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gene regulation in eukaryotes

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https://www.readbyqxmd.com/read/28645773/abc-protein-cgabcf2-is-required-for-asexual-and-sexual-development-appressorial-formation-and-plant-infection-in-colletotrichum-gloeosporioides
#1
Zongshan Zhou, Jianyuan Wu, Meiyu Wang, Junxiang Zhang
ATP-binding cassette (ABC) proteins are exclusively found in both prokaryotes and eukaryotes. In this study, we have characterized a gene from Glomerella leaf spot pathogen Colletotrichum gloeosporioides that encodes an ABC protein, whose function to date remains unknown. We designated this gene as CgABCF2. Deletion of CgABCF2 showed drastic reduction both growing rate and conidial production in C. gloeosporioides. The Δcgabcf2 mutant did not form the appressoria, lost the capability to infect apple and failed to form lesions on the wounded leaves and fruits...
June 20, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28644004/the-intricate-effects-of-alpha-amino-and-lysine-modifications-on-arginine-methylation-on-the-n-terminal-tail-of-histone-h4
#2
Melody D Fulton, Jing Zhang, Maomao He, Meng-Chiao Ho, Y George Zheng
Chemical modifications on the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The "histone code" hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) on the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and over 450 histone PTMs discovered, and the PTMs on lysine and arginine residues account for a crucial part of the histone code. Although significant progress has been achieved in recent years, the molecular basis for the histone code is far from being fully understood...
June 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28641092/nuclear-mechanotransduction-sensing-the-force-from-within
#3
REVIEW
Avathamsa Athirasala, Nivi Hirsch, Amnon Buxboim
The cell nucleus is a hallmark of eukaryotic evolution, where gene expression is regulated and the genome is replicated and repaired. Yet, in addition to complex molecular processes, the nucleus has also evolved to serve physical tasks that utilize its optical and mechanical properties. Nuclear mechanotransduction of externally applied forces and extracellular stiffness is facilitated by the physical connectivity of the extracellular environment, the cytoskeleton and the nucleoskeletal matrix of lamins and chromatin...
June 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28640868/functional-metabolomics-as-a-tool-to-analyze-mediator-function-and-structure-in-plants
#4
Celine Davoine, Ilka N Abreu, Khalil Khajeh, Jeanette Blomberg, Brendan N Kidd, Kemal Kazan, Peer M Schenk, Lorenz Gerber, Ove Nilsson, Thomas Moritz, Stefan Björklund
Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast...
2017: PloS One
https://www.readbyqxmd.com/read/28638059/cis-regulatory-evolution-in-prokaryotes-revealed-by-interspecific-archaeal-hybrids
#5
Carlo G Artieri, Adit Naor, Israela Turgeman-Grott, Yiqi Zhou, Ryan York, Uri Gophna, Hunter B Fraser
The study of allele-specific expression (ASE) in interspecific hybrids has played a central role in our understanding of a wide range of phenomena, including genomic imprinting, X-chromosome inactivation, and cis-regulatory evolution. However across the hundreds of studies of hybrid ASE, all have been restricted to sexually reproducing eukaryotes, leaving a major gap in our understanding of the genomic patterns of cis-regulatory evolution in prokaryotes. Here we introduce a method to generate stable hybrids between two species of halophilic archaea, and measure genome-wide ASE in these hybrids with RNA-seq...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637241/the-chromatin-remodeling-complex-swi-snf-regulates-splicing-of-meiotic-transcripts-in-saccharomyces-cerevisiae
#6
Srivats Venkataramanan, Stephen Douglass, Anoop R Galivanche, Tracy L Johnson
Despite its relatively streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae, such as splicing of meiotic transcripts. Like other eukaryotes, S. cerevisiae undergoes a dramatic reprogramming of gene expression during meiosis, including regulated splicing of a number of crucial meiosis-specific RNAs. Splicing of a subset of these is dependent upon the splicing activator Mer1. Here we show a crucial role for the chromatin remodeler Swi/Snf in regulation of splicing of meiotic genes and find that the complex affects meiotic splicing in two ways...
May 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28636597/phase-separation-drives-heterochromatin-domain-formation
#7
Amy R Strom, Alexander V Emelyanov, Mustafa Mir, Dmitry V Fyodorov, Xavier Darzacq, Gary H Karpen
Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28633563/mammalian-synthetic-biology-engineering-biological-systems
#8
Joshua B Black, Pablo Perez-Pinera, Charles A Gersbach
The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution...
June 21, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28633280/motifhyades-expectation-maximization-for-de-novo-dna-motif-pair-discovery-on-paired-sequences
#9
Ka-Chun Wong
Motivation: In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter-enhancer pairs) systematically. Results: To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences...
June 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#10
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28626565/site-specific-azide-acetyllysine-photochemistry-on-epigenetic-readers-for-interactome-profiling
#11
Babu Sudhamalla, Debasis Dey, Megan Breski, Tiffany Nguyen, Kabirul Islam
Chemical modifications on DNA, RNA and histones are recognized by an array of 'reader' modules to regulate transcriptional programming and cell fate. However, identification of reader-specific interacting partners in a dynamic cellular environment remains a significant challenge. Herein, we report a chemoproteomic approach termed 'interaction-based protein profiling' (IBPP) to characterize novel interacting partners of potentially any reader protein. IBPP harnesses a photosensitive amino acid introduced into the hydrophobic pocket of a reader module to crosslink and enrich transient interacting partners that are inaccessible to traditional methods...
