Results 61 to 70 of about 185,351 (165)

Optimization of carbon and energy utilization through differential translational efficiency

Nature Communications, 2018
Microorganisms must regulate allocation of resources in nutrient-limited conditions. Here, the authors combine Ribo-seq, RNA-seq and TSS-seq to study resource allocation in the acetogen C.
Mahmoud M. Al-Bassam, Ji-Nu Kim, Livia S. Zaramela, Benjamin P. Kellman, Cristal Zuniga, Jacob M. Wozniak, David J. Gonzalez, Karsten Zengler   +7 more
doaj   +1 more source

Transcripts enriched in codons that trigger P‐site tRNA‐mediated mRNA decay possess stable mRNA

FEBS Open Bio, EarlyView.
PTMD codons were first described by Mendel et al. as mediators of an mRNA decay pathway dependent on the human protein CNOT3, homologous to yeast Not5. Our findings confirm that PTMD codons destabilize transcripts; however, unlike in yeast, the human pathway specifically targets and slightly destabilizes primarily stable mRNAs.
Rodolfo Lopes Carneiro, Fernando Lucas Palhano   +1 more
wiley   +1 more source

The Landscape of Long Non‐Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit

Advanced Science, EarlyView.
This study reveals that long non‐coding RNAs represent important regulatory components underlying pear domestication and improvement. Integrative multi‐omics analyses identify selected lncRNAs associated with fruit traits, while functional validation uncovers a lignin‐related lncRNA, lncRNA‐pys, that promotes lignin accumulation.
Bobo Song, Peilin Han, Jiaming Li, Xiaolong Li, Xiang Zhang, Jing Fan, Dongliang Liu, Jianfa Cai, Lingchao Zhang, Jun Wu   +9 more
wiley   +1 more source

Mutant KRAS‐m6A Epitranscriptome Axis Promotes Colorectal Cancer and is a Therapeutic Target

Advanced Science, EarlyView.
Mutant KRAS‐m6A axis promotes colorectal cancer (CRC) progression. Mutant KRAS stabilizes METTL3, leading to increased m6A‐modified BCL9L mRNA and translation of BCL9L protein. BCL9L in turn mediates TGF‐β secretion to induce differentiation of Treg and an immunosuppressive microenvironment.
Danyu Chen, Pingmei Huang, Ruizhi Tao, Fenfen Ji, Qinyao Wei, Lok Hin Ko, Lianxin Zhou, Huarong Chen, Alvin Cheung, Wei Kang, Ko Fai To, Jun Yu, Chi Chun Wong   +12 more
wiley   +1 more source

De novo functional transcriptomics with RNA-seq and Ribo-seq

, 2023
Our genome sequencing and assembly capabilities have hugely increased. However, annotating our genome is still challenging. Genes can produce multiple isoforms, which may have different expression levels and roles. Transcript functions can be elucidated by profiling ribosome positions with the protocol Ribo-seq.
Albanese, Roberto, Campbell, Amy E., Dossena, Francesco, Mancino, Marilena, Sujatha Jagannathan, Calviello, Lorenzo   +5 more
openaire   +1 more source

The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation

Genome Biology
Background Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear.
Chris Papadopoulos, Hugo Arbes, David Cornu, Nicolas Chevrollier, Sandra Blanchet, Paul Roginski, Camille Rabier, Safiya Atia, Olivier Lespinet, Olivier Namy, Anne Lopes   +10 more
doaj   +1 more source

Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii

Microbial Cell Factories, 2021
Background Eukaryotes use distinct networks of biogenesis factors to synthesize, fold, monitor, traffic, and secrete proteins. During heterologous expression, saturation of any of these networks may bottleneck titer and yield.
Troy R. Alva, Melanie Riera, Justin W. Chartron   +2 more
doaj   +1 more source

Thermal Shifts Dominate Single‐Gene Responses to Transcription‐Targeting Antibiotics

Advanced Science, EarlyView.
Thermal shifts reshape bacterial responses to transcription‐targeting antibiotics. In E. coli, temperature can dominate antibiotic‐induced genome‐wide expression, particularly outside 30°C–39°C, through changes in adenosine triphosphate (ATP), nucleoid organization, and drug‐target engagement.
Rahul Jagadeesan, Amir M. Arsh, Vatsala Chauhan, Suchintak Dash, Pooja Ravaria, Andre S. Ribeiro   +5 more
wiley   +1 more source

Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains

Data in Brief, 2019
TMA20 (MCT-1), TMA22 (DENR) and TMA64 (eIF2D) are eukaryotic translation factors involved in ribosome recycling and re-initiation. They operate with P-site bound tRNA in post-termination or (re-)initiation translation complexes, thus participating in the
Desislava S. Makeeva, Andrey S. Lando, Aleksandra Anisimova, Artyom A. Egorov, Maria D. Logacheva, Alexey A. Penin, Dmitry E. Andreev, Pavel G. Sinitcyn, Ilya M. Terenin, Ivan N. Shatsky, Ivan V. Kulakovskiy, Sergey E. Dmitriev   +11 more
doaj   +1 more source

Riborex: fast and flexible identification of differential translation from Ribo-seq data. [PDF]

Bioinformatics, 2017
Abstract Motivation Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample.
Li W, Wang W, Uren PJ, Penalva LOF, Smith AD.   +4 more
europepmc   +5 more sources