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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
...on alternative AUG and nonAUG TIS recognition, the observations also found in a model species, Arabidopsis (Figs. 1⇑⇑–4). We identified CU-rich elements in plant mRNAs that promote translation initiation (Fig. 5) and were evolutionarily conversed for accurate TIS prediction within and across plant species...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...methylated promoters, which might have biased the discovery of proteins binding to these specific loci. In this study, we performed a DNA affinity pull-down experiment followed by mass spectrometry using DNA probes reflecting context-specific DNA methylation states in the Arabidopsis , resulting...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...of haplotype-resolved structural variation in human s. Nat Commun 10: 1784. doi:10.1038/s41467-018-08148-z ↵Chen L, Fish AE, Capra JA. 2018. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput Biol 14: e1006484. doi:10.1371/journal...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...These authors contributed equally to this work. Corresponding authors: wang_yu@nwafu.edu.cn, gaoyuanpeng1990@163.comAbstractUltraconserved elements (UCEs) are the most conserved regions among the s of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs...
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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
...such proximity might not be a prerequisite for intergenic CpG islands to act as alternative promoters to transcribe genes with silenced primary promoters, it does seem likely that it would be a preferred configuration. Finally, the CGIs associated with MethExp genes are evolutionarily much more conserved than...
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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...development of Hi-C and Hi-C-related techniques in recent years have led to the discovery of topologically associated domains (TADs), which are loop-like genomic structures characterized by extensive self-interaction. TADs are established through a dynamic interplay between CTCF and cohesin, influenced...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
.../intron inclusion and exclusion events, as well as by the use of alternative splice sites. The capacity of this gene to generate many alternative isoforms might be important for the ongoing arms race that characterizes the gene family.To quantify the isoform expression levels, we mapped the dRNA reads...
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Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- Kaia Mattioli,
- Pieter-Jan Volders,
- Chiara Gerhardinger,
- James C. Lee,
- Philipp G. Maass,
- Marta Melé,
- and John L. Rinn
Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
..., are evolutionarily conserved, and often comprised of two highly expressed individual core promoter sequences (Trinklein et al. 2004). It remains unclear, however, whether their high expression levels are a byproduct of having two promoters in close proximity or whether it is an inherent property of their DNA...
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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
...) (Supplemental Fig. S9); this proportion is comparable to that of Arabidopsis thaliana (Haudry et al. 2013). Because introns and UTRs have a wide range of conserved functional roles (e.g., to promote gene expression, guide splicing, produce noncoding RNA) (Greene et al. 1994; Akua et al. 2010; Chorev and Carmel...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...RNA targets through base-pairing of the miRNA seed region (miRNA nucleotides [nt] 2–8) and sites in mRNA 3′ untranslated regions (UTRs) (Bartel 2018). Each miRNA has many sites throughout the transcriptome, and more than 60% of human protein-coding genes have evolutionarily conserved sites to at least one...

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