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gene regulation in eukaryotes

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https://www.readbyqxmd.com/read/28230927/crispr-cas9-technologies
#1
Bart O Williams, Matthew L Warman
The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) pathway is revolutionizing biological research. Modifications to this primitive prokaryotic immune system now enable scientists to efficiently edit DNA or modulate gene expression in living eukaryotic cells and organisms. Thus, many laboratories can now perform important experiments that previously were considered scientifically risky or too costly. Here, we describe the components of the CRISPR/Cas system that have been engineered for use in eukaryotes...
February 23, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28230724/alternative-splicing-in-plant-genes-a-means-of-regulating-the-environmental-fitness-of-plants
#2
REVIEW
Xudong Shang, Ying Cao, Ligeng Ma
Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism's transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28230163/ectopic-expression-of-arabidopsis-target-of-rapamycin-attor-improves-water-use-efficiency-and-yield-potential-in-rice
#3
Achala Bakshi, Mazahar Moin, M Udaya Kumar, Aramati Bindu Madhava Reddy, Maozhi Ren, Raju Datla, E A Siddiq, P B Kirti
The target of Rapamycin (TOR) present in all eukaryotes is a multifunctional protein, regulating growth, development, protein translation, ribosome biogenesis, nutrient, and energy signaling. In the present study, ectopic expression of TOR gene of Arabidopsis thaliana in a widely cultivated indica rice resulted in enhanced plant growth under water-limiting conditions conferring agronomically important water-use efficiency (WUE) trait. The AtTOR high expression lines of rice exhibited profuse tillering, increased panicle length, increased plant height, high photosynthetic efficiency, chlorophyll content and low ∆(13)C...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229978/untranslated-regions-of-mrna-and-their-role-in-regulation-of-gene-expression-in-protozoan-parasites
#4
Shilpa J Rao, Sangeeta Chatterjee, Jayantapal K Pal
Protozoan parasites are one of the oldest living entities in this world that throughout their existence have shown excellent resilience to the odds of survival and have adapted beautifully to ever changing rigors of the environment. In view of the dynamic environment encountered by them throughout their life cycle, and in establishing pathogenesis, it is unsurprising that modulation of gene expression plays a fundamental role in their survival. In higher eukaryotes, untranslated regions (UTRs) of transcripts are one of the crucial regulators of gene expression (influencing mRNA stability and translation efficiency)...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28229932/csn5-jab1-suppresses-the-wnt-inhibitor-dkk1-in-colorectal-cancer-cells
#5
Sandra Jumpertz, Thomas Hennes, Yaw Asare, Anke K Schütz, Jürgen Bernhagen
The COP9 signalosome (CSN) is a multi-protein complex that is highly conserved in eukaryotes. Due to its regulatory impact on processes such as cell cycle, DNA damage response and apoptosis, the CSN is essential for mammalian cells. One of the best-studied functions of the CSN is the deNEDDylation of cullin-RING ligases (CRLs) via its catalytically active subunit CSN5/JAB1, thereby triggering the degradation of various target proteins. CSN5 was found to be overexpressed in many human cancer entities, including colon adenocarcinoma...
February 13, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28228471/novel-layers-of-rna-polymerase-iii-control-affecting-trna-gene-transcription-in-eukaryotes
#6
REVIEW
Ewa Leśniewska, Magdalena Boguta
RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28228125/rna-seq-of-life-stages-of-the-oomycete-phytophthora-infestans-reveals-dynamic-changes-in-metabolic-signal-transduction-and-pathogenesis-genes-and-a-major-role-for-calcium-signaling-in-development
#7
Audrey M V Ah-Fong, Kyoung Su Kim, Howard S Judelson
BACKGROUND: The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS: RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P...
