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cis-regulatory elements

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https://www.readbyqxmd.com/read/29149533/monocyte-specific-knockout-of-c-ebp%C3%AE-results-in-osteopetrosis-phenotype-blocks-bone-loss-in-ovariectomized-mice-and-reveals-an-important-function-of-c-ebp%C3%AE-in-osteoclast-differentiation-and-function
#1
Wei Chen, Guochun Zhu, Joel Jules, Diep Nguyen, Yi-Ping Li
CCAAT/enhancer-binding protein α (C/ebpα) is critical for osteoclastogenesis by regulating osteoclast (OC) lineage commitment and is also important for OC differentiation and function in vitro. However, the role of C/ebpα in postnatal skeletal development has not been reported owing to lethality in C/ebpα(-/-) mice from hypoglycemia within 8 hours after birth. Herein, we generated conditional knockout mice by deleting the C/ebpα gene in monocyte via LysM-Cre to examine its role in OC differentiation and function...
November 17, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29148171/identification-and-expression-profiling-of-pht1-phosphate-transporters-in-wheat-in-controlled-environments-and-in-the-field
#2
A Grün, P Buchner, M R Broadley, M J Hawkesford
Phosphorus (P) is an important macronutrient with critical functions in plants. Phosphate (Pi) transporters which mediate Pi acquisition and Pi translocation within the plant are key factors in Pi deficiency responses. However, their relevance for adaptation to long-term Pi limitation under agronomic conditions, particularly in wheat, remains unknown. Here, we describe the identification of the complete Pi transporter gene family (Pht1) in wheat (Triticum aestivum). Gene expression profiles were compared for hydroponic and field-grown plant tissues of wheat at multiple developmental stages...
November 17, 2017: Plant Biology
https://www.readbyqxmd.com/read/29145496/insights-into-soybean-transcriptome-reconfiguration-under-hypoxic-stress-functional-regulatory-structural-and-compositional-characterization
#3
Thiago J Nakayama, Fabiana A Rodrigues, Norman Neumaier, Juliana Marcolino-Gomes, Hugo B C Molinari, Thaís R Santiago, Eduardo F Formighieri, Marcos F Basso, José R B Farias, Beatriz M Emygdio, Ana C B de Oliveira, Ângela D Campos, Aluízio Borém, Frank G Harmon, Liliane M Mertz-Henning, Alexandre L Nepomuceno
Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits...
2017: PloS One
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#4
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133885/a-conserved-stem-of-the-myxococcus-xanthus-srna-pxr-controls-srna-accumulation-and-multicellular-development
#5
Yuen-Tsu N Yu, Elizabeth Cooper, Gregory J Velicer
The small RNA (sRNA) Pxr negatively controls multicellular fruiting body formation in the bacterium Myxococcus xanthus, inhibiting the transition from growth to development when nutrients are abundant. Like many other prokaryotic sRNAs, Pxr is predicted to fold into three stem loops (SL1-SL3). SL1 and SL2 are highly conserved across the myxobacteria, whereas SL3 is much more variable. SL1 is necessary for the regulatory function of Pxr but the importance of SL3 in this regard is unknown. To test for cis genetic elements required for Pxr function, we deleted the entire pxr gene from a developmentally defective strain that fails to remove Pxr-mediated blockage of development and reintroduced variably truncated fragments of the pxr region to test for their ability to block development...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#6
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29123541/rice-seed-germination-underwater-morpho-physiological-responses-and-the-bases-of-differential-expression-of-alcoholic-fermentation-enzymes
#7
Berta Miro, Toshisangba Longkumer, Frederickson D Entila, Ajay Kohli, Abdelbagi M Ismail
The water-, energy-, and labor-intensive system of transplanted puddled rice (Oryza sativa) is steadily being replaced by direct seeding due to the progressive scarcity of these resources. However, the alternate dry direct seeding leads to competition with weeds and poor establishment when soils are flooded. Direct seeded rice capable of anaerobic germination (germination in flooded soil, AG) is ideal, which under rainfed ecosystems would also overcome waterlogging during germination. AG tolerance is associated with faster germination and faster elongation of coleoptiles, with the activities of alcoholic fermentation enzymes replacing aerobic respiration as a source of energy...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29122042/peroxisome-proliferator-activated-receptor-gamma-ppar%C3%AE-agonist-fails-to-overcome-trans-10-cis-12-conjugated-linoleic-acid-cla-inhibition-of-milk-fat-in-dairy-sheep
#8
E C Sandri, M Camêra, E M Sandri, K J Harvatine, D E De Oliveira
The trans-10, cis-12 conjugated linoleic acid (CLA) causes milk fat depression by downregulating expression of genes and transcription factors involved in lipogenesis and it has been proposed that peroxisome proliferator-activated receptor gamma (PPARγ) can be inhibited by trans-10, cis-12 CLA. The PPARγ is a nuclear receptor activated by natural or synthetic ligands and promotes expression of lipogenic genes and its effect on mammary lipogenesis and the interaction with trans-10, cis-12 CLA in lactating ewes was evaluated using thiazolidinedione (TZD), a chemical PPARγ agonist...
