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eukaryotic gene regulation

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https://www.readbyqxmd.com/read/29691989/targeting-of-rna-polymerase-ii-by-a-nuclear-legionella-pneumophila-dot-icm-effector-snpl
#1
Ralf Schuelein, Hugh Spencer, Laura F Dagley, Peng Fei Li, Lin Luo, Jennifer L Stow, Gilu Abraham, Thomas Naderer, Laura Gomez-Valero, Carmen Buchrieser, Chihiro Sugimoto, Junya Yamagishi, Andrew I Webb, Shivani Pasricha, Elizabeth L Hartland
The intracellular pathogen Legionella pneumophila influences numerous eukaryotic cellular processes through the Dot/Icm-dependent translocation of more than 300 effector proteins into the host cell. Although many translocated effectors localize to the Legionella replicative vacuole, other effectors can affect remote intracellular sites. Following infection, a subset of effector proteins localizes to the nucleus where they subvert host cell transcriptional responses to infection. Here we identified Lpg2519 (Lpp2587/Lpw27461), as a new nuclear-localized effector that we have termed SnpL...
April 24, 2018: Cellular Microbiology
https://www.readbyqxmd.com/read/29691548/-study-of-endoplasmic-reticulum-stress-response-in-osteogenic-differentiation-of-human-periodontal-ligament-cells
#2
Li-Fen Li, Yang Wen, Long Jiang, Ya-Qin Zhu
PURPOSE: The aim of this study was to establish whether endoplasmic reticulum (ER) stress is involved in osteogenic differentiation of periodontal ligament cells (PDLCs) and to better understand the mechanism of PDLCs osteogenic differentiation. METHODS: PDLCs were isolated from extracted teeth and cultured in presence or absence of osteogenic medium, which can induce osteogenic differentiation of PDLCs. Alkaline phosphatase and alizarin red S staining were performed to characterize the osteogenic differentiation of PDLCs...
December 2017: Shanghai Kou Qiang Yi Xue, Shanghai Journal of Stomatology
https://www.readbyqxmd.com/read/29688631/a-guide-to-mirnas-in-inflammation-and-innate-immune-responses
#3
REVIEW
Charlotte Nejad, H James Stunden, Michael P Gantier
The discovery of microRNAs (miRNAs) in the early 1990's has revolutionised our thinking of post-transcriptional gene control. miRNAs are involved in the regulation of almost every cellular and developmental process in eukaryotic organisms. In the context of infection and immunity, miRNAs play critical roles controlling processes involved in pathogen clearance, while ensuring a rapid return to homeostasis. In this review, we provide a broad overview of the miRNAs that have been implicated in innate immunity and inflammation in mammals over the past decade...
April 24, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29687907/proton-coupled-oligopeptide-transporter-1-pept1-function-regulation-and-influence-on-the-intestinal-homeostasis
#4
Britta Spanier, Florian Rohm
As the organ with one of the largest surface areas facing the environment and responsible for nutrient uptake, the small intestine expresses numerous transport proteins in its brush-border membrane for efficient absorption and supply of dietary macro- and micronutrients. The understanding of regulation and functional interplay of these nutrient transporters is of emerging interest in nutrition and medical physiology research in respect to development of diabetes, obesity, and inflammatory bowel disease worldwide...
March 25, 2018: Comprehensive Physiology
https://www.readbyqxmd.com/read/29686299/transcriptome-analysis-reveals-genes-involved-in-flavonoid-biosynthesis-and-accumulation-in-dendrobium-catenatum-from-different-locations
#5
Zhouxi Lei, Chunhua Zhou, Xiaoyu Ji, Gang Wei, Yuechun Huang, Wenxia Yu, Yingyi Luo, Yue Qiu
In this study, we applied transcriptome and UHPLC-MS technologies to investigate the flavonoids and their biosynthesis- and accumulation-related genes in Dendrobium catenatum from three different locations. Eight flavonoid glycosides were identified using standard references or previously isolated substances with MS data analysis. The total flavonoid contents were determined by reagents, and all the data were analyzed. In total, 23139 unigenes were obtained using the Dendrobium catenatum genome data. Of these, 10398 were annotated in the Gene Ontology (GO) database, 4203 were annotated in the KEGG database, and 10917 were annotated in the EuKaryotic Orthologous Groups (KOG) database...
