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Corrigendum: Corrigendum: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. May 2022 32: 1015; doi:10.1101/gr.276750.122
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Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
- Rosario Avolio,
- Ilenia Agliarulo,
- Daniela Criscuolo,
- Daniela Sarnataro,
- Margherita Auriemma,
- Sabrina De Lella,
- Sara Pennacchio,
- Giovanni Calice,
- Martin Y. Ng,
- Carlotta Giorgi,
- Paolo Pinton,
- Barry S. Cooperman,
- Matteo Landriscina,
- Franca Esposito,
- and Danilo Swann Matassa
Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
...alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein, we identify the molecular mechanisms involved, showing that TRAP1 (1) binds both mitochondrial and cytosolic ribosomes, as well as translation elongation factors; (2...
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Method: A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
- René A.M. Dirks,
- Peter C. Thomas,
- Haoyu Wu,
- Robert C. Jones,
- Hendrik G. Stunnenberg,
- and Hendrik Marks
Genome Res. May 2021 31: 919-933; Published in Advance March 11, 2021, doi:10.1101/gr.260745.120
..., and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious and time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable...
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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
...to simultaneously profile translation and transcription at both the gene and mRNA isoform levels. We also developed the EditsC metric to quantify editing and leverage the single-molecule, full-length transcript information provided by long-read sequencing. Here, we report concordance between gene-level translation...
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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
...RNA frequency. Gene set enrichment analysis of these genes identified significant enrichment for downregulation of multiple pathways involving mitochondrial function, including electron transport chain and tricarboxylic acid cycle as well as mitochondrial translation, whereas upregulated pathways focused...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...remains limited owing to technical challenges and high costs. Computational approaches for cross-modality translation provide a promising solution to these limitations by enabling the inference of one modality from another. However, existing methods for cross-modality translation between single-cell RNA...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
..., transcriptional regulation of mitochondrial genes in both the nucleus and the mtDNA is pivotal for the developing embryo and for the transition to the neonate.Studies in model organisms support the occurrence of a metabolic shift after birth in certain tissues. Quantification of lactic acid in rat livers revealed...
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Method: NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA
- Michael A. Schon,
- Max J. Kellner,
- Alexandra Plotnikova,
- Falko Hofmann,
- and Michael D. Nodine
Genome Res. December 2018 28: 1931-1942; Published in Advance October 24, 2018, doi:10.1101/gr.239202.118
...in the data sets. To enable the accurate identification and precise classification of RNA 5′ ends from standard and low-input RNA, we developed a next-generation sequencing-based method called nanoPARE and associated software. By integrating RNA 5′ end information from nanoPARE with gene-body mRNA-seq data...
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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
...Arabidopsis (Arabidopsis thaliana) small ORFs initiated at AUG encode hormone-like peptides that regulate morphogenic development and salinity stress tolerance (Hanada et al. 2013; Nakaminami et al. 2018). The tomato (Solanum lycopersicum) valyl-tRNA synthetase gene encodes both mitochondrial and cytosolic...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
....sohn@igb.fraunhofer.deAbstractHere, we present a method for enrichment of double-stranded cfDNA with an average length of ∼40 bp from cfDNA for high-throughput DNA sequencing. This class of cfDNA is enriched at gene promoters and binding sites of transcription factors or structural DNA-binding proteins, so that a -wide DNA footprint...
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