. Zoolog. B...
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