April 23, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29685971/epigenetics-the-first-25-centuries
#6
A Ganesan
Epigenetics is a natural progression of genetics as it aims to understand how genes and other heritable elements are regulated in eukaryotic organisms. The history of epigenetics is briefly reviewed, together with the key issues in the field today. This themed issue brings together a diverse collection of interdisciplinary reviews and research articles that showcase the tremendous recent advances in epigenetic chemical biology and translational research into epigenetic drug discovery.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'...
June 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29676248/rnase-e-and-the-high-fidelity-orchestration-of-rna-metabolism
#7
Katarzyna J Bandyra, Ben F Luisi
The bacterial endoribonuclease RNase E occupies a pivotal position in the control of gene expression, as its actions either commit transcripts to an irreversible fate of rapid destruction or unveil their hidden functions through specific processing. Moreover, the enzyme contributes to quality control of rRNAs. The activity of RNase E can be directed and modulated by signals provided through regulatory RNAs that guide the enzyme to specific transcripts that are to be silenced. Early in its evolutionary history, RNase E acquired a natively unfolded appendage that recruits accessory proteins and RNA...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29675811/systematic-analysis-and-comparison-of-the-phd-finger-gene-family-in-chinese-pear-pyrus-bretschneideri-and-its-role-in-fruit-development
#8
Yunpeng Cao, Yahui Han, Dandan Meng, Muhammad Abdullah, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes...
April 20, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29675586/rapamycin-alleviates-hormone-imbalance-induced-chronic-nonbacterial-inflammation-in-rat-prostate-through-activating-autophagy-via-the-mtor-ulk1-atg13-signaling-pathway
#9
Yang Su, Jingxiao Lu, Xianguo Chen, Chaozhao Liang, Pengcheng Luo, Cong Qin, Jie Zhang
Chronic prostatitis (CP) is a clinically common disease with high morbidity. It affects the patients' quality of life (QoL) as well as physical and mental health seriously due to the recurring symptoms of lower urinary tract and genitalia. As the opinions about the etiology of CP are still not uniform, it is very difficult to be treated or even cured. Autophagy is a highly conserved physiological function which is widely found in eukaryotic cells. In general, cells maintain a certain level of autophagy under physiological conditions, and the basal level of autophagy can be regulated by a variety of autophagy-related genes under stress such as hunger, infection, trauma, and other circumstances...
April 19, 2018: Inflammation
https://www.readbyqxmd.com/read/29673772/widespread-enhancer-activity-from-core-promoters
#10
REVIEW
Alejandra Medina-Rivera, David Santiago-Algarra, Denis Puthier, Salvatore Spicuglia
Gene expression in higher eukaryotes is precisely regulated in time and space through the interplay between promoters and gene-distal regulatory regions, known as enhancers. The original definition of enhancers implies the ability to activate gene expression remotely, while promoters entail the capability to locally induce gene expression. Despite the conventional distinction between them, promoters and enhancers share many genomic and epigenomic features. One intriguing finding in the gene regulation field comes from the observation that many core promoter regions display enhancer activity...
April 16, 2018: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29672999/tagging-of-weakly-expressed-toxoplasma-gondii-calcium-related-genes-with-high-affinity-tags
#11
Miryam A Hortua Triana, Karla M Márquez-Nogueras, Le Chang, Andrew J Stasic, Catherine Li, Kevin A Spiegel, Amrita Sharma, Zhu-Hong Li, Silvia N J Moreno
Calcium ions regulate a diversity of cellular functions in all eukaryotes. The cytosolic Ca2+ concentration is tightly regulated at the physiological cytosolic concentration of 50-100 nM. The Toxoplasma gondii genome predicts the presence of several genes encoding potential Ca2+ channels, pumps and transporters. Many of these genes are weakly expressed and likely tightly regulated due to their potential impact to the physiology of the cell. Endogenous tagging has been widely used to localize proteins in T. gondii but low level of expression of many of them makes visualization of tags difficult and sometimes impossible...
