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1. The Cap-Snatching Mechanism of Bunyaviruses

Author:
Olschewski, Silke; Cusack, Stephen; Rosenthal, Maria
Source:
Trends in microbiology 2020 v.28 no.4 pp. 293-303
ISSN:
0966-842X
Subject:
messenger RNA,   etc   ; Orthobunyavirus; Orthomyxoviridae;     Show all 3 Subjects
Abstract:
... In common with all segmented negative-sense RNA viruses, bunyavirus transcripts contain heterologous sequences at their 5′ termini originating from capped host cell RNAs. These heterologous sequences are acquired by a so-called cap-snatching mechanism. Whereas for nuclear replicating influenza virus the source of capped primers as well as the cap-binding and endonuclease activities of the viral po ...
DOI:
10.1016/j.tim.2019.12.006

2. Messenger RNA delivery to mitoribosomes – hints from a bacterial toxin

Author:
Bruni, Francesco; Proctor‐Kent, Yasmin; Lightowlers, Robert N.; Chrzanowska‐Lightowlers, Zofia M.
Source:
TheFEBS journal 2021 v.288 no.2 pp. 437-451
ISSN:
1742-464X
Subject:
messenger RNA,   etc   ; bacterial toxins; mammals; mitochondria; translation (genetics);     Show all 5 Subjects
Abstract:
... In mammalian mitochondria, messenger RNA is processed and matured from large primary transcripts in structures known as RNA granules. The identity of the factors and process transferring the matured mRNA to the mitoribosome for translation is unclear. Nascent mature transcripts are believed to associate initially with the small mitoribosomal subunit prior to recruitment of the large subunit to for ...
DOI:
10.1111/febs.15342

3. Mind the Gapmer: Implications of Co-transcriptional Cleavage by Antisense Oligonucleotides

Author:
Maranon, David G.; Wilusz, Jeffrey
Source:
Molecular cell 2020 v.77 no.5 pp. 932-933
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; oligonucleotides; transcription (genetics);     Show all 3 Subjects
Abstract:
... While gapmers efficiently knock down as well as terminate transcription of nascent lncRNAs and mRNAs, Lee and Mendell (2020) and Lai et al. (2020) also demonstrate that Pol II termination is not observed with gapmers targeting the 3′ terminal portions of the transcript. ...
DOI:
10.1016/j.molcel.2020.02.010

4. Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription

Author:
Cossa, Giacomo; Roeschert, Isabelle; Prinz, Florian; Baluapuri, Apoorva; Silveira Vidal, Raphael; Schülein-Völk, Christina; Chang, Yun-Chien; Ade, Carsten Patrick; Mastrobuoni, Guido; Girard, Cyrille; Wortmann, Lars; Walz, Susanne; Lührmann, Reinhard; Kempa, Stefan; Kuster, Bernhard; Wolf, Elmar; Mumberg, Dominik; Eilers, Martin
Source:
Molecular cell 2020
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; chromatin; enzymes; spliceosomes;     Show all 4 Subjects
Abstract:
... Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here, we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNU ...
DOI:
10.1016/j.molcel.2020.01.008
PubMed:
32006464
PubMed Central:
PMC7086158

5. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Author:
Chia, Minghao; Li, Cai; Marques, Sueli; Pelechano, Vicente; Luscombe, Nicholas M.; van Werven, Folkert J.
Source:
Genome biology 2021 v.22 no.1 pp. 34
ISSN:
1474-760X
Subject:
messenger RNA,   etc   ; Saccharomyces cerevisiae; chromatin; gene expression; genes; genomics; methodology; protein isoforms; transcription (genetics); yeasts;     Show all 10 Subjects
Abstract:
... BACKGROUND: The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regul ...
DOI:
10.1186/s13059-020-02245-3

6. Enhanced throughput of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR panel by assay multiplexing and specimen pooling

Author:
Lu, Xiaoyan; Sakthivel, Senthilkumar K.; Wang, Lijuan; Lynch, Brian; Dollard, Sheila M.
Source:
Journal of virological methods 2021 v.293 pp. 114149
ISSN:
0166-0934
Subject:
messenger RNA,   etc   ; Severe acute respiratory syndrome coronavirus 2; humans; reverse transcriptase polymerase chain reaction; ribonucleases;     Show all 5 Subjects
Abstract:
... A multiplex real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) assay for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was developed based on the same primer and probe sequences of an existing U.S. CDC Emergency Use authorized test panel, targeting SARS-CoV-2 N1, N2 and human RNase P genes in singleplex. Both singleplex and multiplex assays demonstrated ...
DOI:
10.1016/j.jviromet.2021.114149

7. Inhibition of MTA2 and MTA3 induces mesendoderm specification of human embryonic stem cells

Author:
You, Yu; Cui, Yandi; Li, Yuting; Zhang, Meng; Wang, Xin; Ji, Junxiang; Zhang, Xinbao; Zhou, Min; Zhang, Zhonglin; Ye, Shou-Dong; Wang, Xiaoxiao
Source:
Biochemical and biophysical research communications 2021 v.552 pp. 142-149
ISSN:
0006-291X
Subject:
messenger RNA,   etc   ; humans; phenotype; phosphotransferases (kinases); quantitative polymerase chain reaction; research; tyrosine;     Show all 7 Subjects
Abstract:
... Fully understanding the regulatory network under the pluripotency of embryonic stem cells (ESC) is a prerequisite for their safe application. Here, we addressed the characteristics of metastasis-associated (MTA) family members in human ESCs and found that knockdown of the expression of MTA2 and MTA3, but not MTA1, would induce differentiation. High-throughput sequence and quantitative real-time PC ...
DOI:
10.1016/j.bbrc.2021.03.030

8. A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data

Author:
Wang, Dingjie; Zou, Xiufen; Fai Au, Kin
Source:
Methods 2021 v.189 pp. 54-64
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; alternative splicing; exons; functional diversity; high-throughput nucleotide sequencing; prediction; proteins; sample size;     Show all 8 Subjects
Abstract:
... Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addition to gene-level expression, the advances of high-throughput sequencing offer a chance to estimate isoform-specific exon expression with a high resolution, which ...
DOI:
10.1016/j.ymeth.2020.06.005

9. CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis

Author:
Hou, Yifeng; Sun, Jing; Wu, Baixing; Gao, Yangyang; Nie, Hongbo; Nie, Zhentian; Quan, Shuxuan; Wang, Yong; Cao, Xiaofeng; Li, Sisi
Source:
Molecular plant 2021 v.14 no.4 pp. 688-699
ISSN:
1674-2052
Subject:
messenger RNA,   etc   ; Arabidopsis; genes; light; metabolism; mutants; nitrates; sequence homology; sheds;     Show all 9 Subjects
Abstract:
... N⁶-methyladenosine (m⁶A), a ubiquitous internal modification of eukaryotic mRNAs, plays a vital role in almost every aspect of mRNA metabolism. However, there is little evidence documenting the role of m⁶A in regulating alternative polyadenylation (APA) in plants. APA is controlled by a large protein-RNA complex with many components, including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPS ...
DOI:
10.1016/j.molp.2021.01.013

10. Circular sisRNA identification and characterisation

Author:
Ng, Amanda Yunn Ee; Pek, Jun Wei
Source:
Methods 2021
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; gene expression; non-coding RNA; ribonucleases; ribosomal RNA; transcription (genetics);     Show all 6 Subjects
Abstract:
... Stable Intronic Sequence RNA (sisRNA) is a relatively new class of non-coding RNA. Found in many organisms, these sisRNA produced from their host genes are generally involved in regulatory roles, controlling gene expression at multiple levels through active involvement in regulatory feedback loops. Large scale identification of sisRNA via genome-wide RNA sequencing has been difficult, largely in p ...
DOI:
10.1016/j.ymeth.2021.04.002

11. Boron as Boric Acid Induces mRNA Expression of the Differentiation Factor Tuftelin in Pre-Osteoblastic MC3T3-E1 Cells

Author:
Hakki, Sema S.; Bozkurt, Serife Buket; Hakki, Erdogan E.; Nielsen, Forrest H.
Source:
Biological trace element research 2021 v.199 no.4 pp. 1534-1543
ISSN:
0163-4984
Subject:
messenger RNA,   etc   ; acid treatment; bone formation; boric acid; boron; gene expression; genes; mineralization; research;     Show all 9 Subjects
Abstract:
... The effects of boron on the formation and maintenance of mineralized structures at the molecular level are still not clearly defined. Thus, a study was conducted using MC3T3-E1 cells to determine whether boron affected mRNA expressions of genes associated with bone/alveolar bone formation around the teethMC3T3-E1 (clone 4) cells were cultured in media treated with boric acid at concentrations of 0 ...
DOI:
10.1007/s12011-020-02257-x

12. Messenger RNA vaccines against SARS-CoV-2

Author:
Topol, Eric J.
Source:
Cell 2021 v.184 no.6 pp. 1401
ISSN:
0092-8674
Subject:
messenger RNA,   etc   ; COVID-19 infection; Severe acute respiratory syndrome coronavirus 2; placebos;     Show all 4 Subjects
Abstract:
... The first two vaccines proven to be effective for inhibiting COVID-19 illness were both mRNA, achieving 95% efficacy (and safety) among 74,000 participants (half receiving placebo) after intramuscular delivery of two shots, 3–4 weeks apart. To view this Bench to Bedside, open or download the PDF. ...
DOI:
10.1016/j.cell.2020.12.039

13. The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3

Author:
Lagan Tregaskis, Paula; Devaney, Ryan; Smyth, Victoria J.
Source:
Viruses 2021 v.13 no.2
ISSN:
1999-4915
Subject:
messenger RNA,   etc   ; Avian nephritis virus; capsid; flocks; genome; genotype; metagenomics; nephritis; nucleotides; phylogeny; polyproteins;     Show all 11 Subjects
Abstract:
... Avian nephritis virus (ANV) is classified in the Avastroviridae family with disease associations with nephritis, uneven flock growth and runting stunting syndrome (RSS) in chicken and turkey flocks, and other avian species. The whole genome of ANV genotype 3 (ANV-3) of 6959 nucleotides including the untranslated 5′ and 3′ regions and polyadenylated tail was detected in a metagenomic virome investi ...
DOI:
10.3390/v13020235

14. A circRNA-miRNA-mRNA regulatory network associated with the treatment response to tuberculosis

Author:
Tan, Wei; Zhang, Li; Wang, Shanmei; Jiang, Ping
Source:
Microbial pathogenesis 2021 v.150 pp. 104672
ISSN:
0882-4010
Subject:
messenger RNA,   etc   ; databases; genetic markers; microRNA; morbidity; mortality; pathogenesis; regression analysis; socioeconomics; therapeutics; tuberculosis;     Show all 11 Subjects
Abstract:
... The high morbidity and mortality of tuberculosis (TB) have severe socio-economic consequences, and there is an urgent need to explore the mechanisms driving TB development and progression. The aim of this study was to analyze the regulatory RNAs and target genes involved in TB, in order to identify key genetic biomarkers for diagnosing and treating TB.Circular RNAs (circRNAs), microRNAs (miRNAs) a ...
DOI:
10.1016/j.micpath.2020.104672

15. Identification of differentially expressed long non-coding RNAs and mRNAs in orbital adipose/connective tissue of thyroid-associated ophthalmopathy

Author:
Wu, Lianqun; Li, Lei; Liang, Yu; Chen, Xinxin; Mou, Pei; Liu, Guohua; Sun, Xiantao; Qin, Bing; Zhang, Shujie; Zhao, Chen
Source:
Genomics 2021 v.113 no.1 pp. 440-449
ISSN:
0888-7543
Subject:
messenger RNA,   etc   ; extracellular matrix; gene expression regulation; genes; lipid metabolism; non-coding RNA; pathogenesis; sequence analysis;     Show all 8 Subjects
Abstract:
... Extracellular matrix remodeling and orbital adipose/connective tissue expansion are two key features of thyroid-associated ophthalmopathy (TAO). Recent studies have indicated the critical role of long non-coding RNAs (lncRNAs) in the pathogenesis of ocular disorders. However, little is known about the roles of lncRNAs in orbital adipose/connective tissue of TAO. In this study, the profiles of lncR ...
DOI:
10.1016/j.ygeno.2020.09.001

16. m6A mRNA methylation analysis provides novel insights into heat stress responses in the liver tissue of sheep

Author:
Lu, Zengkui; Liu, Jianbin; Yuan, Chao; Jin, Meilin; Quan, Kai; Chu, Mingxing; Wei, Caihong
Source:
Genomics 2021 v.113 no.1 pp. 484-492
ISSN:
0888-7543
Subject:
messenger RNA,   etc   ; heat shock response; heat stress; lipid metabolism; liver; methylation; sheep; stop codon;     Show all 8 Subjects
Abstract:
... N⁶-methyladenosine (m⁶A) mRNA methylation varies in response to stress. However, no map of m⁶A mRNA methylation has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Here, we obtained m⁶A methylation maps of sheep liver tissues with and without heat stress by MeRIP-seq. In total, 8306 m⁶A peaks associated with 2697 genes were detected in the heat str ...
DOI:
10.1016/j.ygeno.2020.09.038

17. Heterogeneous Dynamics of Protein–RNA Interactions across Transcriptome-Derived Messenger RNA Populations

Author:
Çetin, Burak; Song, Gary J.; O’Leary, Seán E.
Source:
Journal of the American Chemical Society 2020 v.142 no.51 pp. 21249-21253
ISSN:
1520-5126
Subject:
messenger RNA,   etc   ; RNA helicases; fluorescence; kinetics; transcriptome;     Show all 5 Subjects
Abstract:
... Dynamic RNA–protein interactions underpin numerous molecular control mechanisms in biology. However, relatively little is known about the kinetic landscape of protein interactions with full-length RNAs. The extent to which interaction kinetics vary for the same RNA element across the transcriptome and the molecular determinants of variability therefore remain poorly defined. Moreover, it is unclea ...
DOI:
10.1021/jacs.0c09841

18. Protein velocity and acceleration from single-cell multiomics experiments

Author:
Gorin, Gennady; Svensson, Valentine; Pachter, Lior
Source:
Genome biology 2020 v.21 no.1 pp. 39
ISSN:
1474-760X
Subject:
messenger RNA,   etc   ; computer software; models; multiomics;     Show all 4 Subjects
Abstract:
... The simultaneous quantification of protein and RNA makes possible the inference of past, present, and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal single-cell experiments, we introduce an extension of the RNA velocity method that leverages estimates of unprocessed transcript and protein abundances to extrapolate cell states. We apply the m ...
DOI:
10.1186/s13059-020-1945-3
PubMed:
32070398
PubMed Central:
PMC7029606

19. Antisense probing of dynamic RNA structures

Author:
Lukasiewicz, Alexandra J.; Contreras, Lydia M.
Source:
Methods 2020 v.183 pp. 76-83
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; Tetrahymena; introns; regulatory sequences;     Show all 4 Subjects
Abstract:
... RNA regulation is influenced by the dynamic changes in conformational accessibility on the transcript. Here we discuss the initial validation of a cell-free antisense probing method for structured RNAs, using the Tetrahymena group I intron as a control target. We observe changes in signal that qualitatively match prior traditional DMS footprinting experiments. Importantly, we have shown that appli ...
DOI:
10.1016/j.ymeth.2020.01.015

20. Dynamics and Functions of Stress Granules and Processing Bodies in Plants

Author:
Jang, Geng-Jen; Jang, Jyan-Chyun; Wu, Shu-Hsing
Source:
Plants 2020 v.9 no.9
ISSN:
2223-7747
Subject:
messenger RNA,   etc   ; cytoplasmic granules; granules; translation (genetics);     Show all 4 Subjects
Abstract:
... RNA granules, such as stress granules and processing bodies, can balance the storage, degradation, and translation of mRNAs in diverse eukaryotic organisms. The sessile nature of plants demands highly versatile strategies to respond to environmental fluctuations. In this review, we discuss recent findings of the dynamics and functions of these RNA granules in plants undergoing developmental reprog ...
DOI:
10.3390/plants9091122