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1. Understanding m6A Function Through Uncovering the Diversity Roles of YTH Domain-Containing Proteins

Author:
Zhao, Y. L.; Liu, Y. H.; Wu, R. F.; Bi, Z.; Yao, Y. X.; Liu, Q.; Wang, Y. Z.; Wang, X. X.
Source:
Molecular biotechnology 2019 v.61 no.5 pp. 355-364
ISSN:
1073-6085
Subject:
messenger RNA,   etc   ; enzymes; eukaryotic cells; proteins;     Show all 4 Subjects
Abstract:
... N⁶-methyladenosine (m⁶A) is the most abundant—internal modification of eukaryotic mRNA. m⁶A can be installed and removed by specific enzymes. The “writer,” “eraser,” and “reader” of m⁶A modification have been reported. These discoveries facilitate our understanding of the functional significance of m⁶A. m⁶A plays an essential role in diverse biological processes by recruiting the corresponding YTH ...
DOI:
10.1007/s12033-018-00149-z

2. Bacterial Transcription Factors: Regulation by Pick “N” Mix

Author:
Browning, Douglas F.; Butala, Matej; Busby, Stephen J.W.
Source:
Journal of molecular biology 2019
ISSN:
0022-2836
Subject:
messenger RNA,   etc   ; bacteria; transcription (genetics); transcription factors;     Show all 4 Subjects
Abstract:
... Transcription in most bacteria is tightly regulated in order to facilitate bacterial adaptation to different environments, and transcription factors play a key role in this. Here we give a brief overview of the essential features of bacterial transcription factors and how they affect transcript initiation at target promoters. We focus on complex promoters that are regulated by combinations of acti ...
DOI:
10.1016/j.jmb.2019.04.011

3. Structural insights into the 3′-end mRNA maturation machinery: Snapshot on polyadenylation signal recognition

Author:
Thore, Stéphane; Fribourg, Sébastien
Source:
Biochimie 2019
ISSN:
0300-9084
Subject:
messenger RNA,   etc   ; humans; signal peptide; yeasts;     Show all 4 Subjects
Abstract:
... Pre-mRNA 3′-end maturation is achieved by a mechanism requiring four different protein complexes assembled from approximately twenty factors. A global understanding of this essential process is still missing due to the inability to structurally characterize the entire complexes, even though structures of the isolated factors have been obtained. In this review, we summarize recent findings regardin ...
DOI:
10.1016/j.biochi.2019.03.016

4. Determination of enrichment factors for modified RNA in MeRIP experiments

Author:
Slama, Kaouthar; Galliot, Aurellia; Weichmann, Franziska; Hertler, Jasmin; Feederle, Regina; Meister, Gunter; Helm, Mark
Source:
Methods 2019 v.156 pp. 102-109
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; antibodies; isotope labeling; nucleotides;     Show all 4 Subjects
Abstract:
... In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness. Here we present a method to assess enrichment factors after MeRIP-type pulldown experiments, here exemplified with a commercial antibody against N6-methyladenosine (m6A). Testing diffe ...
DOI:
10.1016/j.ymeth.2018.10.020

5. RNA Strand Displacement Responsive CRISPR/Cas9 System for mRNA Sensing

Author:
Li, Yue; Teng, Xucong; Zhang, Kaixiang; Deng, Ruijie; Li, Jinghong
Source:
Analytical chemistry 2019 v.91 no.6 pp. 3989-3996
ISSN:
1520-6882
Subject:
messenger RNA,   etc   ; gene editing; genomics; proteins;     Show all 4 Subjects
Abstract:
... CRISPR/Cas9 has already become a powerful tool for genomic manipulation, and further engineering of the system allows it to be precisely regulated in response to external signals, thus, broadening its application possibilities, such as biosensing or bioimaging. However, most stimuli-responsive CRISPR systems are built based on elaborately designed and engineered inducible Cas9 proteins, and extern ...
DOI:
10.1021/acs.analchem.8b05238

6. Tuning the Orchestra: miRNAs in Plant Immunity

Author:
Wang, Wenyi; Galili, Gad
Source:
Trends in plant science 2019
ISSN:
1360-1385
Subject:
messenger RNA,   etc   ; genes; innate immunity; microRNA;     Show all 4 Subjects
Abstract:
... miRNAs act as negative modulators of target genes and play key roles in post-transcriptional gene regulation through sequence-specific mRNA cleavage and translational inhibition. Two recent reports highlight the orchestrated role of miRNA2111 and miRNA172b in plant innate immunity [1,2] (Science 2018;362:233–236; Plant Cell 2018;30:2779–2794). ...
DOI:
10.1016/j.tplants.2019.01.009

7. Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research

Author:
Boldogkői, Zsolt; Moldován, Norbert; Balázs, Zsolt; Snyder, Michael; Tombácz, Dóra
Source:
Trends in microbiology 2019 v.27 no.7 pp. 578-592
ISSN:
0966-842X
Subject:
messenger RNA,   etc   ; DNA; genome; nanopores; transcription (genetics); transcriptome; transcriptomics; viruses;     Show all 8 Subjects
Abstract:
... Long-read sequencing (LRS) has become increasingly popular due to its strengths in de novo assembly and in resolving complex DNA regions as well as in determining full-length RNA molecules. Two important LRS technologies have been developed during the past few years, including single-molecule, real-time sequencing by Pacific Biosciences, and nanopore sequencing by Oxford Nanopore Technologies. Alt ...
DOI:
10.1016/j.tim.2019.01.010

8. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition

Author:
Modic, Miha; Grosch, Markus; Rot, Gregor; Schirge, Silvia; Lepko, Tjasa; Yamazaki, Tomohiro; Lee, Flora C.Y.; Rusha, Ejona; Shaposhnikov, Dmitry; Palo, Michael; Merl-Pham, Juliane; Cacchiarelli, Davide; Rogelj, Boris; Hauck, Stefanie M.; von Mering, Christian; Meissner, Alexander; Lickert, Heiko; Hirose, Tetsuro; Ule, Jernej; Drukker, Micha
Source:
Molecular cell 2019 v.74 no.5 pp. 951-965.e13
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; RNA-binding proteins; genes; mice; non-coding RNA;     Show all 5 Subjects
Abstract:
... RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment “paraspeckles,” are reciprocal in pluripotent and differentiated ce ...
DOI:
10.1016/j.molcel.2019.03.041

9. Obstacles to Scanning by RNase E Govern Bacterial mRNA Lifetimes by Hindering Access to Distal Cleavage Sites

Author:
Richards, Jamie; Belasco, Joel G.
Source:
Molecular cell 2019 v.74 no.2 pp. 284-295.e5
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; bacteria; genes; regulatory proteins; ribonucleases; ribosomes;     Show all 6 Subjects
Abstract:
... The diversity of mRNA lifetimes in bacterial cells is difficult to reconcile with the relaxed cleavage site specificity of RNase E, the endonuclease most important for governing mRNA degradation. This enzyme has generally been thought to locate cleavage sites by searching freely in three dimensions. However, our results now show that its access to such sites in 5′-monophosphorylated RNA is hindere ...
DOI:
10.1016/j.molcel.2019.01.044

10. Massive cytoplasmic transport and microtubule organization in fertilized chordate eggs

Author:
Nishikata, Takahito; Goto, Toshiyuki; Yagi, Haruka; Ishii, Hirokazu
Source:
Developmental biology 2019 v.448 no.2 pp. 154-160
ISSN:
0012-1606
Subject:
messenger RNA,   etc   ; Chordata; amphibians; early development; eggs; fish; microtubules; proteins;     Show all 8 Subjects
Abstract:
... Eggs have developed their own strategies for early development. Amphibian, teleost fish, and ascidian eggs show cortical rotation and an accompanying structure, a cortical parallel microtubule (MT) array, during the one-cell embryonic stage. Cortical rotation is thought to relocate maternal deposits to a certain compartment of the egg and to polarize the embryo. The common features and differences ...
DOI:
10.1016/j.ydbio.2018.11.019

