Searching journal content for articles similar to Li et al. 32 (5): 1015.

Displaying results 1-10 of 4889

For checked items

view abstracts
download to citation manager

Select this article
Method: 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. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
...we aimed to develop a low-input RNase footprinting approach to rapidly quantify cytosolic and mitochondrial ribosome footprints simultaneously. And we applied our method to characterize the translation landscape in diverse primary tissue samples.ResultsRNase digestion distinguishes RNA fragments...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
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...
Select this article
Corrigendum: Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
- Fei Qin,
- Guoshuai Cai,
- Christopher I. Amos,
- and Feifei Xiao
Genome Res. March 2024 34: 514; doi:10.1101/gr.279293.124
...: 10.1101/gr.279293.124 Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.279293.124 ;34/3/514 ;gr.279293.124 514 gr.279293.124 Corrigendum Corrigendum Corrigenda...
OPEN ACCESS ARTICLE
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Li et al. 32 (5): 1015.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: