A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay by Hu, Z, Yau, C, Ahmed, A

“…Nonsense-mediated decay (NMD) eliminates transcripts with premature termination codons. Although NMD-induced loss-of-function has been shown to contribute to the genesis of particular cancers, its global functional consequence in tumours has not been characterized. …”

Complete mitochondrial genome of Brachionus rubens from wuhu, China (Rotifera, Brachionidae) by Yi Zhang, Hai Ying Zhang, Jin Jin Yan, Meng Ning Xia, Ying Long Liu, Yan Mei Lu, Yun Zhi Yan, Shuang Huai Cheng

“…Four of the 12 PCGs had an incomplete stop codons, TA（cob, atp6, nd3）or T(cox3). The A + T content of B. rubens mitochondrial genome was apparently higher (mtDNA-I 70.2% and mtDNA II 70.4%) than that of the mitochondrial genome of B. plicatilis (mtDNA-I 63.9% and mtDNA-II 62.9%).…”
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ELOE: A WEB APPLICATION FOR ESTIMATION OF GENE TRANSLATION ELONGATION EFFICIENCY by V. S. Sokolov, B. S. Zuraev, S. A. Lashin, Yu. G. Matushkin

“…In addition, the program identifies preferential codons in a genome and defines the distribution of stability of potential secondary structures in 5′ and 3′ regions of mRNA. …”
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Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae by Jenna E. Smith, Juan R. Alvarez-Dominguez, Nicholas Kline, Nathan J. Huynh, Sarah Geisler, Wenqian Hu, Jeff Coller, Kristian E. Baker

“…Ribosome profiling demonstrates that many bind translocating ribosomes within predicted open reading frames 10–96 codons in size. We validate expression of peptides encoded within a subset of these RNAs and provide evidence for conservation among yeast species. …”
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Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay by Alicia A. Bicknell, David W. Reid, Marissa C. Licata, Adriana K. Jones, Yi Min Cheng, Mengying Li, Chiaowen Joyce Hsiao, Christopher S. Pepin, Mihir Metkar, Yevgen Levdansky, Brian R. Fritz, Elizaveta A. Andrianova, Ruchi Jain, Eugene Valkov, Caroline Köhrer, Melissa J. Moore

“…We previously found that coding sequence (CDS) design can substantially affect protein output, with mRNA variants containing more optimal codons and higher secondary structure yielding the highest protein outputs due to their slow rates of mRNA decay. …”
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Newly Designed Primers for the Sequencing of the <i>inlA</i> Gene of Lineage I and II <i>Listeria monocytogenes</i> Isolates by Giulia Magagna, Guido Finazzi, Virginia Filipello

“…The virulence factor Internalin A (inlA) has a key role in the invasion of <i>L. monocytogenes</i> into the human intestinal epithelium, and the presence of premature stop-codons (PMSC) mutations in the <i>inlA</i> gene sequence is correlated with attenuated virulence. …”
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Arp GENE NUCLEOTID SEQUENCES VARIABILITY IN RUSSIAN TREPONEMA PALLIDUM ISOLATES by O. A. Obraztsova, K. A. Aleinikova, A. A. Kubanov, D. G. Deryabin

“…Four variants of 60-nucleotide repeats in the internal arp fragment are described, which differing in 6, 8 and 15 — 17 codons compositions. Various combinations of these repeats, corresponding to the reference Nichols strain, globally distributed Street 14 genogroup, and the firstly described Stavropol regional variant are shown. …”
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Characterization of the complete mitochondrial genome of Silurus soldatovi in Korean river by Md. Jobaidul Alam, Mahmoud Aboalyamin Soliman Khalil, Kyung Su Kim, Sapto Andriyono, Chang Geun Choi, Hyun-Woo Kim

“…Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, S. soldatovi showed highest identity (99.38%) to the Chinese haplotype of S. soldatovi (NC022723) followed by the Chinese haplotype of Silurus asotus (JX087351). …”
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The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules? by Maciej Stasiak, Tomasz Kolenda, Joanna Kozłowska-Masłoń, Joanna Sobocińska, Paulina Poter, Kacper Guglas, Anna Paszkowska, Renata Bliźniak, Anna Teresiak, Urszula Kazimierczak, Katarzyna Lamperska

“…Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. …”
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The complete mitochondrial genome of Metaphycus eriococci (Timberlake) (Hymenoptera: Encyrtidae) by Qing-Song Zhou, Mei Xiong, Arong Luo, Yan-Zhou Zhang, Chao-Dong Zhu

“…All the 13 PCGs begin with typical ATN codons. Among them, 12 PCG genes terminate with TAA, only one with TAG. …”
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The switch-like expression of heme-regulated kinase 1 mediates neuronal proteostasis following proteasome inhibition by Beatriz Alvarez-Castelao, Susanne tom Dieck, Claudia M Fusco, Paul Donlin-Asp, Julio D Perez, Erin M Schuman

“…Following proteasome inhibition, HRI protein levels increase owing to stabilization of HRI and enhanced translation, likely via the increased availability of tRNAs for its rare codons. Once expressed, HRI is constitutively active in neurons because endogenous heme levels are so low; HRI activity results in eIF2α phosphorylation and the resulting inhibition of translation. …”
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Mutation Spectra of the MRN (MRE11, RAD50, NBS1/NBN) Break Sensor in Cancer Cells by Matthew T. McPherson, Ashton S. Holub, Aman Y. Husbands, Ruben C. Petreaca

“…This analysis revealed several hotspot frameshift mutations in all three genes that introduce premature stop codons and truncate large regions of the C-termini. …”
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Plasma proteome profiling combined with clinical and genetic features reveals the pathophysiological characteristics of β-thalassemia by Na Li, Peng An, Jifeng Wang, Tingting Zhang, Xiaoqing Qing, Bowen Wu, Lang Sun, Xiang Ding, Lili Niu, Zhensheng Xie, Mengmeng Zhang, Xiaojing Guo, Xiulan Chen, Tanxi Cai, Jianming Luo, Fudi Wang, Fuquan Yang

“…The combination of proteome and patients' clinical data revealed patients with codons 41/42 -TTCT mutations have an elevated risk of higher iron burden, dysplasia, and osteoporosis than patients with other genotypes. …”
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Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1 by Voigt, Christopher A.

“…This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.…”
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Titin-truncating variants affect heart function in disease cohorts and the general population by Schafer, S, de Marvao, A, Adami, E, Fiedler, LR, Ng, B, Khin, E, Rackham, OJL, van Heesch, S, Pua, CJ, Kui, M, Walsh, R, Tayal, U, Prasad, SK, Dawes, TJW, Ko, NSJ, Sim, D, Chan, LLH, Chin, CWL, Mazzarotto, F, Barton, PJ, Kreuchwig, F, de Kleijn, DPV, Totman, T, Biffi, C, Tee, N, Rueckert, D, Schneider, V, Faber, A, Regitz-Zagrosek, V, Seidman, JG, Seidman, CE, Linke, WA, Kovalik, J-P, O'Regan, D, Ware, JS, Hubner, N, Cook, SA

“…Ribosomal profiling in rat showed the translational footprint of premature stop codons in Ttn, TTNtv-position-independent nonsense-mediated degradation of the mutant allele and a signature of perturbed cardiac metabolism. …”

Complete mitochondrial genome of Eurema blanda and phylogenetic relationship with its congener E. hecabe and other pierid butterflies by Yong, Hoi Sen, Song, Sze Looi, Lim, Phaik Eem, Eamsobhana, Praphathip, Suana, I. Wayan

“…It had a total length of 15,123�bp. The start codons ATA and ATC present in E. hecabe were not represented in E. blanda. …”

A snapshot of the prevalence of dihydropteroate synthase-431V mutation and other sulfadoxine-pyrimethamine resistance markers in Plasmodium falciparum isolates in Nigeria by Adebanjo J. Adegbola, Omotade A. Ijarotimi, Akaninyene E. Ubom, Bukola A. Adesoji, Olajide E. Babalola, Emma F. Hocke, Helle Hansson, Andria Mousa, Oluseye O. Bolaji, Michael Alifrangis, Cally Roper

“…The Pfdhps gene carried mutations at codons resulting in amino acid changes at 431–436-437–540-581–613; I431V [45.9%, (28/61)], A581G [31.1% (19/61)] and A613S [49.2% (30/61)]. …”
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MUTATIONAL STATUS OF ONCOGENE KRAS AND RISK OF VENOUS THROMBOSIS IN PATIENTS WITH METASTATIC COLORECTAL CANCER by EC Malafaia, P Doria, L Teixeira, G Pita, Y Zollinger, P Almeida

“…Seven mutations within codons 12 e 13 of KRAS detected by PCR (Idylla technique) or were considered for this study. …”
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Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria) by Jan-Niklas Macher, Nicole L. Coots, Yu-Ping Poh, Elsa B. Girard, Anouk Langerak, Sergio A. Muñoz-Gómez, Savar D. Sinha, Dagmar Jirsová, Rutger Vos, Richard Wissels, Gillian H. Gile, Willem Renema, Jeremy G. Wideman

“…In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. …”
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Development of an Efficient C-to-T Base-Editing System and Its Application to Cellulase Transcription Factor Precise Engineering in Thermophilic Fungus Myceliophthora thermophila by Chenyang Zhang, Nan Li, Lang Rao, Jingen Li, Qian Liu, Chaoguang Tian

“…Here, for the first time, we constructed three cytosine base editors (CBEs) in M. thermophila, namely, evolved apolipoprotein B mRNA-editing enzyme catalytic subunit 1 (APOBEC1) cytosine base editor 4 max (Mtevo-BE4max), bacteriophage Mu Gam protein cytosine base editor 4 max (MtGAM-BE4max), and evolved CDA1 deaminase cytosine base editor (Mtevo-CDA1), and efficiently inactivated genes by precisely converting three codons (CAA, CAG, and CGA) into stop codons without DSB formation. …”
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