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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
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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
...-1, (UN2) unknown-2. (D) Genome browser views showing the aggregated and normalized snATAC-seq signals at promoter regions (±1 kb from transcription start site) of selected cell-type marker genes. Tracks are colored with the same color code as in B and C.After quality control, a total of 83,281 high...
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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
...for the study of vertebrate development, and over half of its consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data...
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Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
....View larger version: In this window In a new window Figure 6. Prominent mosquito piRNA cluster loci. (A) Genome browser snapshots of notably large piRNA Cluster Loci (piRCL) in mosquitoes. Genes and repeats (TEs) tracks are at the bottom of each snapshot. (B) A dynamically evolving Mosquito-Conserved pi...
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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
...in development. After augmenting the reference transcriptome with the NTRs discovered by long-read sequencing, we mapped short-read data (see Methods) to the augmented transcriptome. An NTR example of a UCSC Genome Browser track is shown in Supplemental Figure S1A (Kent et al. 2002). This example illustrates...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...Enabling functional genomics with genome engineering Isaac B. Hilton 1 , 2 and Charles A. Gersbach 1 , 2 , 3 1Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; 2Center for Genomic and Computational...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
..., USA; 4Department of Systems Biology, Columbia University, New York, New York 10032, USA; 5Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA; 6New York Genome Center, New York, New York 10013, USA; 7Department of Biological Sciences...
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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
...in zebrafish embryos Genome Research 1185 www..org of UV+ and UV− samples in two distinct clusters (Supplemental Fig. S1A,B; Supplemental Table S1). Furthermore, 200 and 247 proteins were quantified from at least two replicates in UV+ purifications, whereas 176 and 212 proteins were enriched in UV+ samples...
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Perspective: Defining cell types and states with single-cell genomics
- Cole Trapnell
Genome Res. October 2015 25: 1491-1498; doi:10.1101/gr.190595.115
...Defining cell types and states with single-cell genomics Cole Trapnell Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA Corresponding author: coletrap@uw.edu Abstract A revolution in cellular measurement...
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Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
...in the F1 generation by inbreeding founders, reducing the time needed for phenotyping screening by a generation (≈3–4 mo). Results Genome-wide identification of CRISPR targets To assist in the design of CRISPR targets in zebrafish,we produced a browser extensible data (BED) track computationally predicting...
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