11. Mechanisms of Bacterial Transcription Termination

Author:
Roberts, Jeffrey W.
Source:
Journal of molecular biology 2019
ISSN:
0022-2836
Subject:
messenger RNA,   etc   ; DNA; Escherichia coli; enzymes; torque; transcription termination;     Show all 6 Subjects
Abstract:
... Bacterial transcription termination, described mostly for Escherichia coli, occurs in three recognized ways: intrinsic termination, an activity only of the core RNAP enzyme and transcript sequences that encode an RNA hairpin and terminal uridine-rich segment; termination by the enzyme Rho, an ATP-dependent RNA translocase that releases RNA by forcing uncharacterized structural changes in the elong ...
DOI:
10.1016/j.jmb.2019.04.003

12. Crosslinking catalytic hairpin assembly for high-contrast imaging of multiple mRNAs in living cells

Author:
Huang, Du-Juan; Cao, Ting; Huang, Zhi-Mei; Wu, Zhenkun; Tang, Li-Juan; Jiang, Jian-Hui
Source:
Chemical communications 2019 v.55 no.27 pp. 3899-3902
ISSN:
1364-548X
Subject:
messenger RNA,   etc   ; DNA; chemical compounds; chemical reactions; crosslinking; image analysis;     Show all 6 Subjects
Abstract:
... A novel DNA nanotetrad mediated crosslinking catalytic hairpin assembly (CCHA) is reported to generate clumps of cross-linked mesh products for high-contrast and simultaneous imaging of multiple mRNAs in living cells. ...
DOI:
10.1039/c9cc01033e

13. Eukaryotic Initiation Factor 4E (eIF4E) sequestration mediates 4E-BP1 response to rapamycin

Author:
Batool, Asiya; Majeed, Sheikh Tahir; Aashaq, Sabreena; Majeed, Rabiya; Shah, Ghazia; Nazir, Nadiem; Andrabi, Khurshid Iqbal
Source:
International journal of biological macromolecules 2019 v.125 pp. 651-659
ISSN:
0141-8130
Subject:
messenger RNA,   etc   ; glucose; nutrients; phosphorylation; rapamycin; translation (genetics);     Show all 6 Subjects
Abstract:
... The cap dependent translation initiation is a tightly controlled process of cooperative ternary complex formation by 4E-BP1, eIF4E and the 5′ cap of eukaryotic mRNA in response to environmental cues like glucose, nutrients and growth factor levels. Based on the well-described effects of mTORC1/rapamycin complex on 4E-BP1 phosphorylation/s, it is generally accepted that rapamycin is a global inhibi ...
DOI:
10.1016/j.ijbiomac.2018.12.102

14. R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes

Author:
Skourti-Stathaki, Konstantina; Torlai Triglia, Elena; Warburton, Marie; Voigt, Philipp; Bird, Adrian; Pombo, Ana
Source:
Molecular cell 2019 v.73 no.5 pp. 930-945.e4
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; embryonic stem cells; mice; regulator genes; transcription (genetics);     Show all 5 Subjects
Abstract:
... R-loops are three-stranded nucleic acid structures that form during transcription, especially over unmethylated CpG-rich promoters of active genes. In mouse embryonic stem cells (mESCs), CpG-rich developmental regulator genes are repressed by the Polycomb complexes PRC1 and PRC2. Here, we show that R-loops form at a subset of Polycomb target genes, and we investigate their contribution to Polycomb ...
DOI:
10.1016/j.molcel.2018.12.016

15. Nucleoside analogs in the study of the epitranscriptome

Author:
Palumbo, Cody M.; Beal, Peter A.
Source:
Methods 2019 v.156 pp. 46-52
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; DNA-directed RNA polymerase; nucleosides; nucleotides; synthesis;     Show all 5 Subjects
Abstract:
... Over 150 unique RNA modifications are now known including several nonstandard nucleotides present in the body of messenger RNAs. These modifications can alter a transcript’s function and are collectively referred to as the epitrancriptome. Chemically modified nucleoside analogs are poised to play an important role in the study of these epitranscriptomic marks. Introduced chemical features on nucle ...
DOI:
10.1016/j.ymeth.2018.10.014

