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Resource: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
- Chirag Nepal,
- Yavor Hadzhiev,
- Christopher Previti,
- Vanja Haberle,
- Nan Li,
- Hazuki Takahashi,
- Ana Maria M. Suzuki,
- Ying Sheng,
- Rehab F. Abdelhamid,
- Santosh Anand,
- Jochen Gehrig,
- Altuna Akalin,
- Christel E.M. Kockx,
- Antoine A.J. van der Sloot,
- Wilfred F.J. van IJcken,
- Olivier Armant,
- Sepand Rastegar,
- Craig Watson,
- Uwe Strähle,
- Elia Stupka,
- Piero Carninci,
- Boris Lenhard,
- and Ferenc Müller
Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112
...-seq supports the bulk of transcripts detectable in embryogenesis, improves preFigure 1. Mapping of transcription initiation in zebrafish embryo development. (A–C ) Genome browser view of ncalda gene with CAGE-seq, ChIP-seq, and RNA-seq tracks from selected developmental stages. Schematic representation...
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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
...% of zebrafish genes. Comparison of the patterns of 39 end usage in different stages revealed several significant trends, such as the usage of shorter 39 UTRs in the ovaries, preferential depletion of short 39 UTRs in the early embryo, and widespread polyadenylation at noncanonical sites, which appears to occur...
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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
...). Based on integrative analysis of EST, SAGE, and microarray data, tandem 39 UTR lengthening has been observed during mouse embryogenesis ( Ji et al. 2009). However, the specific genes directly regulated by APA during vertebrate development remain unknown. Several high-throughput sequencing methods have...
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LETTER: Genetic variation in the zebrafish
- Victor Guryev,
- Marco J. Koudijs,
- Eugene Berezikov,
- Stephen L. Johnson,
- Ronald H.A. Plasterk,
- Fredericus J.M. van Eeden,
- and Edwin Cuppen
Genome Res. April 2006 16: 491-497; Published in Advance March 13, 2006, doi:10.1101/gr.4791006
.... , Eun A. , He Y. , Ma W. , Wang W. , Wen Z. , et al. ( 2003 ) 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res. 13 : 455 – 466 . ↵ Moriyama E.N. , Powell F.R. ( 1996 ) Intraspecific nuclear DNA variation...
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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
...this potential variability, we show many of the Iso-Seq TSSs were accurate, confirmed by patterns of accessible chromatin from ATAC-seq. Correct TSSs/TTSs are particularly important for future work in threespine stickleback fish in understanding gene regulation. Additional work mapping accessible chromatin...
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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
...found that 24% of them (or 36 genes) are also activated prior to themidblastula transition in zebrafish (Aanes et al. 2011). The list of 150 genes, together with their expression profiles and associated GO terms, are provided in Supplemental File S4. We used quantitative real-time PCR (RT...
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PERSPECTIVE: Xenomics
- Enrique Amaya
Genome Res. December 2005 15: 1683-1691; doi:10.1101/gr.3801805
...is now available, in the form of ESTs in both X. laevis and X. tropicalis , as well as sequence information in the case of X. tropicalis . Therefore, in the next phase of screens, it would seem prudent to use a unique set of genes, rather than randomly selected clones for the screen. The Ueno group...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...the author’s laboratory) to establish a comprehensive EST database via analysis of mRNAs from a broad range of opossum tissues and life stages that can be used to seek novel opossum transcripts, augment and refine the current annotation, and guide the design of basic gene-expression microarrays for -wide...
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REVIEW: Functional Genomics in the Mouse: Phenotype-Based Mutagenesis Screens
- John Schimenti and
- Maja Bucan
Genome Res. July 1, 1998 8: 698-710; doi:10.1101/gr.8.7.698
...if expression profiles were available on all the ESTs. “The joy of screening” will come not only from finding new interesting phenotypes, but from the knowledge that the genes responsible for these phenotypes have been isolated already. Acknowledgments We thank members of our laboratories and many colleagues...

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