April 19, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29670105/viral-proteins-as-a-potential-driver-of-histone-depletion-in-dinoflagellates
#12
Nicholas A T Irwin, Benjamin J E Martin, Barry P Young, Martin J G Browne, Andrew Flaus, Christopher J R Loewen, Patrick J Keeling, LeAnn J Howe
Within canonical eukaryotic nuclei, DNA is packaged with highly conserved histone proteins into nucleosomes, which facilitate DNA condensation and contribute to genomic regulation. Yet the dinoflagellates, a group of unicellular algae, are a striking exception to this otherwise universal feature as they have largely abandoned histones and acquired apparently viral-derived substitutes termed DVNPs (dinoflagellate-viral-nucleoproteins). Despite the magnitude of this transition, its evolutionary drivers remain unknown...
April 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29670053/testosterone-dependent-mir-26a-5p-and-let-7g-5p-act-as-signaling-mediators-to-regulate-sperm-apoptosis-via-targeting-pten-and-pmaip1
#13
Jideng Ma, Yu Fan, Jinwei Zhang, Siyuan Feng, Zihui Hu, Wanling Qiu, Keren Long, Long Jin, Qianzi Tang, Xun Wang, Qi Zhou, Yiren Gu, Weihang Xiao, Lingyan Liu, Xuewei Li, Mingzhou Li
Recent evidence suggests that testosterone deficiency can dramatically decrease the quality of sperm. MicroRNAs (miRNAs) are conserved mediators of post-transcriptional gene regulation in eukaryotes. However, the systemic regulation and function of miRNAs in sperm quality decline induced by testosterone deficiency has not been investigated. Here, we found that the sperm apoptosis was significantly enhanced and the sperm motility was dramatically decreased in hemicastrated pigs. We then used small RNA sequencing to detect miRNA profiles of sperm from pigs with prepubertal hemicastration (HC) and compared them with control libraries...
April 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29668857/de-novo-mutations-of-the-atp6v1a-gene-cause-developmental-encephalopathy-with-epilepsy
#14
Anna Fassio, Alessandro Esposito, Mitsuhiro Kato, Hirotomo Saitsu, Davide Mei, Carla Marini, Valerio Conti, Mitsuko Nakashima, Nobuhiko Okamoto, Akgun Olmez Turker, Burcu Albuz, C Nur Semerci Gündüz, Keiko Yanagihara, Elisa Belmonte, Luca Maragliano, Keri Ramsey, Chris Balak, Ashley Siniard, Vinodh Narayanan, Chihiro Ohba, Masaaki Shiina, Kazuhiro Ogata, Naomichi Matsumoto, Fabio Benfenati, Renzo Guerrini
V-type proton (H+) ATPase (v-ATPase) is a multi-subunit proton pump that regulates pH homeostasis in all eukaryotic cells; in neurons, v-ATPase plays additional and unique roles in synapse function. Through whole exome sequencing, we identified de novo heterozygous mutations (p.Pro27Arg, p.Asp100Tyr, p.Asp349Asn, p.Asp371Gly) in ATP6V1A, encoding the A subunit of v-ATPase, in four patients with developmental encephalopathy with epilepsy. Early manifestations, observed in all patients, were developmental delay and febrile seizures, evolving to encephalopathy with profound delay, hypotonic/dyskinetic quadriparesis and intractable multiple seizure types in two patients (p...
