keyword
MENU ▼
Read by QxMD icon Read
search

eukaryotic gene regulation

keyword
https://www.readbyqxmd.com/read/28716048/transcriptome-analysis-uncovers-arabidopsis-f-box-stress-induced-1-as-a-regulator-of-jasmonic-acid-and-abscisic-acid-stress-gene-expression
#1
Lauren E Gonzalez, Kristen Keller, Karen X Chan, Megan M Gessel, Bryan C Thines
BACKGROUND: The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells. F-box proteins are substrate adaptors within the UPS and are responsible for the diversity of potential protein targets. Plant genomes are enriched in F-box genes, but the vast majority of these have unknown roles. This work investigated the Arabidopsis F-box gene F-BOX STRESS INDUCED 1 (FBS1) for its effects on gene expression in order elucidate its previously unknown biological function...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28715365/analysis-of-the-c-kit-ligand-promoter-using-chromatin-immunoprecipitation
#2
Pingyu Zhang, Andres Rojas, Boris Blechacz
Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. Therefore, DNA-protein interactions regulate multiple physiological, pathophysiological, and biological functions, such as cell differentiation, cell proliferation, cell cycle control, chromosome stability, epigenetic gene regulation, and cell transformation. In eukaryotic cells, the DNA interacts with histone and nonhistone proteins and is condensed into chromatin...
June 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28713400/overexpression-of-e3-ubiquitin-ligase-gene-adbil-contributes-to-resistance-against-chilling-stress-and-leaf-mold-disease-in-tomato
#3
Shuangchen Chen, Hongjiao Zhao, Mengmeng Wang, Jidi Li, Zhonghong Wang, Fenghua Wang, Airong Liu, Golam J Ahammed
Ubiquitination is a common regulatory mechanism, playing a critical role in diverse cellular and developmental processes in eukaryotes. However, a few reports on the functional correlation between E3 ubiquitin ligases and reactive oxygen species (ROS) or reactive nitrogen species (RNS) metabolism in response to stress are currently available in plants. In the present study, the E3 ubiquitin ligase gene AdBiL (Adi3 Binding E3 Ligase) was introduced into tomato line Ailsa Craig via Agrobacterium-mediated method...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28710288/post-transcriptional-control-of-gene-expression-following-stress-the-role-of-rna-binding-proteins
#4
REVIEW
Robert Harvey, Veronica Dezi, Mariavittoria Pizzinga, Anne E Willis
The ability of mammalian cells to modulate global protein synthesis in response to cellular stress is essential for cell survival. While control of protein synthesis is mediated by the regulation of eukaryotic initiation and elongation factors, RNA-binding proteins (RBPs) provide a crucial additional layer to post-transcriptional regulation. RBPs bind specific RNA through conserved RNA-binding domains and ensure that the information contained within the genome and transcribed in the form of RNA is exported to the cytoplasm, chemically modified, and translated prior to folding into a functional protein...
July 14, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28707092/the-determinants-of-alternative-rna-splicing-in-human-cells
#5
REVIEW
Tatsiana V Ramanouskaya, Vasily V Grinev
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body...
July 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28706527/localization-of-sphingolipid-enriched-plasma-membrane-regions-and-long-chain-base-composition-during-mature-fruit-abscission-in-olive
#6
Maria C Parra-Lobato, Miguel A Paredes, Juana Labrador, Mariana Saucedo-García, Marina Gavilanes-Ruiz, Maria C Gomez-Jimenez
Sphingolipids, found in membranes of eukaryotic cells, have been demonstrated to carry out functions in various processes in plant cells. However, the roles of these lipids in fruit abscission remain to be determined in plants. Biochemical and fluorescence microscopy imaging approach has been adopted to investigate the accumulation and distribution of sphingolipids during mature-fruit abscission in olive (Olea europaea L. cv. Picual). Here, a lipid-content analysis in live protoplasts of the olive abscission zone (AZ) was made with fluorescent dyes and lipid analogs, particularly plasma membrane sphingolipid-enriched domains, and their dynamics were investigated in relation to the timing of mature-fruit abscission...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28702278/prima-a-gene-centered-rna-to-protein-method-for-mapping-rna-protein-interactions
#7
Alex M Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D Holdorf, Sean P Ryder, Albertha J M Walhout
Interactions between RNA binding proteins (RBPs) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts...
2017: Translation
https://www.readbyqxmd.com/read/28701485/gt-rich-promoters-can-drive-rna-pol-ii-transcription-and-deposition-of-h2a-z-in-african-trypanosomes
#8
Carolin Wedel, Konrad U Förstner, Ramona Derr, T Nicolai Siegel
Genome-wide transcription studies are revealing an increasing number of "dispersed promoters" that, unlike "focused promoters", lack well-conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well-defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation...
