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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: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...in populations and determine their degree of evolutionary conservation over time.In this study, we identified the exonized L1 elements that give rise to ORF1p fusion proteins and are evolutionarily conserved in vertebrate s for periods ranging from tens of millions to more than 280 million years. These findings...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...timeframe for appearance of RIDLs is consistent with the wide diversity of TE types, from ancient MIR elements to presently active LINE-1 (Jurka et al. 1995; Konkel et al. 2010; Smith et al. 2013).Instances of genomic TE insertions typically represent a fragment of the full consensus sequence. We...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...of these incipient de novo genes with the dominance of ancient gene families in individual s. Here, we test this rapid turnover hypothesis in the context of the nematode model organism Pristionchus pacificus. We extended the existing species-level phylogenomic framework by sequencing the s of six divergent P...
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Research: Comparative transcriptomics of primary cells in vertebrates
- Tanvir Alam,
- Saumya Agrawal,
- Jessica Severin,
- Robert S. Young,
- Robin Andersson,
- Erik Arner,
- Akira Hasegawa,
- Marina Lizio,
- Jordan A. Ramilowski,
- Imad Abugessaisa,
- Yuri Ishizu,
- Shohei Noma,
- Hiroshi Tarui,
- Martin S. Taylor,
- Timo Lassmann,
- Masayoshi Itoh,
- Takeya Kasukawa,
- Hideya Kawaji,
- Luigi Marchionni,
- Guojun Sheng,
- Alistair R.R. Forrest,
- Levon M. Khachigian,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Michiel J.L. de Hoon
Genome Res. July 2020 30: 951-961; Published in Advance July 27, 2020, doi:10.1101/gr.255679.119
...the dominant promoter did not have an orthologous region (Fisher combined P < 10−100) (Supplemental Figs. S7, S8), as well as for evolutionarily ancient genes compared to recent genes (Fisher combined P < 10−100) (Supplemental Figs. S9, S10). A Gene Ontology analysis of correlation values again showed...
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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
...identified evolutionarily conserved elements (ECEs) in vocal nonlearning birds using phastCons (most-conserved criterion; PHAST v1.4) (Siepel et al. 2005). After filtering regions with ambiguous orthology between chicken and vocal learners, we retained 276,412 ECEs of at least 100 bp, spanning a combined 51...
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Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
- Leeban Yusuf,
- Matthew C. Heatley,
- Joseph P.G. Palmer,
- Henry J. Barton,
- Christopher R. Cooney,
- and Toni I. Gossmann
Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
...to noncoding regions that are specific to birds or highly divergent relative to vertebrates (Seki et al. 2017). Whether anciently conserved elements, such as vertebrate specific regulatory regions (Lowe et al. 2015), may play a role in avian beak shape remains an open question. Equally, because the noncoding...
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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
...An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement Ignacio Maeso 1 , 6 , 8 , 9 , Manuel Irimia 1 , 7 , 8 , 9 , Juan J. Tena 2 , 8 , Esther González-Pérez 3 , 8...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
.... Ancient transposable elements transformed the uterine regulatory landscape and transcriptome...
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