April 13, 2018: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29665941/-research-on-ralation-of-long-non-coding-rna-with-diffuse-large-b-cell-lymphomas-review
#15
Yan-Yuan Wu, Yi-Ran Xing, Duo-Nan Yu
Diffuse large B-cell lymphoma (DLBCL) accounts for approximately 30% of the non-Hodgkin's lymphoma patients. The underlying molecular mechanism of its pathogenesis is not well defined and the survival rate of DLBCL patients is very low. Moreover, the annual incidence and mortality of DLBCL is still rising. Accordingly, identification and characterization of new molecular pathways of DLBCL will lead to the development of novel diagnostic markers and molecular therapeutic targets. Long non-coding RNAs (LncRNA) are non-coding RNAs with a length greater than 200 bp in eukaryotic cells, which can regulate the expression of their target genes at the transcriptional and post transcriptional levels...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/29663663/modular-ligation-extension-of-guide-rna-operons-lego-for-multiplexed-dcas9-regulation-of-metabolic-pathways-in-saccharomyces-cerevisiae
#16
Matthew Deaner, Allison Holzman, Hal S Alper
Metabolic engineering typically utilizes a suboptimal step-wise gene target optimization approach to parse a highly connected and regulated cellular metabolism. While the endonuclease-null CRISPR/Cas system has enabled gene expression perturbations without genetic modification, it has been mostly limited to small sets of gene targets in eukaryotes due to inefficient methods to assemble and express large sgRNA operons. In this work, we develop a TEF1p-tRNA expression system and demonstrate that the use of tRNAs as splicing elements flanking sgRNAs provides higher efficiency than both Pol III and ribozyme-based expression across a variety of single sgRNA and multiplexed contexts...
April 16, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29662072/a-firefly-luciferase-dual-color-bioluminescence-reporter-assay-using-two-substrates-to-simultaneously-monitor-two-gene-expression-events
#17
Bruce R Branchini, Tara L Southworth, Danielle M Fontaine, Dawn Kohrt, Catherine M Florentine, Martha J Grossel
Effective methods for monitoring eukaryotic gene expression and regulation based on bioluminescence - the emission of light by living organisms - are well established. Typically, the expression of a gene of interest is reported on with high sensitivity and over a wide dynamic range by the emission of light from a variety of engineered luciferase genes from beetles and marine organisms. The luciferase reporter genes are expressed downstream of the target gene or promoter and detected after exogenous addition of luciferin substrates...
April 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29661850/distinct-3-utrs-regulate-the-life-cycle-specific-expression-of-two-tctp-paralogs-in-trypanosoma-brucei
#18
Borka Jojic, Simona Amodeo, Irina Bregy, Torsten Ochsenreiter
The translationally controlled tumor protein (TCTP) is highly conserved and ubiquitously expressed in eukaryotes. It is involved in growth and development, cell cycle progression, protection against cellular stresses and apoptosis, indicating the multifunctional role of the protein. Here, for the first time we characterize the expression and function of TCTP in the human and animal pathogen, Trypanosoma brucei We identified two paralogs ( TCTP1 and TCTP2 ) that are differentially expressed in the life cycle of the parasite...
April 16, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29659634/genome-wide-analysis-of-basic-helix-loop-helix-superfamily-members-in-peach
#19
Chunhua Zhang, Ruchao Feng, Ruijuan Ma, Zhijun Shen, Zhixiang Cai, Zhizhong Song, Bin Peng, Mingliang Yu
The basic helix-loop-helix (bHLH) transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. Over the past several decades, many bHLH superfamily genes have been identified and characterized in herbaceous and woody plants. However, the genes belonging to the bHLH superfamily in peach (Prunus persica) have not yet been comprehensively identified and characterized. Here, we identified 95 members of the bHLH superfamily in the peach genome, and these genes were classified into 19 subfamilies based on a phylogenetic comparison with bHLH proteins from Arabidopsis...
2018: PloS One
https://www.readbyqxmd.com/read/29659627/n6-methyladenosine-modification-and-the-ythdf2-reader-protein-play-cell-type-specific-roles-in-lytic-viral-gene-expression-during-kaposi-s-sarcoma-associated-herpesvirus-infection
#20
Charles Hesser, John Karijolich, Dan Dominissini, Chuan He, Britt A Glaunsinger
Methylation at the N6 position of adenosine (m6A) is a highly prevalent and reversible modification within eukaryotic mRNAs that has been linked to many stages of RNA processing and fate. Recent studies suggest that m6A deposition and proteins involved in the m6A pathway play a diverse set of roles in either restricting or modulating the lifecycles of select viruses. Here, we report that m6A levels are significantly increased in cells infected with the oncogenic human DNA virus Kaposi's sarcoma-associated herpesvirus (KSHV)...
April 16, 2018: PLoS Pathogens
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