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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
..., by adapting mRNA interactome capture to living zebrafish embryos at specific time points before and during ZGA. To determine the contribution of an identified mRNA interactome component—the known splicing factor Hnrnpa1—to the regulation of maternal and zygotic RNAs, individual nucleotide resolution...
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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
...extensively used to study embryonic development (Howe et al. 2013). The first stage of zebrafish development is characterized by rapid cleavage of the embryonic cells and is entirely driven by the maternally provided mRNA and proteins as the zygotic is transcriptionally inactive until about 3 h post...
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Resource: RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
- Meng How Tan,
- Kin Fai Au,
- Arielle L. Yablonovitch,
- Andrea E. Wills,
- Jason Chuang,
- Julie C. Baker,
- Wing Hung Wong,
- and Jin Billy Li
Genome Res. January 2013 23: 201-216; Published in Advance September 7, 2012, doi:10.1101/gr.141424.112
.... 2006); and the splicing machinery is not error-free (Hsu and Hertel 2009), thereby generating debate over the likelihood that stochastic noise contributes to much of the observed mRNA diversity arising from alternative splicing (Melamud and Moult 2009). To obtain an estimate of the percentage of novel...
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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
...preferentially accumulating the shortest isoform. Thus, in zebrafish ovaries and early embryo, APAmediated truncation of the papolb coding sequence acts concordantly with altered mRNA levels to shift productive expression nearly exclusively to the papolg homolog. Preferential loss of ovary transcripts with very...
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Research: Dynamic landscape of tandem 3′ UTRs during zebrafish development
- Yuxin Li,
- Yu Sun,
- Yonggui Fu,
- Mengzhen Li,
- Guangrui Huang,
- Chenxu Zhang,
- Jiahui Liang,
- Shengfeng Huang,
- Gaoyang Shen,
- Shaochun Yuan,
- Liangfu Chen,
- Shangwu Chen,
- and Anlong Xu
Genome Res. October 2012 22: 1899-1906; Published in Advance September 5, 2012, doi:10.1101/gr.128488.111
.... 30730089 to A.X.), Fundamental Research Funds for the Central Universities (to Y.F.), and the China Postdoctoral Science Foundation (no. 2012M511618 to Y.S.). References Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, Lee SG, Lim AY, Hajan HS, Collas P, Bourque G, et al. 2011. Zebrafish mRNA sequencing...
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Resource: Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
- Andrea Pauli,
- Eivind Valen,
- Michael F. Lin,
- Manuel Garber,
- Nadine L. Vastenhouw,
- Joshua Z. Levin,
- Lin Fan,
- Albin Sandelin,
- John L. Rinn,
- Aviv Regev,
- and Alexander F. Schier
Genome Res. March 2012 22: 577-591; Published in Advance November 22, 2011, doi:10.1101/gr.133009.111
...contributed equally to this work. Abstract Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the mouse have annotated lncRNAs expressed in cell lines and adult tissues...
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Research: DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation
- Joseph C. Siefert,
- Constantin Georgescu,
- Jonathan D. Wren,
- Amnon Koren,
- and Christopher L. Sansam
Genome Res. August 2017 27: 1406-1416; Published in Advance May 16, 2017, doi:10.1101/gr.218602.116
...and edited the manuscript. References AanesH,WinataCL, LinCH, Chen JP, SrinivasanKG, Lee SG, LimAY,Hajan HS, Collas P, Bourque G, et al. 2011. Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res 21: 1328–1338. Aday AW, Zhu LJ, Lakshmanan A...
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Method: MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq
- Jonathon T. Hill,
- Bradley L. Demarest,
- Brent W. Bisgrove,
- Bushra Gorsi,
- Yi-Chu Su,
- and H. Joseph Yost
Genome Res. April 2013 23: 687-697; Published in Advance January 8, 2013, doi:10.1101/gr.146936.112
...(0.98 cM) Hill et al. 692 Genome Research www..org PCR-based DNA sequencing confirmed the presence of a nonsense mutation in the ctr9 gene that appears to cause nonsense-mediated decay, and the ability to rescue themutant phenotype by injection of wild-type ctr9 mRNA confirmed ctr9 as the causative...
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