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cis-regulatory elements

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https://www.readbyqxmd.com/read/28817121/meganuclease-assisted-generation-of-stable-transgenics-in-the-sea-anemone-nematostella-vectensis
#1
Eduard Renfer, Ulrich Technau
The sea anemone Nematostella vectensis is a model system used by a rapidly growing research community for comparative genomics, developmental biology and ecology. Here, we describe a microinjection procedure for creating stable transgenic lines in Nematostella based on meganuclease (I-SceI)-assisted integration of a transgenic cassette into the genome. The procedure describes the preparation of the reagents, microinjection of the transgenesis vector and the husbandry of transgenic animals. The microinjection setup differs from those of previously published protocols by the use of a holding capillary mounted on an inverted fluorescence microscope...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28814792/genetic-regulatory-effects-modified-by-immune-activation-contribute-to-autoimmune-disease-associations
#2
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane E Castel, Markus M Nöthen, Luis B Barreiro, Joseph K Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28808972/chromosome-conformation-capture-for-research-on-innate-antiviral-immunity
#3
Yoon Jung Kim, Tae Hoon Kim
Chromosome conformation capture (3C) technology has revolutionized our knowledge on chromatin folding and nuclear organization. This cis-loop detection approach can be used to identify candidate regulatory elements interacting with target gene of interest. This chapter introduces the application of 3C technique to investigate a dynamic alteration in the chromosome folding structure or genomic architecture resulting from interaction changes between the enhancer and its target gene. Innate antiviral immunity is one of the well-known gene induction systems, involving rapid first-line response to virus or pathogen to trigger gene expression changes in order to protect cells and to limit further infection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28802259/cis-regulatory-elements-explain-most-of-the-mrna-stability-variation-across-genes-in-yeast
#4
Jun Cheng, Kerstin C Maier, Ziga Avsec, Petra Rus, Julien Gagneur
The stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model for Saccharomyces cerevisiae based on functional mRNA sequence features that explains 59% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3'UTR motif, ATATTC, which we functionally validated...
August 11, 2017: RNA
https://www.readbyqxmd.com/read/28802165/the-world-according-to-garp-transcription-factors
#5
REVIEW
Alaeddine Safi, Anna Medici, Wojciech Szponarski, Sandrine Ruffel, Benoît Lacombe, Gabriel Krouk
Plant specific GARP transcription factor family (made of ARR-B and G2-like) contains genes with very diverse in planta functions: nutrient sensing, root and shoot development, floral transition, chloroplast development, circadian clock oscillation maintenance, hormonal transport and signaling. In this work we review: first, their structural but distant relationships with MYB transcription factors, second, their role in planta, third, the diversity of their Cis-regulatory elements, fourth, their potential protein partners...
August 10, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28801902/bioinformatically-informed-design-of-synthetic-mammalian-promoters
#6
Michael L Roberts, Polyxeni Katsoupi, Vivian Tseveleki, Era Taoufik
Synthetic promoters have been developed in a number of different organisms and are capable of mediating specific and enhanced levels of gene expression. Typically, cis-regulatory regions from a few genes are randomly combined to generate a synthetic promoter library, and the sequences with the highest activity are selected for in target cell lines. Here we describe a novel approach that can be employed in the construction of synthetic promoters . Specifically, we use gene expression profiles obtained from microarray datasets to select the cis-regulatory elements that comprise the synthetic promoter library...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801900/monitoring-promoter-activity-by-flow-cytometry
#7
Taher E I Taher
Genetic reporters have become invaluable tools for indirectly monitoring promoter activities. The quantitative measurement of promoter activities using reporter gene systems is fundamental for pharmaceutical, biomedical, and molecular biology research. Genetic reporters are used not only for measuring promoter activities but also for understanding the mechanisms controlling gene transcription and in the identification, and characterization of cis-acting regulatory elements. Fluorescent reporter proteins including enhanced green fluorescent protein (EGFP ) are reliable for monitoring quantitative underlying differences in promoter activities...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801786/the-grapevine-vvcax3-is-a-cation-h-exchanger-involved-in-vacuolar-ca-2-homeostasis
#8
Viviana Martins, Filipa Carneiro, Carlos Conde, Mariana Sottomayor, Hernâni Gerós
The grapevine VvCAX3 mediates calcium transport in the vacuole and is mostly expressed in green grape berries and upregulated by Ca (2+) , Na (+) and methyl jasmonate. Calcium is an essential plant nutrient with important regulatory and structural roles in the berries of grapevine (Vitis vinifera L.). On the other hand, the proton-cation exchanger CAX proteins have been shown to impact Ca(2+) homeostasis with important consequences for fruit integrity and resistance to biotic/abiotic stress. Here, the CAX gene found in transcriptomic databases as having one of the highest expressions in grapevine tissues, VvCAX3, was cloned and functionally characterized...