16. CAPAM: The mRNA Cap Adenosine N6-Methyltransferase

Author:
Cowling, Victoria H.
Source:
Trends in biochemical sciences 2019 v.44 no.3 pp. 183-185
ISSN:
0968-0004
Subject:
messenger RNA,   etc   ; adenosine; methylation; transcription (genetics); transferases; translation (genetics);     Show all 6 Subjects
Abstract:
... The mRNA cap is a structure that protects mRNA from degradation and recruits processing and translation factors. A new mRNA capping enzyme has been identified, PCIF1/CAPAM, which methylates adenosine when it is the first transcribed nucleotide. This discovery is crucial for understanding the function of cap adenosine methylation. ...
DOI:
10.1016/j.tibs.2019.01.002

17. Efficient Pre-mRNA Cleavage Prevents Replication-Stress-Associated Genome Instability

Author:
Teloni, Federico; Michelena, Jone; Lezaja, Aleksandra; Kilic, Sinan; Ambrosi, Christina; Menon, Shruti; Dobrovolna, Jana; Imhof, Ralph; Janscak, Pavel; Baubec, Tuncay; Altmeyer, Matthias
Source:
Molecular cell 2019 v.73 no.4 pp. 670-683.e12
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; DNA damage; genes; genomics; neoplasms; transcription (genetics); viability;     Show all 7 Subjects
Abstract:
... Cellular mechanisms that safeguard genome integrity are often subverted in cancer. To identify cancer-related genome caretakers, we employed a convergent multi-screening strategy coupled to quantitative image-based cytometry and ranked candidate genes according to multivariate readouts reflecting viability, proliferative capacity, replisome integrity, and DNA damage signaling. This unveiled regula ...
DOI:
10.1016/j.molcel.2018.11.036

18. Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing

Author:
Wolfe, Michael B.; Goldstrohm, Aaron C.; Freddolino, Peter L.
Source:
Methods 2019 v.155 pp. 88-103
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; high-throughput nucleotide sequencing; metabolism; transcription (genetics); transcriptome;     Show all 5 Subjects
Abstract:
... Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only g ...
DOI:
10.1016/j.ymeth.2018.12.001

19. Thermodynamic investigation of kissing-loop interactions

Author:
Carr, Carolyn E.; Marky, Luis A.
Source:
Biochimie 2019 v.157 pp. 177-183
ISSN:
0300-9084
Subject:
messenger RNA,   etc   ; DNA; biotechnology; dimerization; oligonucleotides; stems; therapeutics; thermodynamics; vaccines;     Show all 9 Subjects
Abstract:
... Kissing loop interactions (KLIs) are a common motif that is critical in retroviral dimerization, viroid replication, mRNA, and riboswitches. In addition, KLIs are currently used in a variety of biotechnology applications, such as in aptamer sensors, RNA scaffolds and to stabilize vaccines for therapeutics. Here we describe the thermodynamics of a basic intramolecular DNA capable of engaging in a K ...
DOI:
10.1016/j.biochi.2018.11.012

20. The Pat1-Lsm Complex Stabilizes ATG mRNA during Nitrogen Starvation-Induced Autophagy

Author:
Gatica, Damián; Hu, Guowu; Liu, Xu; Zhang, Nannan; Williamson, Peter R.; Klionsky, Daniel J.
Source:
Molecular cell 2019 v.73 no.2 pp. 314-324.e4
ISSN:
1097-2765
Subject:
messenger RNA,   etc   ; autophagy; dephosphorylation; exosomes; homeostasis; nitrogen; proteins;     Show all 7 Subjects
Abstract:
... Macroautophagy/autophagy is a key catabolic recycling pathway that requires fine-tuned regulation to prevent pathologies and preserve homeostasis. Here, we report a new post-transcriptional pathway regulating autophagy involving the Pat1-Lsm (Lsm1 to Lsm7) mRNA-binding complex. Under nitrogen-starvation conditions, Pat1-Lsm binds a specific subset of autophagy-related (ATG) transcripts and prevent ...
DOI:
10.1016/j.molcel.2018.11.002