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1. Vive ut Numquam Moriturus: Tweaking Translational Control to Regulate Longevity

Author:
Bar-Ziv, Raz; Nguyen, Ngoc-Tram; Dillin, Andrew
Source:
Molecular cell 2019 v.73 no.4 pp. 643-644
ISSN:
1097-2765
Subject:
transcription (genetics),   etc   ; homeostasis; longevity; mitochondria;     Show all 4 Subjects
Abstract:
... Molecular mechanisms regulating aging at the post-transcriptional level are not clear. In this issue of Molecular Cell,D’Amico et al. (2019) demonstrate that the translational inhibition of mitochondrial fission factor (MFF) regulates cellular homeostasis and aging. ...
DOI:
10.1016/j.molcel.2019.02.006

2. Replication Timing Becomes Intertwined with 3D Genome Organization

Author:
Ma, Jian; Duan, Zhijun
Source:
Cell 2019 v.176 no.4 pp. 681-684
ISSN:
0092-8674
Subject:
transcription (genetics),   etc   ; DNA replication; genome; regulatory sequences;     Show all 4 Subjects
Abstract:
... Through dissecting the link between spatial genome organization and DNA replication timing, Sima et al. (2018) discover early replicating control elements (ERCEs), a new type of cis-acting elements that regulate replication timing, transcription, and multiple layers of three-dimensional features of genome organization. The study has important implications for unraveling control elements of high-or ...
DOI:
10.1016/j.cell.2019.01.027

3. To regenerate or not to regenerate: factors that drive plant regeneration

Author:
Sugimoto, Kaoru; Temman, Haruka; Kadokura, Satoshi; Matsunaga, Sachihiro
Source:
Current opinion in plant biology 2019 v.47 pp. 138-150
ISSN:
1369-5266
Subject:
transcription (genetics),   etc   ; epigenetics; meristems; stem cells;     Show all 4 Subjects
Abstract:
... Plants have a remarkable regenerative capacity, but it varies widely among species and tissue types. Whether plant cells/tissues initiate regeneration largely depends on the extent to which they are constrained to their original tissue fate. Once cells start the regeneration program, they acquire a new fate, form meristems, and develop into organs. During these processes, the cells must continuous ...
DOI:
10.1016/j.pbi.2018.12.002

4. Temporal evolution of Acinetobacter baumannii ST107 clone: conversion of blaOXA-143 into blaOXA-231 coupled with mobilization of ISAba1 upstream occAB1

Author:
Rodrigues-Costa, Fernanda; Cayô, Rodrigo; Matos, Adriana Pereira; Girardello, Raquel; Martins, Willames M.B.S.; Carrara-Marroni, Floristher Elaine; Gales, Ana Cristina
Source:
Research in microbiology 2019 v.170 no.1 pp. 53-59
ISSN:
0923-2508
Subject:
transcription (genetics),   etc   ; Acinetobacter baumannii; carbapenems; mutation;     Show all 4 Subjects
Abstract:
... Nine carbapenem-resistant Acinetobacter baumannii isolates carrying blaOXA-231 and an ISAba1 upstream occAB1 were evaluated. They were clonally related and belonged to ST107. An OXA-143-producing A. baumannii ST107 strain (Ac-148) that did not possess ISAba1 upstream occAB1 was included in the analysis. Reduction in the expression of occAB1 and a 4-fold increase of carbapenem MICs were observed fo ...
DOI:
10.1016/j.resmic.2018.07.001

5. Correction: Study on the transcriptional regulatory mechanism of the MyoD1 gene in Guanling bovine

Author:
Zhou, Di; Xu, Houqiang; Chen, Wei; Wang, Yuanyuan; Zhang, Ming; Yang, Tao
Source:
RSC advances 2018 v.8 no.73 pp. 41775
ISSN:
2046-2069
Subject:
transcription (genetics),   etc   ; cattle; genes;     Show all 3 Subjects
Abstract:
... Correction for ‘Study on the transcriptional regulatory mechanism of the MyoD1 gene in Guanling bovine’ by Di Zhou et al., RSC Adv., 2018, 8, 12409–12419. ...
DOI:
10.1039/c8ra90096e

6. Cell-free microcompartmentalised transcription–translation for the prototyping of synthetic communication networks

Author:
Dubuc, Emilien; Pieters, Pascal A; van der Linden, Ardjan J; van Hest, Jan CM; Huck, Wilhelm TS; de Greef, Tom FA
Source:
Current opinion in biotechnology 2019 v.58 pp. 72-80
ISSN:
0958-1669
Subject:
transcription (genetics),   etc   ; cells; gene expression; synthetic biology; translation (genetics);     Show all 5 Subjects
Abstract:
... Recent efforts in synthetic biology have shown the possibility of engineering distributed functions in populations of living cells, which requires the development of highly orthogonal, genetically encoded communication pathways. Cell-free transcription-translation (TXTL) reactions encapsulated in microcompartments enable prototyping of molecular communication channels and their integration into en ...
DOI:
10.1016/j.copbio.2018.10.006

7. Meeting report from the first European OddPols meeting: Toulouse 2018

Author:
Dauban, Lise; Cerezo, Emilie; Henras, Anthony; Gadal, Olivier
Source:
Gene 2019 v.702 pp. 215-219
ISSN:
0378-1119
Subject:
transcription (genetics),   etc   ; RNA; botanical gardens; enzymes; public speaking; France;     Show all 6 Subjects
Abstract:
... The eleventh international conference on transcription by RNA polymerases I, III, IV and V (the OddPols) was held from June 26th to June 29th 2018 at the Museum of Natural History of Toulouse, France and organized by Anthony Henras and Olivier Gadal. The scientific committee was composed of David Engelke, Joachim Griesenbeck, Ross Hannan, Deborah Johnson, Richard Maraia, Christoph Müller, Craig Pi ...
DOI:
10.1016/j.gene.2018.12.051

8. New Technologies To Enhance In Vivo Reprogramming for Regenerative Medicine

Author:
Larouche, Jacqueline; Aguilar, Carlos A.
Source:
Trends in biotechnology 2019 v.37 no.6 pp. 604-617
ISSN:
0167-7799
Subject:
transcription (genetics),   etc   ; chromatin; gene expression; medicine; somatic cells; technology; therapeutics;     Show all 7 Subjects
Abstract:
... Cellular identity and state are determined by a collection of molecular components that are specified during development and stabilized thereafter to maintain and protect tissue functions. Alteration of the molecular elements (gene expression program and chromatin state) as a result of disease or age can induce somatic cells to assume different identities or modulate functions. Therapeutic use of ...
DOI:
10.1016/j.tibtech.2018.11.003

9. The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Author:
Carreres, Benoit M.; León-Saiki, G. Mitsue; Schaap, Peter J.; Remmers, Ilse M.; van der Veen, Douwe; Martins dos Santos, Vitor A.P.; Wijffels, René H.; Martens, Dirk E.; Suarez-Diez, Maria
Source:
Algal research 2019 v.40 pp. 101477
ISSN:
2211-9264
Subject:
transcription (genetics),   etc   ; Tetradesmus; energy; genome; microalgae; mutants; phenotype; scotophase; starch;     Show all 9 Subjects
Abstract:
... Tetradesmus obliquus is a promising oleaginous microalga. We functionally annotated its genome and characterized the transcriptional landscape of T. obliquus adapted to 16:8 h light dark (LD) cycles in turbidostat culture conditions at very high temporal resolution (1 h intervals). Revealing a cycle of cellular events, six distinct expression profiles were obtained, each with transcriptional pheno ...
DOI:
10.1016/j.algal.2019.101477

10. Assembly of TALE-based DNA scaffold for the enhancement of exogenous multi-enzymatic pathway

Author:
Xie, Si-si; Qiu, Xin-yuan; Zhu, Lv-yun; Zhu, Chu-shu; Liu, Chuan-yang; Wu, Xiao-min; Zhu, Lingyun; Zhang, Dong-yi
Source:
Journal of biotechnology 2019 v.296 pp. 69-74
ISSN:
0168-1656
Subject:
transcription (genetics),   etc   ; Escherichia coli; biochemical pathways; enzymes; plasmids;     Show all 5 Subjects
Abstract:
... Synthetic scaffold systems, which exhibit enzyme clustering effect, have been considered as an important parallel approach for metabolic flux control and pathway enhancement. Here, we described an improved DNA-based scaffold system for synthetic tri-enzymatic pathway in Escherichia coli. With plasmid DNA serving as scaffold and exogenous enzymes fused with rationally designed transcription activat ...
DOI:
10.1016/j.jbiotec.2019.03.008

11. Gene-Specific H1 Eviction through a Transcriptional Activator→p300→NAP1→H1 Pathway

Author:
Shimada, Miho; Chen, Wei-Yi; Nakadai, Tomoyoshi; Onikubo, Takashi; Guermah, Mohamed; Rhodes, Daniela; Roeder, Robert G.
Source:
Molecular cell 2019 v.74 no.2 pp. 268-283.e5
ISSN:
1097-2765
Subject:
transcription (genetics),   etc   ; B-lymphocytes; acetylation; chromatin; gene activation; genes; histones;     Show all 7 Subjects
Abstract:
... Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by ...
DOI:
10.1016/j.molcel.2019.02.016

12. Ordering up gene expression by slowing down transcription factor binding kinetics

Author:
Culyba, Matthew J.
Source:
Current genetics 2019 v.65 no.2 pp. 401-406
ISSN:
0172-8083
Subject:
transcription (genetics),   etc   ; gene expression; genes; thermodynamics; transcription factors;     Show all 5 Subjects
Abstract:
... Efficient regulation of a complex genetic response requires that the gene products, which catalyze the response, be synthesized in a temporally ordered manner to match the sequential nature of the reaction pathway they act upon. Transcription regulation networks coordinate this aspect of cellular control by modulating transcription factor (TF) concentrations through time. The effect a TF has on th ...
DOI:
10.1007/s00294-018-0896-7

13. A computational system for identifying operons based on RNA-seq data

Author:
Tjaden, Brian
Source:
Methods 2019
ISSN:
1046-2023
Subject:
transcription (genetics),   etc   ; biochemical pathways; databases; operon; probabilistic models; sequence analysis;     Show all 6 Subjects
Abstract:
... An operon is a set of neighboring genes in a genome that is transcribed as a single polycistronic message. Genes that are part of the same operon often have related functional roles or participate in the same metabolic pathways. The majority of all bacterial genes are co-transcribed with one or more other genes as part of a multi-gene operon. Thus, accurate identification of operons is important i ...
DOI:
10.1016/j.ymeth.2019.03.026

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:
transcription (genetics),   etc   ; embryonic stem cells; messenger RNA; mice; regulator genes;     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. 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:
transcription (genetics),   etc   ; adenosine; messenger RNA; methylation; 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

16. Genomic 3D compartments emerge from unfolding mitotic chromosomes

Author:
Kumar, Rajendra; Lizana, Ludvig; Stenberg, Per
Source:
Chromosoma 2019 v.128 no.1 pp. 15-20
ISSN:
0009-5915
Subject:
transcription (genetics),   etc   ; DNA; chromatin; genome; genomics; interphase; mitosis; models; polymers;     Show all 9 Subjects
Abstract:
... The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and whe ...
DOI:
10.1007/s00412-018-0684-7

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:
transcription (genetics),   etc   ; DNA damage; genes; genomics; messenger RNA; neoplasms; 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. Combinatorial Control through Allostery

Author:
Galstyan, Vahe; Funk, Luke; Einav, Tal; Phillips, Rob
Source:
TheJournal of physical chemistry 2019 v.123 no.13 pp. 2792-2800
ISSN:
1520-5207
Subject:
transcription (genetics),   etc   ; binding sites; cell communication; ligands; mechanical models;     Show all 5 Subjects
Abstract:
... Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these responses come about and how they can be harnessed, we develop a statistical mechanical model to characterize the types of Boolean logic that can arise from allosteric molecules following the Monod–Wyman–Changeux (MWC) mode ...
DOI:
10.1021/acs.jpcb.8b12517

19. 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:
transcription (genetics),   etc   ; high-throughput nucleotide sequencing; messenger RNA; metabolism; 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

20. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Author:
Sima, Jiao; Chakraborty, Abhijit; Dileep, Vishnu; Michalski, Marco; Klein, Kyle N.; Holcomb, Nicolas P.; Turner, Jesse L.; Paulsen, Michelle T.; Rivera-Mulia, Juan Carlos; Trevilla-Garcia, Claudia; Bartlett, Daniel A.; Zhao, Peiyao A.; Washburn, Brian K.; Nora, Elphège P.; Kraft, Katerina; Mundlos, Stefan; Bruneau, Benoit G.; Ljungman, Mats; Fraser, Peter; Ay, Ferhat; Gilbert, David M.
Source:
Cell 2019 v.176 no.4 pp. 816-830.e18
ISSN:
0092-8674
Subject:
transcription (genetics),   etc   ; DNA replication; genome; mice; protein depletion; regulatory sequences;     Show all 6 Subjects
Abstract:
... The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened mos ...
DOI:
10.1016/j.cell.2018.11.036