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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
...that downstream alternative initiation is a strategy used in plants for achieving organ-specific targeting.Together our findings suggest that alternative translation initiation is an evolutionarily conserved strategy that generates different protein isoforms with diverse N termini to achieve the removal...
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Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- J. Omar Yáñez-Cuna,
- Huy Q. Dinh,
- Evgeny Z. Kvon,
- Daria Shlyueva,
- and Alexander Stark
Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
...predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes ( cis -regulatory signatures), which appear to be conserved during evolution. Taken together...
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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
...; Ricci et al. 2019), although not all cis-regulatory sequences are evolutionarily conserved (Ross et al. 1994; Wittkopp et al. 2002; McLean et al. 2011). We observed enrichment of lead eQTLs in CNS regions and association between CNS absence and gene expression (Fig. 5C,D). In terms of the regulation...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...inside a gene, but would code for a protein that does not correspond to any protein in the gene. Most likely, these ORFs were nested into an alternative frame of the main genic ORF. To avoid any bias, neORFs that emerged inside an exon were removed from the analysis in the study of synteny. Concerning ne...
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Research: Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
- Pieter Spealman,
- Armaghan W. Naik,
- Gemma E. May,
- Scott Kuersten,
- Lindsay Freeberg,
- Robert F. Murphy,
- and Joel McManus
Genome Res. February 2018 28: 214-222; Published in Advance December 18, 2017, doi:10.1101/gr.221507.117
...ORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs. Proc Natl Acad Sci 105: 10079–10084. ↵Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. 2011. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...), and mRNA processing ( Golovkin and Reddy 1996 ; Kalyna et al. 2006 ), and AS impacts many important plant process such as photosynthesis, defense response, flowering, and cereal grain quality (for review, see Reddy 2007 ). Conservation of alternatively spliced genes between evolutionarily distant plant...
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LETTER: Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
...site predictions and enumerate the target gene cohort. We show that it is possible to begin with a single biologically defined, evolutionarily conserved NRSF/ REST site, then use conservation among mouse, human, and dog s to develop a refined model for NRSF sites. The resulting model is compared...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...address this issue by developing deep learning models to deconvolute degenerate cis-regulatory elements and quantify their positional importance in mediating yeast poly(A) site formation, cleavage heterogeneity, and strength. In S. cerevisiae, cleavage heterogeneity is promoted by the depletion of U...
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Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- Danny Zeevi,
- Shai Lubliner,
- Maya Lotan-Pompan,
- Eran Hodis,
- Rita Vesterman,
- Adina Weinberger,
- and Eran Segal
Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
...protein (RP) promoters from nine different yeast species into S. cerevisiae and accurately measuring their activity. We found that orthologous RP promoters have extreme expression conservation even across evolutionarily distinct yeast species. Notably, our measurements reveal two distinct mechanisms...
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Research: Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality
- Daniel F. Simola,
- Lothar Wissler,
- Greg Donahue,
- Robert M. Waterhouse,
- Martin Helmkampf,
- Julien Roux,
- Sanne Nygaard,
- Karl M. Glastad,
- Darren E. Hagen,
- Lumi Viljakainen,
- Justin T. Reese,
- Brendan G. Hunt,
- Dan Graur,
- Eran Elhaik,
- Evgenia V. Kriventseva,
- Jiayu Wen,
- Brian J. Parker,
- Elizabeth Cash,
- Eyal Privman,
- Christopher P. Childers,
- Monica C. Muñoz-Torres,
- Jacobus J. Boomsma,
- Erich Bornberg-Bauer,
- Cameron R. Currie,
- Christine G. Elsik,
- Garret Suen,
- Michael A.D. Goodisman,
- Laurent Keller,
- Jürgen Liebig,
- Alan Rawls,
- Danny Reinberg,
- Chris D. Smith,
- Chris R. Smith,
- Neil Tsutsui,
- Yannick Wurm,
- Evgeny M. Zdobnov,
- Shelley L. Berger,
- and Jürgen Gadau
Genome Res. August 2013 23: 1235-1247; Published in Advance May 1, 2013, doi:10.1101/gr.155408.113
...ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying...

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