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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...also helped characterize novel cis-regulatory DNA elements and their combined effects in regulating transcription and associating genetic variation with differential gene expression and phenotypic diversity (Azodi et al. 2020a,b). Therefore, integrating high-throughput translation initiation sequencing...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...Studies examining how evolutionary forces mold the genomic TE-landscape underscore the significant role of purifying selection in limiting TE accumulation within protein-coding gene sequences (Bartolomé et al. 2002; Rizzon et al. 2003), but also in noncoding regions (Hollister and Gaut 2009; Bergthorsson et al...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...al. 2012; Fueyo et al. 2022). TE coding sequences give rise to alterations in host gene expression (Babarinde et al. 2021) by encoding transposases and transcription factors, etc. (Joly-Lopez and Bureau 2018). A plethora of instances have shown that TE insertions with regulatory functions...
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Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
...for AT composition) (Supplemental Fig. S4). Altogether, maize R-loops showed conserved sequence characters compared with those in humans and Arabidopsis (Ginno et al. 2012; Xu et al. 2017).In our data, we identified numerous antisense R-loops in the maize , even more than sense R-loops (Supplemental Fig. S5A,B). We...
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Research: Regulatory modules controlling maize inflorescence architecture
- Andrea L. Eveland,
- Alexander Goldshmidt,
- Michael Pautler,
- Kengo Morohashi,
- Christophe Liseron-Monfils,
- Michael W. Lewis,
- Sunita Kumari,
- Susumu Hiraga,
- Fang Yang,
- Erica Unger-Wallace,
- Andrew Olson,
- Sarah Hake,
- Erik Vollbrecht,
- Erich Grotewold,
- Doreen Ware,
- and David Jackson
Genome Res. March 2014 24: 431-443; Published in Advance December 4, 2013, doi:10.1101/gr.166397.113
...cereal and bioenergy crops (Vollbrecht et al. 2005; Doust 2007). While classical genetics has uncovered regulators of maize inflorescence architecture (Vollbrecht and Schmidt 2009), the molecular mechanisms and gene regulatory networks underlying this grass-specific morphology remain elusive. Branching...
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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
...Table S4; Supplemental Figs. S7, S8). The four assemblies showed similar numbers (around 20,000) of annotated protein-coding genes, with an average length of ∼47.89 kb for a gene, ∼1645.20 bp for a coding sequence, and ∼176.88 bp for an exon (Supplemental Table S5). Additionally, we predicted a number...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
...in the maize apex, a pipeline was produced implementing the TargetFinder tool and degradome (PARE) analysis, which assesses enrichment of 5′ uncapped transcript ends at the predicted cleavage site over chance occurrence (Methods). Altogether, 106 target genes were identified, 104 of which are conserved...
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Resource: A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing
- Bo Wang,
- Michael Regulski,
- Elizabeth Tseng,
- Andrew Olson,
- Sara Goodwin,
- W. Richard McCombie,
- and Doreen Ware
Genome Res. June 2018 28: 921-932; Published in Advance April 30, 2018, doi:10.1101/gr.227462.117
...rapidly in humans. Nature 443: 167–172. Pophaly SD, Tellier A. 2015. Population level purifying selection and gene expression shape sub evolution in maize. Mol Biol Evol 32: 3226–3235. Prabhakar S, Noonan JP, Pääbo S, Rubin EM. 2006. Accelerated evolution of conserved noncoding sequences in humans...
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Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
- Ya-Ru Li and
- Ming-Jung Liu
Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
...-AUG TISs, a phenomenon also found in mammals. In addition, although alternative TISs were usually found in both orthologous genes, the TIS sequences were not conserved, suggesting the conservation of alternative initiation mechanisms but flexibility in using TISs. Unlike upstream AUG TISs, the presence...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
..., in the current study we have taken advantage of the specific capture of H3K27me3-labeled chromatin loops to provide evidence of the role of this covalent histone modification in the spatial organization of chromatin. A similar approach has been used in maize to identify cis-regulatory elements, revealing that H3...

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