June 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28625986/the-irr-and-rira-proteins-participate-in-a-complex-regulatory-circuit-and-act-in-concert-to-modulate-bacterioferritin-expression-in-ensifer-meliloti-1021
#12
Daniela Costa, Vanesa Amarelle, Claudio Valverde, Mark R O'Brian, Elena Fabiano
In this work we found that the bfr gene of the rhizobial species Ensifer meliloti, encoding a bacterioferritin iron storage protein, is involved in iron homeostasis and oxidative stress response. This gene is located downstream and overlapping the smc03787 ORF. No well predicted RirA or Irr boxes were found in the region immediately upstream the bfr gene although two presumptive RirA boxes and one presumptive Irr box were present in the putative promoter of smc03787 We demonstrate that bfr gene expression is enhanced under iron sufficient condition and that Irr and RirA modulate this expression...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28624850/the-plant-lim-proteins-unlocking-the-hidden-attractions
#13
REVIEW
Vikas Srivastava, Praveen Kumar Verma
The plant LIMs comprise two sub-families with one (DA1/DAR) and two (2LIM) LIM domains. This review comprehensively discussed the structure and potential role of this protein family in diverse area of plant biology. The description of first eukaryote lineage-specific plant LIM domain (LIN11, ISL1, and MEC3) proteins was observed in Helianthus long back. The successive study of LIM proteins in diverse plants has shown its vital relation to development, metabolism and defence. This nascent gene family has been worked out for their role in actin dynamics, organ size determination and transcription regulation...
June 17, 2017: Planta
https://www.readbyqxmd.com/read/28624538/analysis-of-mrna-deadenylation-by-multi-protein-complexes
#14
Michael W Webster, James A W Stowell, Terence T L Tang, Lori A Passmore
Poly(A) tails are found at the 3' end of almost every eukaryotic mRNA and are important for the stability of mRNAs and their translation into proteins. Thus, removal of the poly(A) tail, a process called deadenylation, is critical for regulation of gene expression. Most deadenylation enzymes are components of large multi-protein complexes. Here, we describe an in vitro deadenylation assay developed to study the exonucleolytic activities of the multi-protein Ccr4-Not and Pan2-Pan3 complexes. We discuss how this assay can be used with short synthetic RNAs, as well as longer RNA substrates generated using in vitro transcription...
June 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28623575/from-genes-to-networks-characterizing-gene-regulatory-interactions-in-plants
#15
Kerstin Kaufmann, Dijun Chen
Plants, like other eukaryotes, have evolved complex mechanisms to coordinate gene expression during development, environmental response, and cellular homeostasis. Transcription factors (TFs), accompanied by basic cofactors and posttranscriptional regulators, are key players in gene-regulatory networks (GRNs). The coordinated control of gene activity is achieved by the interplay of these factors and by physical interactions between TFs and DNA. Here, we will briefly outline recent technological progress made to elucidate GRNs in plants...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28622506/dynamic-rna-modifications-in-gene-expression-regulation
#16
REVIEW
Ian A Roundtree, Molly E Evans, Tao Pan, Chuan He
Over 100 types of chemical modifications have been identified in cellular RNAs. While the 5' cap modification and the poly(A) tail of eukaryotic mRNA play key roles in regulation, internal modifications are gaining attention for their roles in mRNA metabolism. The most abundant internal mRNA modification is N(6)-methyladenosine (m(6)A), and identification of proteins that install, recognize, and remove this and other marks have revealed roles for mRNA modification in nearly every aspect of the mRNA life cycle, as well as in various cellular, developmental, and disease processes...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28620758/transcriptome-analysis-of-drought-responsive-genes-regulated-by-hydrogen-sulfide-in-wheat-triticum-aestivum-l-leaves
#17
Hua Li, Min Li, Xingliang Wei, Xia Zhang, Ruili Xue, Yidan Zhao, Huijie Zhao
Drought is an environmental factor that deeply impacts wheat yield and quality. Hydrogen sulfide (H2S) is a known regulator of drought resistance in plants. To preliminarily elucidate the regulatory mechanisms of H2S on drought tolerance, the effects of H2S on drought-responsive genes were investigated by transcriptome analysis. As a result, a total of 7552 transcripts not only responded to drought stress but also exhibited differential expression relative to the polyethylene glycol (PEG) treatment (P) and the NaHS pretreatment with PEG treatment (SP)...
June 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28620688/controlling-microbial-phb-synthesis-via-crispri
#18
Dan Li, Li Lv, Jin-Chun Chen, Guo-Qiang Chen
Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively...
June 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28619535/evolution-and-regulation-of-bigelowiella-natans-light-harvesting-antenna-system
#19
Jonathan A D Neilson, Pattarasiri Rangsrikitphoti, Dion G Durnford
Bigelowiella natans is a mixotrophic flagellate and member of the chlorarachniophytes (Rhizaria), whose plastid is derived from a green algal endosymbiont. With the completion of the B. natans nuclear genome we are able to begin the analysis of the structure, function and evolution of the photosynthetic apparatus. B. natans has undergone substantial changes in photosystem structure during the evolution of the plastid from a green alga. While Photosystem II (PSII) composition is well conserved, Photosystem I (PSI) composition has undergone a dramatic reduction in accessory protein subunits...
May 31, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28617232/tigeri-modeling-and-visualizing-the-responses-to-perturbation-of-a-transcription-factor-network
#20
Namshik Han, Harry A Noyes, Andy Brass
BACKGROUND: Transcription factor (TF) networks play a key role in controlling the transfer of genetic information from gene to mRNA. Much progress has been made on understanding and reverse-engineering TF network topologies using a range of experimental and theoretical methodologies. Less work has focused on using these models to examine how TF networks respond to changes in the cellular environment. METHODS: In this paper, we have developed a simple, pragmatic methodology, TIGERi (Transcription-factor-activity Illustrator for Global Explanation of Regulatory interaction), to model the response of an inferred TF network to changes in cellular environment...
May 31, 2017: BMC Bioinformatics
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