February 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28224922/multiple-garlic-allium-sativum-l-micrornas-regulate-the-immunity-against-the-basal-rot-fungus-fusarium-oxysporum-f-sp-cepae
#8
Subodh Kumar Chand, Satyabrata Nanda, Rukmini Mishra, Raj Kumar Joshi
The basal plate rot fungus, Fusarium oxysporum f. sp. cepae (FOC), is the most devastating pathogen posing a serious threat to garlic (Allium sativum L.) production worldwide. MicroRNAs (miRNAs) are key modulators of gene expression related to development and defense responses in eukaryotes. However, the miRNA species associated with garlic immunity against FOC are yet to be explored. In the present study, a small RNA library developed from FOC infected resistant garlic line was sequenced to identify immune responsive miRNAs...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28223993/diacylglycerol-kinases-are-widespread-in-higher-plants-and-display-inducible-gene-expression-in-response-to-beneficial-elements-metal-and-metalloid-ions
#9
Hugo F Escobar-Sepúlveda, Libia I Trejo-Téllez, Paulino Pérez-Rodríguez, Juan V Hidalgo-Contreras, Fernando C Gómez-Merino
Diacylglycerol kinases (DGKs) are pivotal signaling enzymes that phosphorylate diacylglycerol (DAG) to yield phosphatidic acid (PA). The biosynthesis of PA from phospholipase D (PLD) and the coupled phospholipase C (PLC)/DGK route is a crucial signaling process in eukaryotic cells. Next to PLD, the PLC/DGK pathway is the second most important generator of PA in response to biotic and abiotic stresses. In eukaryotic cells, DGK, DAG, and PA are implicated in vital processes such as growth, development, and responses to environmental cues...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223359/peptide-recognition-by-hp1-chromoshadow-domains-revisited-plasticity-in-the-pseudosymmetric-histone-binding-site-of-human-hp1
#10
Yanli Liu, Su Qin, Ming Lei, Wolfram Tempel, Yuzhe Zhang, Peter Loppnau, Yanjun Li, Jinrong Min
Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PxVxL motif, but also with a region of histone H3 that bears the similar PxxVxL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PxxVxL motif of histone H3...
February 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28220899/group-a-streptococcal-m1-protein-provides-resistance-against-the-antimicrobial-activity-of-histones
#11
Simon Döhrmann, Christopher N LaRock, Ericka L Anderson, Jason N Cole, Brinda Ryali, Chelsea Stewart, Poochit Nonejuie, Joe Pogliano, Ross Corriden, Partho Ghosh, Victor Nizet
Histones are essential elements of chromatin structure and gene regulation in eukaryotes. An unexpected attribute of these nuclear proteins is their antimicrobial activity. A framework for histone release and function in host defense in vivo was revealed with the discovery of neutrophil extracellular traps, a specialized cell death process in which DNA-based structures containing histones are extruded to ensnare and kill bacteria. Investigating the susceptibility of various Gram-positive pathogens to histones, we found high-level resistance by one leading human pathogen, group A Streptococcus (GAS)...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220432/genome-wide-analysis-of-chromatin-accessibility-in-arabidopsis-infected-with-pseudomonas-syringae
#12
Yogendra Bordiya, Hong-Gu Kang
Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28219769/epitranscriptomic-regulation-of-viral-replication
#13
REVIEW
Camila Pereira-Montecinos, Fernando Valiente-Echeverría, Ricardo Soto-Rifo
RNA plays central roles in biology and novel functions and regulation mechanisms are constantly emerging. To accomplish some of their functions within the cell, RNA molecules undergo hundreds of chemical modifications from which N6-methyladenosine (m(6)A), inosine (I), pseudouridine (ψ) and 5-methylcytosine (5mC) have been described in eukaryotic mRNA. Interestingly, the m(6)A modification was shown to be reversible, adding novel layers of regulation of gene expression through what is now recognized as epitranscriptomics...
February 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28219680/the-regulation-of-transcriptional-repression-in-hypoxia
#14
Miguel A S Cavadas, Alex Cheong, Cormac T Taylor
A sufficient supply molecular oxygen is essential for the maintenance of physiologic metabolism and bioenergetic homeostasis for most metazoans. For this reason, mechanisms have evolved for eukaryotic cells to adapt to conditions where oxygen demand exceeds supply (hypoxia). These mechanisms rely on the modification of pre-existing proteins, translational arrest and transcriptional changes. The hypoxia inducible factor (HIF; a master regulator of gene induction in response to hypoxia) is responsible for the majority of induced gene expression in hypoxia...