August 11, 2017: Planta
https://www.readbyqxmd.com/read/28800289/viral-master-circuits-from-discovery-to-new-therapy-targets
#9
Anand Pai, Leor S Weinberger
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates)...
August 11, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28793263/the-conserved-sonic-hedgehog-limb-enhancer-consists-of-discrete-functional-elements-that-regulate-precise-spatial-expression
#10
Laura A Lettice, Paul Devenney, Carlo De Angelis, Robert E Hill
Expression of sonic hedgehog (Shh) in the limb bud is regulated by an enhancer called the zone of polarizing activity regulatory sequence (ZRS), which, in evolution, belongs to an ancient group of highly conserved cis regulators found in all classes of vertebrates. Here, we examined the endogenous ZRS in mice, using genome editing to establish the relationship between enhancer composition and embryonic phenotype. We show that enhancer activity is a consolidation of distinct activity domains. Spatial restriction of Shh expression is mediated by a discrete repressor module, whereas levels of gene expression are controlled by large overlapping domains containing varying numbers of HOXD binding sites...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28783165/tmprss2-erg-fusion-co-opts-master-transcription-factors-and-activates-notch-signaling-in-primary-prostate-cancer
#11
Ken J Kron, Alexander Murison, Stanley Zhou, Vincent Huang, Takafumi N Yamaguchi, Yu-Jia Shiah, Michael Fraser, Theodorus van der Kwast, Paul C Boutros, Robert G Bristow, Mathieu Lupien
TMPRSS2-ERG (T2E) structural rearrangements typify ∼50% of prostate tumors and result in overexpression of the ERG transcription factor. Using chromatin, genomic and expression data, we show distinct cis-regulatory landscapes between T2E-positive and non-T2E primary prostate tumors, which include clusters of regulatory elements (COREs). This difference is mediated by ERG co-option of HOXB13 and FOXA1, implementing a T2E-specific transcriptional profile. We also report a T2E-specific CORE on the structurally rearranged ERG locus arising from spreading of the TMPRSS2 locus pre-existing CORE, assisting in its overexpression...
August 7, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28780864/predicting-ion-effects-in-rna-conformational-equilibrium
#12
Lizhen Sun, Clayton Kranawetter, Xiao Heng, Shi-Jie Chen
We develop a partial charge-based Tightly Bound Ion (PCTBI) model for the ion effects in RNA folding. Based on the Monte Carlo Tightly Bound Ion (MCTBI) approach, the model can account for ion fluctuation and correlation effects , and can predict the ion distribution around the RNA. Furthermore, unlike the previous coarse-grained RNA charge models, where negative charges are placed on the phosphates only, the current new model considers the detailed all-atom partial charge distribution on the RNA. Thus, the model not only keeps the advantage of the MCTBI model but also has the potential to provide important detailed information unattainable by the previousMCTBI models...
August 5, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28776093/identification-of-an-atypical-microdeletion-generating-the-rnf135-suz12-chimeric-gene-and-causing-a-position-effect-in-an-nf1-patient-with-overgrowth
#13
Luca Ferrari, Giulietta Scuvera, Arianna Tucci, Donatella Bianchessi, Francesco Rusconi, Francesca Menni, Elena Battaglioli, Donatella Milani, Paola Riva
Neurofibromatosis type I (NF1) microdeletion syndrome, which is present in 4-11% of NF1 patients, is associated with a severe phenotype as it is caused by the deletion of NF1 and other genes in the 17q11.2 region. The variable expressivity of the disease makes it challenging to establish genotype-phenotype correlations, which also affects prognosis and counselling. We here describe a 3-year-old NF1 patient with an atypical deletion and a complex phenotype. The patient showed overgrowth, café au lait spots, inguinal freckling, and neurological abnormalities...
August 3, 2017: Human Genetics
https://www.readbyqxmd.com/read/28774878/the-actin-binding-protein-profilin-2-is-a-novel-regulator-of-iron-homeostasis
#14
Sara Luscieti, Bruno Galy, Lucia Gutierrez, Michael Reinke, Jorge Couso, Maya Shvartsman, Antonio Di Pascale, Walter Witke, Matthias W Hentze, Pietro Pilo Boyl, Mayka Sanchez
Cellular iron homeostasis is controlled by the iron regulatory proteins (IRPs) 1 and 2 that bind cis-regulatory iron-responsive elements (IRE) on target mRNAs. We identified the profilin2 (Pfn2) mRNA, which encodes an actin binding protein involved in endocytosis and neurotransmitters release, as a novel IRP-interacting transcript and studied its role in iron metabolism. Combination of EMSA experiments and bioinformatic analyses led to the identification of an atypical and conserved IRE in the 3' untranslated region of Pfn2 mRNA...