July 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28701416/eukaryotic-transcription-factors-paradigms-of-protein-intrinsic-disorder
#9
REVIEW
Lasse Staby, Charlotte O'Shea, Martin Willemoës, Frederik Theisen, Birthe B Kragelund, Karen Skriver
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from 'negative noodles' to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities...
July 12, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28700213/enabling-graded-and-large-scale-multiplex-of-desired-genes-using-a-dual-mode-dcas9-activator-in-saccharomyces-cerevisiae
#10
Matthew Deaner, Julio Mejia, Hal S Alper
Standard approaches for dCas9-based modification of gene expression are limited in the ability to multiplex targets, establish streamlined cassettes, and utilize commonly studied Pol II promoters. In this work, we re-purpose the dCas9-VPR activator to act as a dual-mode activator/repressor that can be programmed based solely on target position at gene loci. Furthermore, we implement this approach using a streamlined Pol II-ribozyme system that allows expression of many sgRNAs from a single transcript. By "stepping" dCas9-VPR within the promoter region and ORF we create graded activation and repression (respectively) of target genes, allowing precise control over multiplexed gene modulation...
July 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28699129/shikonin-changes-the-lipopolysaccharide-induced-expression-of-inflammation-related-genes-in-macrophages
#11
Lucia Satiko Yoshida, Tomohito Kakegawa, Yasukatsu Yuda, Hiromi Takano-Ohmuro
We aimed to find candidate molecules possibly involved in the anti-inflammatory activity of shikonin (active compound of "Shikon") by analyzing its effects on gene expression of lipopolysaccharide (LPS)-treated THP-1 macrophages. Polysome-associated mRNAs (those expected to be under translation: translatome) from cells treated with LPS alone (LPS: 5 µg/mL), shikonin alone (S: 100 nM), or LPS plus shikonin (LPS&S) for 3 h were analyzed by DNA microarray followed by detection of enriched pathways/gene ontologies using the tools of the STRING database...
July 11, 2017: Journal of Natural Medicines
https://www.readbyqxmd.com/read/28696216/regulation-of-lysosomal-function-by-the-daf-16-forkhead-transcription-factor-couples-reproduction-to-aging-in-caenorhabditis-elegans
#12
Kunal Baxi, Ata Ghavidel, Brandon Waddell, Troy A Harkness, Carlos E de Carvalho
Aging in eukaryotes is accompanied by widespread deterioration of the somatic tissue. Yet, abolishing germ cells delays the age-dependent somatic decline in Caenorhabditis elegans In adult worms lacking germ cells, the activation of the DAF-9/DAF-12 steroid signalling pathway in the gonad recruits DAF-16 activity in the intestine to promote longevity-associated phenotypes. However, the impact of this pathway on the fitness of normally reproducing animals is less clear. Here, we explore the link between progeny production and somatic aging and identify the loss of lysosomal acidity, a critical regulator of the proteolytic output of these organelles, as a novel biomarker of aging in C...
July 10, 2017: Genetics
https://www.readbyqxmd.com/read/28692326/deletion-of-eif2%C3%AE-lysine-stretches-creates-a-dominant-negative-that-affects-the-translation-and-proliferation-in-human-cell-line-a-tool-for-arresting-the-cell-growth
#13
Gabrielle Dias Salton, Claudia Cilene Fernandes Correia Laurino, Nicolás Oliveira Mega, Andrés Delgado-Cañedo, Niclas Setterblad, Maryvonnick Carmagnat, Ricardo Machado Xavier, Elizabeth Cirne-Lima, Guido Lenz, João Antonio Pêgas Henriques, Jomar Pereira Laurino
BACKGROUND: Eukaryote initiation factor 2 subunit β (eIF2β) plays a crucial role in regulation protein synthesis, which mediates the interaction of eIF2 with mRNA. eIF2β contains evolutionarily conserved polylysine stretches in amino-terminal region and a zinc finger motif in the carboxy-terminus. METHODS: The gene eIF2β was cloned under tetracycline transcription control and the polylysine stretches were deleted by site-directed mutagenesis (eIF2βΔ3K). The plasmid was transfected into HEK 293 TetR cells...
July 10, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28690840/making-the-clock-tick-the-transcriptional-landscape-of-the-plant-circadian-clock
#14
REVIEW
James Ronald, Seth J Davis
Circadian clocks are molecular timekeepers that synchronise internal physiological processes with the external environment by integrating light and temperature stimuli. As in other eukaryotic organisms, circadian rhythms in plants are largely generated by an array of nuclear transcriptional regulators and associated co-regulators that are arranged into a series of interconnected molecular loops. These transcriptional regulators recruit chromatin-modifying enzymes that adjust the structure of the nucleosome to promote or inhibit DNA accessibility and thus guide transcription rates...