November 10, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29121266/stress-inducible-galactinol-synthase-of-chickpea-cagols-implicates-in-heat-and-oxidative-stress-tolerance-through-reducing-stress-induced-excessive-reactive-oxygen-species-accumulation
#9
Prafull Salvi, Nitin Uttam Kamble, Manoj Majee
Raffinose Family Oligosaccharides (RFOs) participates in various aspects of plant physiology and galactinol synthase (GolS, EC 2.4.1.123) catalyzes the key step of RFO biosynthesis. Stress induced accumulation of RFOs particularly galactinol and raffinose has been reported in few plants; however their precise role and mechanistic insight in stress adaptation remain elusive. In present study, we have shown that the GolS activity as well as galactinol and raffinose content are significantly increased in response to various abiotic stresses in chickpea...
November 7, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29110697/exutr-a-novel-pipeline-for-large-scale-prediction-of-3-utr-sequences-from-ngs-data
#10
Zixia Huang, Emma C Teeling
BACKGROUND: The three prime untranslated region (3'-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA. Many crucial developmental events, such as mammalian spermatogenesis, tissue patterning, sex determination and neurogenesis, rely heavily on post-transcriptional regulation by the 3'-UTR. However, 3'-UTR biology seems to be a relatively untapped field, with only limited tools and 3'-UTR resources available. To elucidate the regulatory mechanisms of the 3'-UTR on gene expression, firstly the 3'-UTR sequences must be identified...
November 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29107972/rna-seq-analysis-reveals-insight-into-enhanced-rice-xa7-mediated-bacterial-blight-resistance-at-high-temperature
#11
Stephen P Cohen, Hongxia Liu, Cristiana T Argueso, Andy Pereira, Casiana Vera Cruz, Valerie Verdier, Jan E Leach
Plant disease is a major challenge to agriculture worldwide, and it is exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress allows pathogens to overcome host resistance, a phenomenon which could severely impact crop productivity considering the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the underlying molecular mechanisms. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants (cultivar IRBB61) containing Xa7, a bacterial blight disease resistance (R) gene, that were infected with Xanthomonas oryzae, the bacterial blight pathogen of rice, during high temperature stress...
2017: PloS One
https://www.readbyqxmd.com/read/29101849/molecular-characterization-of-the-bovine-ier3-gene-down-regulation-of-il-8-by-blocking-nf-%C3%AE%C2%BAb-activity-mediated-by-ier3-overexpression-in-mdbk-cells-infected-with-bovine-viral-diarrhea-virus-1
#12
Melina Villalba, Fernanda Fredericksen, Carola Otth, Víctor H Olavarría
The immediate early response 3 (IER3) is a key regulatory factor in the immune response, particularly as related to homeostasis immunomodulation via the nuclear factor kappa B (NF-κB) signaling pathway. The IER3 gene has been identified in mammals and, more recently, in other higher vertebrates. Nevertheless, relatively little is known about this regulator in bovines. Therefore, this study explored, characterized, and compared the genetic context of bovine IER3 to homologous genes in the human, mouse, and canine chromosomes...
