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Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Related publications (57)
Formaldehyde regulates one-carbon metabolism and epigenetics
Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...
Cell Press2024Statistical learning quantifies transposable element-mediated cis-regulation
Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Cyril David Son-Tuyên Pulver, Shaoline Sheppard
Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...
2023Chromatin modules and their implication in genomic organization and gene regulation
Bart Deplancke, Guido Van Mierlo, Judith Franziska Kribelbauer
Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...
ELSEVIER SCIENCE LONDON2023Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase
The substrate-reducing proteins of all nitrogenases (MoFe, VFe, and FeFe) are organized as alpha 2ss2(gamma 2) multimers with two functional halves. While their dimeric organization could afford improved structural stability of nitrogenases in vivo, previo ...
AMER CHEMICAL SOC2023GCN2 adapts protein synthesis to scavenging-dependent growth
Pancreatic cancer cells with limited access to free amino acids can grow by scavenging extracellular protein. In a murine model of pancreatic cancer, we performed a genome-wide CRISPR screen for genes required for scavenging-dependent growth. The screen id ...
2022RNA Sequencing of Arabidopsis thaliana Seedlings after Non-Thermal Plasma-Seed Treatment Reveals Upregulation in Plant Stress and Defense Pathways
Ivo Furno, Alan Howling, Alexandra Waskow
Not all agricultural practices are sustainable; however, non-thermal plasma treatment of seeds may be an eco-friendly alternative to improve macroscopic plant growth parameters. Despite the numerous successful results of plasma-seed treatments reported in ...
MDPI2022Circadian dynamics of RNA localisation in the mammalian liver
Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...
EPFL2021Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex
Daniel Constam, Benjamin Marcel Daniel Rothé
Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examin ...
NATURE PORTFOLIO2021The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy
Dominant mutations in ubiquitously expressed transfer RNA (tRNA) synthetase genes cause axonal peripheral neuropathy, accounting for at least six forms of Charcot-Marie-Tooth (CMT) disease. Genetic evidence in mouse and Drosophila models suggests a gain-of ...
AMER ASSOC ADVANCEMENT SCIENCE2021Mechanistic insights into AMP-activated protein kinase-dependent gene expression
AMP-activated protein kinase (AMPK) is a fundamental enzyme that controls energy homeostasis, through orchestrating the cellular response to a reduction in energy availability. Under conditions of cellular energy stress AMPK senses the decrease in ATP leve ...
EPFL2019