February 17, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28216641/targeted-rp9-ablation-and-mutagenesis-in-mouse-photoreceptor-cells-by-crispr-cas9
#15
Ji-Neng Lv, Gao-Hui Zhou, Xuejiao Chen, Hui Chen, Kun-Chao Wu, Lue Xiang, Xin-Lan Lei, Xiao Zhang, Rong-Han Wu, Zi-Bing Jin
Precursor messenger RNA (Pre-mRNA) splicing is an essential biological process in eukaryotic cells. Genetic mutations in many spliceosome genes confer human eye diseases. Mutations in the pre-mRNA splicing factor, RP9 (also known as PAP1), predispose autosomal dominant retinitis pigmentosa (adRP) with an early onset and severe vision loss. However, underlying molecular mechanisms of the RP9 mutation causing photoreceptor degeneration remains fully unknown. Here, we utilize the CRISPR/Cas9 system to generate both the Rp9 gene knockout (KO) and point mutation knock in (KI) (Rp9, c...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28215355/differential-dna-methylation-may-contribute-to-temporal-and-spatial-regulation-of-gene-expression-and-the-development-of-mycelia-and-conidia-in-entomopathogenic-fungus-metarhizium-robertsii
#16
Wanzhen Li, Yulong Wang, Jianyu Zhu, Zhangxun Wang, Guiliang Tang, Bo Huang
Conidia and mycelia are two important developmental stages in the asexual life cycle of entomopathogenic fungus Metarhizium. Despite the crucial role that DNA methylation plays in many biological processes, its role in regulation of gene expression and development in fungi is not yet fully understood. We performed genome-wide analysis of DNA methylation patterns of an M. robertsii strain with single base pair resolution. Specifically, we examined for changes in methylation patterns between the conidia and mycelia stages...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28214582/structural-changes-induced-by-l50p-and-i61t-single-mutations-of-ubiquitin-affect-cell-cycle-progression-while-impairing-its-regulatory-and-degradative-functions-in-saccharomyces-cerevisiae
#17
Ankita Doshi, Mrinal Sharma, C Ratna Prabha
Posttranslational conjugation of ubiquitin to proteins either regulates their function directly or concentration through ubiquitination dependent degradation. High degree of conservation of ubiquitin's sequence implies structural and functional importance of the conserved residues. Ubiquitin gene of Saccharomyces cerevisiae was evolved in vitro by us to study the significance of conserved residues. Present study investigates the structural changes in the protein resulting from the single mutations UbS20F, UbA46S, UbL50P, UbI61T and their functional consequences in the SUB60 strain of S...
February 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28213158/pink1-parkin-mitophagy-and-neurodegeneration-what-do-we-really-know-in-vivo
#18
REVIEW
Alexander J Whitworth, Leo J Pallanck
Mitochondria are essential organelles that provide cellular energy and buffer cytoplasmic calcium. At the same time they produce damaging reactive oxygen species and sequester pro-apoptotic factors. Hence, eukaryotes have evolved exquisite homeostatic processes that maintain mitochondrial integrity, or ultimately remove damaged organelles. This subject has garnered intense interest recently following the discovery that two Parkinson's disease genes, PINK1 and parkin, regulate mitochondrial degradation (mitophagy)...
February 14, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#19
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28207814/jmjd-5-kdm8-regulates-h3k36me2-and-is-required-for-late-steps-of-homologous-recombination-and-genome-integrity
#20
Pier Giorgio Amendola, Nico Zaghet, João J Ramalho, Jens Vilstrup Johansen, Mike Boxem, Anna Elisabetta Salcini
The eukaryotic genome is organized in a three-dimensional structure called chromatin, constituted by DNA and associated proteins, the majority of which are histones. Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes. Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair. Here, we show that the JMJD-5 regulates H3K36 di-methylation and it is required at late stages of double strand break repair mediated by homologous recombination...
February 16, 2017: PLoS Genetics
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