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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...of a transposable element (TE) for the divergent function of gsdfY. By insertion within the gsdfY promoter region, this TE generated allelic diversification by bringing cis-regulatory modules that led to transcriptional rewiring and thus creation of a new MSD gene. This points out, for the first time...
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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
.... 2014; Machado et al. 2016; Sackton et al. 2019). Thus, relatively little is currently known about the genetics underpinning the macroevolution of beak shape. The current lack of insight connecting species or clade-specific candidate genes to large-scale evolutionary time may be explained by two main...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...–specific activation of TE-derived alternative promoters driving the expression of neurogenesis-associated genes. Long-read sequencing confirmed these TE-driven isoforms as significant contributors to neurogenic transcripts. We also show experimentally that a co-opted antisense L2 element drives temporal protein...
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LETTER: Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters
- Daehyun Baek,
- Colleen Davis,
- Brent Ewing,
- David Gordon,
- and Phil Green
Genome Res. February 2007 17: 145-155; Published in Advance January 8, 2007, doi:10.1101/gr.5872707
.... ↵ Kimura, K. , Wakamatsu, A. , Suzuki, Y. , Ota, T. , Nishikawa, T. , Yamashita, R. , Yamamoto, J. , Sekine, M. , Tsuritani, K. , Wakaguri, H. , et al. ( 2006 ) Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes...
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LETTER: Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes
- Katsuki Tsuritani,
- Takuma Irie,
- Riu Yamashita,
- Yuta Sakakibara,
- Hiroyuki Wakaguri,
- Akinori Kanai,
- Junko Mizushima-Sugano,
- Sumio Sugano,
- Kenta Nakai,
- and Yutaka Suzuki
Genome Res. July 2007 17: 1005-1014; Published in Advance June 13, 2007, doi:10.1101/gr.6030107
...revealed that the majority of human genes are subject to regulation of alternative promoters, the biological relevance of this phenomenon remains unclear. We have also demonstrated that roughly half of the human RefSeq genes examined contain putative alternative promoters (PAPs). Here we report large-scale...
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Resource: Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
- Riu Yamashita,
- Nuankanya P. Sathira,
- Akinori Kanai,
- Kousuke Tanimoto,
- Takako Arauchi,
- Yoshiaki Tanaka,
- Shin-ichi Hashimoto,
- Sumio Sugano,
- Kenta Nakai,
- and Yutaka Suzuki
Genome Res. May 2011 21: 775-789; Published in Advance March 3, 2011, doi:10.1101/gr.110254.110
...(Keene 2007). Further systematic analysis of the TSS-seq and RNA-seq data should also be useful for examining post-transcriptional expression regulation, about which relatively little knowledge has been accumulated. Possible functions of putative alternative promoters We attempted to infer possible...
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Research: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
- Sharmistha Pal,
- Ravi Gupta,
- Hyunsoo Kim,
- Priyankara Wickramasinghe,
- Valérie Baubet,
- Louise C. Showe,
- Nadia Dahmane,
- and Ramana V. Davuluri
Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
...for understanding the isoform-specific functions of a gene and identification of disease-relevant gene isoforms from bystander alternative forms of a gene. The role of alternative promoter is particularly critical in transcriptional regulation, since their precise utilization allows the balanced expression...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...of euchromatic regions and facilitates transcription elongation. In contrast, Ash1-mediated H3K36me3 localizes to promoters within facultative heterochromatin and represses transcription. Notably, Ash1-mediated H3K36me3 cooperates with Polycomb repressive complex 2 (PRC2)-dependent H3K27me3 to silence secondary...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
...Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles Jianbin Wang 1 , Benjamin Czech 2 , Amanda Crunk 1 , Adam Wallace 1 , Makedonka Mitreva 3 , Gregory...
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Method: High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- Philippe Batut,
- Alexander Dobin,
- Charles Plessy,
- Piero Carninci,
- and Thomas R. Gingeras
Genome Res. January 2013 23: 169-180; Published in Advance August 30, 2012, doi:10.1101/gr.139618.112
...). The regulatory blueprints that orchestrate the spatiotemporal dynamics of eukaryotic transcriptomes mirror this complexity. Large-scale surveys of chromatin modifications and transcription factor occupancy in diverse organisms have started to shed light on the abundance of cis-regulatory modules (Ernst et al...

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