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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...with varied number of vertebrae and validated the causal mutation by whole- association analysis. We verified its function using CRISPR-Cas9 editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other...
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Perspective: Diversifying the genomic data science research community
- The Genomic Data Science Community Network
Genome Res. July 2022 32: 1231-1241; Published in Advance July 20, 2022, doi:10.1101/gr.276496.121
...Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES; https://seaphages.org/) network is both an inclusive research education community and the developer of the two-term laboratory CURE studying viral diversity, evolution, annotation, and bioinformatic analyses (Jordan et al. 2014...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...enabled functional annotation of genomic regions (The ENCODE Project Consortium 2012; Roadmap Epigenomics Consortium et al. 2015; Bujold et al. 2016; Dekker et al. 2017). Based on whole- alignment between species, orthologous regions can be directly compared, and insights on the conservation...
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Research: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification
- Megan Rothstein and
- Marcos Simoes-Costa
Genome Res. January 2020 30: 35-48; Published in Advance December 17, 2019, doi:10.1101/gr.249680.119
...development. Our results show that TFAP2A activates distinct sets of genomic regions during induction of the neural plate border and specification of neural crest cells. Genomic occupancy analysis revealed that the repertoire of TFAP2A targets depends upon its dimerization with paralogous proteins TFAP2C...
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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
...), was discovered as a specific marker of the neural crest (Rubinstein et al. 2000; Luo et al. 2001). Despite these observations, BHIKHARI elements have not been characterized further, and there is a general dearth of information regarding the genomic characteristics and expression of individual TE families...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian structure and sex chromosomes in three...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
..., Santa Cruz, California 95064, USA; 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; 4Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Corresponding authors: jcahill@rockefeller.edu, ejarvis@rockefeller.eduAbstractVocal learning, the ability...
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Research: Birth, evolution, and transmission of satellite-free mammalian centromeric domains
- Solomon G. Nergadze,
- Francesca M. Piras,
- Riccardo Gamba,
- Marco Corbo,
- Federico Cerutti,
- Joseph G.W. McCarter,
- Eleonora Cappelletti,
- Francesco Gozzo,
- Rebecca M. Harman,
- Douglas F. Antczak,
- Donald Miller,
- Maren Scharfe,
- Giulio Pavesi,
- Elena Raimondi,
- Kevin F. Sullivan,
- and Elena Giulotto
Genome Res. June 2018 28: 789-799; Published in Advance April 30, 2018, doi:10.1101/gr.231159.117
...) or with a CREST serum (green). Peak overlapping appears in yellow. The y-axis reports the normalized read counts, whereas the x-axis reports the genomic coordinates (Mb). The E. caballus satellite-free centromere from Chromosome 11 (A) and the 16 satellite-free E. asinus centromeres (B) are shown; for each E...
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Research: Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network
- Marcos Simões-Costa,
- Joanne Tan-Cabugao,
- Igor Antoshechkin,
- Tatjana Sauka-Spengler,
- and Marianne E. Bronner
Genome Res. February 2014 24: 281-290; Published in Advance January 3, 2014, doi:10.1101/gr.161182.113
...embryo. Methods Cell Biol 87: 237–256. Sauka-Spengler T, Bronner-Fraser M. 2008. A gene regulatory network orchestrates neural crest formation. Nat Rev Mol Cell Biol 9: 557–568. Simo˜es-Costa M, Bronner M. 2013. Insights into neural crest development and evolution from genomic analysis. Genome Res 23...
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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
...2 functional genomics approaches to identify highly conserved endodermal cis-regulatory 30 modules (CRMs) functioning across the 400 million years of evolution separating zebrafish 31 and humans. Our analyses suggest that there are few endoderm-specific CRMs, with many 32 CRMs governing pancreas...
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