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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...Corresponding authors: twang@wustl.edu, gzhao@wustl.eduAbstractFollowing amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs...
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Resource: Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear
- Henriëtte van Beijnum,
- Tim Koopmans,
- Antonio Tomasso,
- Vanessa Disela,
- Severin te Lindert,
- Jeroen Bakkers,
- Anna Alemany,
- Eugene Berezikov,
- and Kerstin Bartscherer
Genome Res. August 2023 33: 1424-1437; Published in Advance September 19, 2023, doi:10.1101/gr.277538.122
...gene vimentin (Vim) and annexin A1 (Anxa1), revealed expression patterns untypical for muscle cells (Supplemental Fig. S5B), indicating that the exclusion of the muscle gene set may have excluded genes outside of our target group.Next, we performed differential expression analysis with the remaining...
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LETTER: Expression Profiling and Comparative Genomics Identify a Conserved Regulatory Region Controlling Midline Expression in the Zebrafish Embryo
- Thomas Dickmeis,
- Charles Plessy,
- Sepand Rastegar,
- Pia Aanstad,
- Ralf Herwig,
- Frédéric Chalmel,
- Nadine Fischer,
- and Uwe Strähle
Genome Res. February 2004 14: 228-238; Published in Advance January 12, 2004, doi:10.1101/gr.1819204
...in genomes. We tested this approach to identify regulatory sequences that control expression in the midline of the zebrafish embryo. We first isolated a set of genes that are coexpressed in the midline of the zebrafish embryo during somitogenesis stages by gene array analysis and subsequent rescreens...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
..., the annexin genes anxa1a/anxa1b and anxa3a/anxa3b, the ATPase genes atp2a2a/ atp2a2b, and the calbindin 2 genes calb2/calb2l.Many other genes retained in duplicate in zebrafish have annotated functions during development and include, for example, fzd8a and fzd8b and otx1 and otx1lb. Expression localization...
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LETTER: Identification, Characterization, and Mapping of Expressed Sequence Tags from an Embryonic Zebrafish Heart cDNA Library
- Christopher Ton,
- David M. Hwang,
- Adam A. Dempsey,
- Hong-Chang Tang,
- Jennifer Yoon,
- Mindy Lim,
- John D. Mably,
- Mark C. Fishman,
- and Choong-Chin Liew
Genome Res. December 1, 2000 10: 1915-1927; doi:10.1101/gr.154000
...to be a rapid and economical approach by which to identify and characterize expressed genes. We generated 5102 ESTs from a 3-d-old embryonic zebrafish heart cDNA library. Of these, 57.6% matched to known genes, 14.2% matched only to other ESTs, and 27.8% showed no match to any ESTs or known genes. Clustering...
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LETTER: Evolution of the Neuropeptide Y Receptor Family: Gene and Chromosome Duplications Deduced from the Cloning and Mapping of the Five Receptor Subtype Genes in Pig
- Amanda Wraith,
- Anna Törnsten,
- Patrick Chardon,
- Ingrid Harbitz,
- Bhanu P. Chowdhary,
- Leif Andersson,
- Lars-Gustav Lundin,
- and Dan Larhammar
Genome Res. March 1, 2000 10: 302-310; doi:10.1101/gr.10.3.302
...genes were subsequently lost. An example of this type of gene loss was suggested for the teleost fish that have undergone a recent tetraploidization that resulted in seven Hox cluster chromosomes in the zebrafish, of which only four seem to remain in the puffer fish (Amores et al. 1998). The NPY...
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Resource: Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data
- Fabian A. Buske,
- Denis C. Bauer,
- John S. Mattick,
- and Timothy L. Bailey
Genome Res. July 2012 22: 1372-1381; Published in Advance May 1, 2012, doi:10.1101/gr.130237.111
...immediate off-targets (Table 1, column 12, x = 0). In less complex species, the number of genes lacking any unique TTSs rises above 30% (Table 1, column 9, x = 0), which could be due to the more compact gene encoding in these species, the smaller quantity of annotated RefSeq genes (14,482 in zebrafish...
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Research: Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
- Michael R. Tallack,
- Graham W. Magor,
- Benjamin Dartigues,
- Lei Sun,
- Stephen Huang,
- Jessica M. Fittock,
- Sally V. Fry,
- Evgeny A. Glazov,
- Timothy L. Bailey,
- and Andrew C. Perkins
Genome Res. December 2012 22: 2385-2398; Published in Advance July 26, 2012, doi:10.1101/gr.135707.111
...) regulates the development of erythroid cells from bi-potent progenitor cells via the transcriptional activation of a diverse set of genes. Mice lacking Klf1 die in utero prior to E15 from severe anemia due to the inadequate expression of genes controlling hemoglobin production, cell membrane...
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RESOURCE: The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes
- Bhanu P. Chowdhary,
- Terje Raudsepp,
- Srinivas R. Kata,
- Glenda Goh,
- Lee V. Millon,
- Veronica Allan,
- François Piumi,
- Gérard Guérin,
- June Swinburne,
- Matthew Binns,
- Teri L. Lear,
- Jim Mickelson,
- James Murray,
- Douglas F. Antczak,
- James E. Womack,
- and Loren C. Skow
Genome Res. April 1, 2003 13: 742-751; doi:10.1101/gr.917503
...over previous maps. With 69 new FISH assignments, a total of 253 cytogenetically mapped loci physically anchor the RH map to various chromosomal segments. Synteny assignments of 39 gene loci complemented the RH mapping of 27 genes. The results added 12 new loci to the horse gene map. Lastly, comparison...
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LETTER: Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation
- Natalia Martin,
- Satyakam Patel,
- and Julia A. Segre
Genome Res. December 2004 14: 2430-2438; doi:10.1101/gr.2709404
...genes or the flanking genes ( Loricrin and Involucrin ) in the zebrafish and pufferfish sequences. As expected, based on the shorter evolutionary distance between two rodents, comparing the mouse Sprr locus sequence with rat produced long blocks of conserved sequence with high percent similarity...

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