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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...development also likely acting within the nervous system. 33 Furthermore, these highly conserved CRMs are strongly enriched for binding sites of “neuro-34 pancreatic” transcription factors governing both pancreas and nervous system development, 35 potentially suggesting function across these distinct organ...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...transcription and contribute to proteome diversity through processes such as leaky scanning, reinitiation, inclusion of upstream open reading frame (uORF) usage, and utilization of varied ribosomal entry sites (Kochetov 2008; Lee et al. 2012; Tamarkin-Ben-Harush et al. 2014; Johnstone et al. 2016). Although...
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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
...with protein coding transcripts, particularly those that overlap canonical CDSs in an alternative reading frame (altCDSs), followed by full overlaps with ncRNA transcripts, then by partial transcript overlaps, and finally intronic or intergenic regions. Our detailed prioritization summary is shown...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...myelogenous leukemia led to the development of BCR–ABL inhibitors that are the mainstay of treatment (Wong and Witte 2004). More recently, with the advent of RNA-seq and transcriptomic analyses, nuclear chimeric RNAs are being found in normal cells (Singh et al. 2020). In contrast, mtRNA transcripts...
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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
...′ UTR location), 9443 downstream ORFs (dORFs; for 3′ UTR location), 36,732 coding sequence-sORFs (CDS-sORFs; sORFs overlapping with main ORFs [+1 frame] in noncanonical +2 and +3 reading frames), and 3485 interlaced-sORFs (overlapping with both the CDS and 5′ UTR or CDS and 3′ UTR on the same transcript...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...-seq and RNA-seq and additional complex algorithms to assemble previously uncharacterized transcripts for the purpose of identifying open reading frames and predicting unannotated peptide sequences (Boley et al. 2014). These methods are often ad hoc, with highly variable performance, and are difficult...
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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
...novo gene to emerge, at least two events must occur: the emergence of a new open reading frame (ORF), and the gain of transcription. Nonetheless, s and synteny between two closely related species can be extensively reshuffled during evolution.The extensive divergence of noncoding regions because...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...establish transcriptional codependencies, i.e. coexistence of distinct features (e.g. specific splice junctions and untranslated regions—UTRs) on the same transcript. Long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) have emerged as transformative methodological alternatives to overcome...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...—specifically, if the exon is a multiple of 3 nt (Fig. 8A). Tissue-regulated alternative exons have been shown to have increased selection pressure to be frame-preserving in order to be included or skipped in transcripts without causing a shift in reading frame (Modrek et al. 2001). Consistent with these observations, we...
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