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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
...of translation in humans alone (Ma et al. 2014; Chen et al. 2020; Erady et al. 2021). These ORFs are mostly under 100 codons and found in diverse regions of the , including in long noncoding RNAs (lncRNAs), pseudogenes, 3′ UTRs, 5′ UTRs, and alternative reading frames of canonical protein coding exons...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...of centromere tandem repeat arrays has been limited in many species, as they could not be fully assembled using short-read sequencing (Miga and Sullivan 2021). However, Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio) HiFi long-read sequencing now allow complete assembly of complex centromere...
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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
...sister s. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating s. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...generations. We found unexpected consequences on the structure and stability, as well as on its 3D organization. We also show the short-term consequences of gene copy number variation (CNV) on their expression and potentially their role in plant phenotypic traits such as pathogen responses.View larger version...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...queried (chicken, zebra finch, and turkey). This implies that H2A.Rs and short histone H2A variants evolved exclusively in the mammalian lineage, after the split from birds. Like canonical H2A, H2A.R, H2A.B, H2A.L, H2A.P, and H2A.Q sequences all have intronless open reading frames.The four clades...
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LETTER: Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
- James P. Kastenmayer,
- Li Ni,
- Angela Chu,
- Lauren E. Kitchen,
- Wei-Chun Au,
- Hui Yang,
- Carole D. Carter,
- David Wheeler,
- Ronald W. Davis,
- Jef D. Boeke,
- Michael A. Snyder,
- and Munira A. Basrai
Genome Res. March 2006 16: 365-373; doi:10.1101/gr.4355406
...Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae James P. Kastenmayer 1 , 6 , Li Ni 2 , 6 , Angela Chu 3 , Lauren E. Kitchen 1 , Wei-Chun Au 1 , Hui Yang 2 , Carole D. Carter 1...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, s hort t andem r epeat profiling using f lank-based m apping, a computational pipeline that can detect...
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Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...Terminal Repeat [LTR] and non-LTR groups) and their approximate representation in the human (in parentheses). While all sharing a polyA tail, the non-LTR retrotransposons are structurally distinct. The autonomous LINE-1 element (L1) contains two open reading frames while Alu and SVA do not. Alu is instead...
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LETTER: Cloning and Functional Analysis of cDNAs with Open Reading Frames for 300 Previously Undefined Genes Expressed in CD34+ Hematopoietic Stem/Progenitor Cells
- Qing-Hua Zhang,
- Min Ye,
- Xin-Yan Wu,
- Shuang-Xi Ren,
- Meng Zhao,
- Chun-Jun Zhao,
- Gang Fu,
- Yu Shen,
- Hui-Yong Fan,
- Gang Lu,
- Ming Zhong,
- Xiang-Ru Xu,
- Ze-Guang Han,
- Ji-Wang Zhang,
- Jiong Tao,
- Qiu-Hua Huang,
- Jun Zhou,
- Geng-Xi Hu,
- Jian Gu,
- Sai-Juan Chen,
- and Zhu Chen
Genome Res. October 1, 2000 10: 1546-1560; doi:10.1101/gr.140200
...Cloning and Functional Analysis of cDNAs with Open Reading Frames for 300 Previously Undefined Genes Expressed in CD34+ Hematopoietic Stem/Progenitor Cells Qing-Hua Zhang 1 , 4 , Min Ye 1 , 4 , Xin-Yan Wu 1 , 4 , Shuang-Xi Ren 2 , 4 , Meng...
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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
...3 nt periodicity, a hallmark of translating ribosomes, within a gene-structure context, including introns and untranslated regions, enabling the study of novel open reading frames (ORFs), translation of different isoforms, and mechanisms of translational regulation. ggRibo can plot multiple Ribo...
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