Searching journal content for articles similar to Kikuta et al. 17 (5): 545.

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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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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...formation within PSM. Furthermore, SE sequences showed higher enrichment for conserved DNA elements across 103 mammalian species from the Ensembl database compared to TEs (Supplemental Fig. S3E). Previous studies have highlighted the importance of conserved noncoding DNA elements in vertebrate development...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...that the remaining Hox genes maintain physical association in three dimensions and are thus under conserved regulation (Krefting et al. 2018). Similarly, although the ro gene has moved to be adjacent to the rest of the Hox cluster, it has not been encompassed within the same TAD. Consistent with this conclusion...
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12 Drosophila Genomes/Letter: Genomic regulatory blocks underlie extensive microsynteny conservation in insects
- Pär G. Engström,
- Shannan J. Ho Sui,
- Øyvind Drivenes,
- Thomas S. Becker,
- and Boris Lenhard
Genome Res. December 2007 17: 1898-1908; Published in Advance November 7, 2007, doi:10.1101/gr.6669607
...“genomic regulatory blocks” (GRBs) and found GRBs to correspond to the longest regions of conserved gene order across vertebrate s. In this paper, we use the term “microsynteny conservation” to denote the preservation of close proximity among genes through evolution, and we refer to chromosomal regions...
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Resource: Automated identification of conserved synteny after whole-genome duplication
- Julian M. Catchen,
- John S. Conery,
- and John H. Postlethwait
Genome Res. August 2009 19: 1497-1505; Published in Advance May 22, 2009, doi:10.1101/gr.090480.108
...duplication events can cause anciently related homologs to appear in some assays as orthologs. Conserved synteny—the tendency of neighboring genes to retain their relative positions and orders on chromosomes over evolutionary time—can help resolve such errors. Several previous studies examined genome...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
..., Toronto, Ontario, Canada M5S 3E1. ↵ 8 These authors contributed equally to this work. Abstract Developmental genes are regulated by complex, distantly located cis -regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates...
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Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...Genome-wide identification of conserved regulatory function in diverged sequences Leila Taher 1 , David M. McGaughey 2 , Samantha Maragh 2 , 3 , Ivy Aneas 4 , Seneca L. Bessling 2 , Webb Miller 5 , Marcelo A. Nobrega 4...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...in transgenic zebrafish assays—including examples from vertebrates and amphioxus—and find that the majority are functional enhancers. We find that PCNEs are enriched around genes with ancient synteny conservation, and that this association is strongest for extragenic PCNEs, suggesting that cis -regulatory...
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Research: Functional and topological characteristics of mammalian regulatory domains
- Orsolya Symmons,
- Veli Vural Uslu,
- Taro Tsujimura,
- Sandra Ruf,
- Sonya Nassari,
- Wibke Schwarzer,
- Laurence Ettwiller,
- and François Spitz
Genome Res. March 2014 24: 390-400; Published in Advance January 7, 2014, doi:10.1101/gr.163519.113
...described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within...
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Method: Discovery and assessment of conserved Pax6 target genes and enhancers
- Pedro Coutinho,
- Sofia Pavlou,
- Shipra Bhatia,
- Kevin J. Chalmers,
- Dirk A. Kleinjan,
- and Veronica van Heyningen
Genome Res. August 2011 21: 1349-1359; Published in Advance May 26, 2011, doi:10.1101/gr.124115.111
...Shipra, Bhatia Dirk A Kleinjan Veronica Coutinho, P Pedro, Coutinho Kevin J Chalmers, Kevin J Kleinjan van Heyningen, V DirkA Kleinjan Chalmers, K.J DA Kleinjan 1088-9051 genome;gr.124115.111 10.1101/gr.124115.111 Discovery and assessment of conserved Pax6 target genes and enhancers Method Discovery...

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