Searching journal content for articles similar to Oyama et al. 14 (10b): 2048.

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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
...the similarity of the translation initiation regulation in both species. To characterize the CU-rich elements in plant mRNAs, we swapped the TIS upstream regions between WT and mCU mutants from the 5′ to 3′ end in the 5′ UTR–AUG TIS of Solyc03g096920.3.1 (Fig. 5C). The protein signals of the GFP reporter were...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...(Prabakaran et al. 2014; Plaza et al. 2017; Brunet et al. 2018).Based on their genomic location and their size, these unannotated ORFs have been defined in numerous ways including as short ORFs (sORFs), small ORFs (smORFs), alternative ORFs (altORFs), and upstream/downstream ORFs (u/dORFs). The definitions...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
..., tumor biomarker levels, and survival outcomes of patients who underwent organoid-based drug screening. (D) Comparison of ATAC-seq signals located within 3 kb upstream of and downstream from DETEs between organoid tumor and normal samples. Unchanged TE regions (2000 randomly selected) were used...
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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
...) neORFs partially overlapped to an existing gene and the upstream/downstream noncoding region. Finally, 4.4% (ES) to 6.7% (ZI) neORFs emerged inside an annotated intron. Most of these introns were antisense in all lines (64.2% [FI] to 80.6% [ES]). These percentages followed the same trends in all...
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Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
...profiles obtained with long-read and short-read Ribo-STAMP. We show that LR-Ribo-STAMP successfully profiles translation of mRNA isoforms and links regulatory features, such as upstream open reading frames (uORFs), to translation measurements. We apply LR-Ribo-STAMP to discovering translational differences...
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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
...on their 5′ end, plotting 1 kb upstream and 6 kb downstream.To quantitatively analyze the binding profiles of these proteins, we next investigated the chromatin states to which these proteins bind. To do so, we generated a chromatin-state model with ChromHMM (Ernst and Kellis 2017), using the mC reader Ch...
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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...ORFs). As the occurrence of sORFs downstream from or upstream of the main ORF can be deleterious to its translation or induce nonsense-mediated decay (NMD), we cannot rule out the possibility that this may cause strong selection pressure and the rapid elimination of uORFs and dORFs (Iacono et al. 2005; Neafsey and Galagan...
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Research: Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
- Peggy Janich,
- Alaaddin Bulak Arpat,
- Violeta Castelo-Szekely,
- Maykel Lopes,
- and David Gatfield
Genome Res. December 2015 25: 1848-1859; Published in Advance October 20, 2015, doi:10.1101/gr.195404.115
...Research 25:1848–1859 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/15; www..org www..org calculated translation efficiencies transcriptome-wide. Moreover, we inferred the relative levels of clock protein biosynthesis and identified upstream open reading frame (uORF) translation...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
....1101/601468 ↵Calviello L, Hirsekorn A, Ohler U. 2020. Quantification of translation uncovers the functions of the alternative transcriptome. Nat Struct Mol Biol 27: 717–725. doi:10.1038/s41594-020-0450-4 ↵Calvo SE, Pagliarini DJ, Mootha VK. 2009. Upstream open reading frames cause widespread reduction of protein...
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Research: Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context
- Maria S. Benitez-Cantos,
- Martina M. Yordanova,
- Patrick B.F. O'Connor,
- Alexander V. Zhdanov,
- Sergey I. Kovalchuk,
- Dmitri B. Papkovsky,
- Dmitry E. Andreev,
- and Pavel V. Baranov
Genome Res. July 2020 30: 974-984; Published in Advance July 15, 2020, doi:10.1101/gr.257352.119
...). Only manually curated mRNA sequences were used (those with accession prefix NM_). Sequences without an AUG translation initiation codon and without at least 6 nt upstream of AUG were discarded. To avoid the redundancy caused by multiple transcript variants, we took advantage of APPRIS database...
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