August 3, 2017: Blood
https://www.readbyqxmd.com/read/28771698/molecular-and-functional-genetics-of-the-proopiomelanocortin-gene-food-intake-regulation-and-obesity
#15
REVIEW
Marcelo Rubinstein, Malcolm J Low
During the last decade, the obesity pandemia has skyrocketed, and the spectre is threatening children, adolescents and lower income families worldwide. Although driven by an increase in the consumption of ultra-processed edibles of poor nutritional value, the obesogenic changes in contemporary human lifestyle affect people differently, revealing that some individuals are more prone to developing increased adiposity. During the last years, we performed a variety of genetic, evolutionary, biochemical and behavioral experiments that allowed us to understand how a group of neurons present in the arcuate nucleus of the hypothalamus regulate the expression of the proopiomelanocortin (Pomc) gene and induce satiety...
August 3, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28766300/a-cell-based-high-throughput-method-for-identifying-modulators-of-alternative-splicing
#16
Sika Zheng
Alternative splicing, a key regulatory process of gene expression, is controlled by trans-acting factors that recognize cis-elements in premature RNA transcripts to affect spliceosome assembly and splice site choices. Extracellular stimuli and signaling cascades can converge on RNA binding splicing regulators to affect alternative splicing. Defects in splicing regulation have been associated with various human diseases, and modification of disease-causing splicing events presents great therapeutic promise. Determining splicing regulators and/or upstream modulators has been difficult with low throughput, low sensitivity, and low specificity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28756947/two-element-transcriptional-regulation-in-the-canonical-wnt-pathway
#17
Kibeom Kim, Jaehyoung Cho, Thomas S Hilzinger, Harry Nunns, Andrew Liu, Bryan E Ryba, Lea Goentoro
The canonical Wnt pathway regulates numerous fundamental processes throughout development and adult physiology and is often disrupted in diseases [1-4]. Signal in the pathway is transduced by β-catenin, which in complex with Tcf/Lef regulates transcription. Despite the many processes that the Wnt pathway governs, β-catenin acts primarily on a single cis element in the DNA, the Wnt-responsive element (WRE), at times potentiated by a nearby Helper site. In this study, working with Xenopus, mouse, and human systems, we identified a cis element, distinct from WRE, upon which β-catenin and Tcf act...
August 7, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28756583/phytopathogen-induced-changes-to-plant-methylomes
#18
REVIEW
Tarek Hewezi, Vince Pantalone, Morgan Bennett, C Neal Stewart, Tessa M Burch-Smith
DNA methylation is a dynamic and reversible type of epigenetic mark that contributes to cellular physiology by affecting transcription activity, transposon mobility and genome stability. When plants are infected with pathogens, plant DNA methylation patterns can change, indicating an epigenetic interplay between plant host and pathogen. In most cases methylation can change susceptibility. While DNA hypomethylation appears to be a common phenomenon during the susceptible interaction, the levels and patterns of hypomethylation in transposable elements and genic regions may mediate distinct responses against various plant pathogens...
July 29, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28755320/evaluation-of-the-mature-grain-phytase-candidate-hvpaphy_a-gene-in-barley-hordeum-vulgare-l-using-crispr-cas9-and-talens
#19
Inger B Holme, Toni Wendt, Javier Gil-Humanes, Lise C Deleuran, Colby G Starker, Daniel F Voytas, Henrik Brinch-Pedersen
In the present study, we utilized TALEN- and CRISPR/Cas9-induced mutations to analyze the promoter of the barley phytase gene HvPAPhy_a. The purpose of the study was dual, validation of the PAPhy_a enzyme as the main contributor of the mature grain phytase activity (MGPA), as well as validating the importance of a specific promoter region of the PAPhy_a gene which contains three overlapping cis-acting regulatory elements (GCN4, Skn1 and the RY-element) known to be involved in gene expression during grain filling...
July 28, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28751609/control-of-species-dependent-cortico-motoneuronal-connections-underlying-manual-dexterity
#20
Zirong Gu, John Kalamboglas, Shin Yoshioka, Wenqi Han, Zhuo Li, Yuka Imamura Kawasawa, Sirisha Pochareddy, Zhen Li, Fuchen Liu, Xuming Xu, Sagara Wijeratne, Masaki Ueno, Emily Blatz, Joseph Salomone, Atsushi Kumanogoh, Mladen-Roko Rasin, Brian Gebelein, Matthew T Weirauch, Nenad Sestan, John H Martin, Yutaka Yoshida
Superior manual dexterity in higher primates emerged together with the appearance of cortico-motoneuronal (CM) connections during the evolution of the mammalian corticospinal (CS) system. Previously thought to be specific to higher primates, we identified transient CM connections in early postnatal mice, which are eventually eliminated by Sema6D-PlexA1 signaling. PlexA1 mutant mice maintain CM connections into adulthood and exhibit superior manual dexterity as compared with that of controls. Last, differing PlexA1 expression in layer 5 of the motor cortex, which is strong in wild-type mice but weak in humans, may be explained by FEZF2-mediated cis-regulatory elements that are found only in higher primates...
July 28, 2017: Science
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