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Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
.... 2011, 2014; Pauli et al. 2012; Heyn et al. 2014). In part, this can be attributed to the use of short-read sequencing as the principal technology for understanding developmentally regulated genes expressed in the early embryo and for zebrafish transcriptome annotation (Pauli et al. 2012; Pruitt et al...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...been shown to be the source of new protein coding exons, RNA-binding motifs, and microRNA target sites (Lev-Maor et al. 2003; Zarnack et al. 2013; Petri et al. 2019; Cosby et al. 2021). Our analyses reveal that DNA transposon transcription is more often gene-dependent than retroelement transcription...
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Research: A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness
- A. Maxwell Burroughs,
- Yoshinari Ando,
- Michiel J.L. de Hoon,
- Yasuhiro Tomaru,
- Takahiro Nishibu,
- Ryo Ukekawa,
- Taku Funakoshi,
- Tsutomu Kurokawa,
- Harukazu Suzuki,
- Yoshihide Hayashizaki,
- and Carsten O. Daub
Genome Res. October 2010 20: 1398-1410; Published in Advance August 18, 2010, doi:10.1101/gr.106054.110
...These authors contributed equally to this work. Abstract Animal microRNA sequences are subject to 3′ nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates...
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Resource: A single-base resolution map of an archaeal transcriptome
- Omri Wurtzel,
- Rajat Sapra,
- Feng Chen,
- Yiwen Zhu,
- Blake A. Simmons,
- and Rotem Sorek
Genome Res. January 2010 20: 133-141; Published in Advance November 2, 2009, doi:10.1101/gr.100396.109
...Escherichia coli. Prog Mol Biol Transl Sci 85: 275–317. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. 2008. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 18: 957–964. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW...
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Research: Discovery of hundreds of mirtrons in mouse and human small RNA data
- Erik Ladewig,
- Katsutomo Okamura,
- Alex S. Flynt,
- Jakub O. Westholm,
- and Eric C. Lai
Genome Res. September 2012 22: 1634-1645; doi:10.1101/gr.133553.111
...al. 2009), these have mostly been superseded by deep sequencing. This is in large part due to the fact that effective computational methods rely on comparative genomics and are ill-suited to identify species-specific miRNAs with reasonable specificity and sensitivity. Another limitation...
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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
...substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mirtrons from...
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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...distribution across random sites in matched exons shown (red). (D) Frequency of CAGE tags mapping across microRNA hairpin with mature and star sequences indicated. 1640 Genome Research www..org Mercer et al. in the frequency of exonic CAGE tags relative to nonconserved sites, and account for;10.6% and 9.6%of...

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