2017: F1000Research
https://www.readbyqxmd.com/read/28690838/recent-advances-in-high-throughput-approaches-to-dissect-enhancer-function
#15
REVIEW
David Santiago-Algarra, Lan T M Dao, Lydie Pradel, Alexandre España, Salvatore Spicuglia
The regulation of gene transcription in higher eukaryotes is accomplished through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. It is now well acknowledged that enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Many strategies have been developed to identify and characterize enhancers. Here, we discuss recent advances in high-throughput approaches to assess enhancer activity, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies...
2017: F1000Research
https://www.readbyqxmd.com/read/28689066/roles-of-a-mitochondrial-accsco2-gene-from-apis-cerana-cerana-in-oxidative-stress-responses
#16
Haihong Jia, Manli Ma, Na Zhai, Zhenguo Liu, Hongfang Wang, Xingqi Guo, Baohua Xu
In eukaryotes, cytochrome c oxidase (COX) is a multimeric protein complex that is the last enzyme in the respiratory electron transport chain of mitochondria. Syntheses of cytochrome c oxidase (SCO) proteins are copper-donor chaperones involved in metalation of the CuA redox center of COX. However, its other precise actions are not yet understood. Here, we report the characterization of AccSCO2 from Apis cerana cerana (Acc). Our data showed that AccSCO2 expression was induced by cold (4°C), CdCl2, HgCl2, ultraviolet (UV) light, and H2O2 and was inhibited by different pesticide treatments...
July 2, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28686223/regulation-of-autophagy-through-torc1-and-mtorc1
#17
REVIEW
Takeshi Noda
Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated by the target of rapamycin complex 1 (TORC1/mTORC1). In this review, a history of this regulation and recent advances in such regulation both in yeast and mammals will be discussed...
July 7, 2017: Biomolecules
https://www.readbyqxmd.com/read/28681362/protein-phosphatases-1-and-2a-and-their-naturally-occurring-inhibitors-current-topics-in-smooth-muscle-physiology-and-chemical-biology
#18
REVIEW
Akira Takai, Masumi Eto, Katsuya Hirano, Kosuke Takeya, Toshiyuki Wakimoto, Masaru Watanabe
Protein phosphatases 1 and 2A (PP1 and PP2A) are the most ubiquitous and abundant serine/threonine phosphatases in eukaryotic cells. They play fundamental roles in the regulation of various cellular functions. This review focuses on recent advances in the functional studies of these enzymes in the field of smooth muscle physiology. Many naturally occurring protein phosphatase inhibitors with different relative PP1/PP2A affinities have been discovered and are widely used as powerful research tools. Current topics in the chemical biology of PP1/PP2A inhibitors are introduced and discussed, highlighting the identification of the gene cluster responsible for the biosynthesis of calyculin A in a symbiont microorganism of a marine sponge...
July 5, 2017: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/28681113/structure-and-mechanisms-of-viral-transcription-factors-in-archaea
#19
REVIEW
Carol Sheppard, Finn Werner
Virus-encoded transcription factors have been pivotal in exploring the molecular mechanisms and regulation of gene expression in bacteria and eukaryotes since the birth of molecular biology, while our understanding of viral transcription in archaea is still in its infancy. Archaeal viruses do not encode their own RNA polymerases (RNAPs) and are consequently entirely dependent on their hosts for gene expression; this is fundamentally different from many bacteriophages and requires alternative regulatory strategies...
July 5, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28678890/platinum-sensitive-2-like-impacts-growth-root-morphology-seed-set-and-stress-responses
#20
Amr R A Kataya, Maria T Creighton, Toga P Napitupulu, Christine Sætre, Behzad Heidari, Peter Ruoff, Cathrine Lillo
Eukaryotic protein phosphatase 4 (PP4) is a PP2A-type protein phosphatase that is part of a conserved complex with regulatory factors PSY2 and PP4R2. Various lines of Arabidopsis thaliana with mutated PP4 subunit genes were constructed to study the so far completely unknown functions of PP4 in plants. Mutants with knocked out putative functional homolog of the PSY2 LIKE (PSY2L) gene were dwarf and bushy, while plants with knocked out PP4R2 LIKE (PP4R2L) looked very similar to WT. The psy2l seedlings had short roots with disorganized morphology and impaired meristem...
2017: PloS One
keyword
keyword
83233
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"