November 1, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29101371/identification-of-novel-cis-regulatory-elements-of-eya1-in-xenopus-laevis-using-bac-recombineering
#13
Santosh Kumar Maharana, Nicolas Pollet, Gerhard Schlosser
The multifunctional Eya1 protein plays important roles during the development of cranial sensory organs and ganglia, kidneys, hypaxial muscles and several other organs in vertebrates. Eya1 is encoded by a complex locus with candidate cis-regulatory elements distributed over a 329 kbp wide genomic region in Xenopus. Consequently, very little is currently known about how expression of Eya1 is controlled by upstream regulators. Here we use a library of Xenopus tropicalis genomic sequences in bacterial artificial chromosomes (BAC) to analyze the genomic region surrounding the Eya1 locus for enhancer activity...
November 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29095557/developmental-genetic-and-genomic-insights-into-the-evolutionary-loss-of-limbs-in-snakes
#14
REVIEW
Francisca Leal, Martin J Cohn
The evolution of snakes involved dramatic modifications to the ancestral lizard body plan. Limb loss and elongation of the trunk are hallmarks of snakes, although convergent evolution of limb-reduced and trunk-elongated forms occurred multiple times in snake-like lizards. Advanced snakes are completely limbless, but intermediate and basal snakes have retained rudiments of hindlimbs and pelvic girdles. Moreover, the snake fossil record indicates that complete legs were re-acquired at least once, suggesting that the potential for limb development was retained in some limb-reduced taxa...
November 2, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/29093084/characterization-of-elements-regulating-the-nuclear-to-cytoplasmic-translocation-of-icp0-in-late-hsv-1-infection
#15
Subodh Kumar Samrat, Binh L Ha, Yi Zheng, Haidong Gu
Infected cell protein 0 (ICP0) of HSV-1 is an immediate early protein containing a RING-type E3 ubiquitin ligase. It targets several host factors for proteasomal degradation and subsequently activates viral expression. ICP0 has a nuclear localization sequence and functions in the nucleus at early infection. However, later in infection, ICP0 is found solely in the cytoplasm. The molecular mechanism and biological function of ICP0 nuclear to cytoplasmic translocation is not well understood. In this study, we sought to characterize elements important for this translocation...
November 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29091423/emergent-properties-in-complex-synthetic-bacterial-promoters
#16
Lummy Maria Oliveira Monteiro, Letícia Magalhães Arruda, Rafael Silva-Rocha
Regulation of gene expression in bacteria results from the interplay between hundreds of transcriptional factors (TFs) at target promoters. However, how the arrangement of binding sites for TFs generates the regulatory logic of promoters is not well-known. Here, we generated and fully characterized a library of synthetic complex promoters for the global regulators, CRP and IHF, in Escherichia coli, which are formed by a weak -35/-10 consensus sequence preceded by four combinatorial binding sites for these two TFs...
November 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29090330/characterization-of-promoter-of-egpal1-a-novel-pal-gene-from-the-oil-palm-elaeis-guineensis-jacq
#17
Chong Yu Lok Yusuf, Janna Ong Abdullah, Noor Azmi Shaharuddin, Idris Abu Seman, Mohd Puad Abdullah
The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop...
October 31, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29089431/in-vivo-behavior-of-the-tandem-glycine-riboswitch-in-bacillus-subtilis
#18
Arianne M Babina, Nicholas E Lea, Michelle M Meyer
In many bacterial species, the glycine riboswitch is composed of two homologous ligand-binding domains (aptamers) that each bind glycine and act together to regulate the expression of glycine metabolic and transport genes. While the structure and molecular dynamics of the tandem glycine riboswitch have been the subject of numerous in vitro studies, the in vivo behavior of the riboswitch remains largely uncharacterized. To examine the proposed models of tandem glycine riboswitch function in a biologically relevant context, we characterized the regulatory activity of mutations to the riboswitch structure in Bacillus subtilis using β-galactosidase assays...
October 31, 2017: MBio
https://www.readbyqxmd.com/read/29083488/c-ebp%C3%AE-controls-osteoclast-terminal-differentiation-activation-function-and-postnatal-bone-homeostasis-through-direct-regulation-of-nfatc1
#19
Wei Chen, Guochun Zhu, Jun Tang, Hou-De Zhou, Yi-Ping Li
Osteoclast lineage commitment and differentiation have been studied extensively, although the mechanism by which transcription factor(s) control osteoclast terminal differentiation, activation and function remains unclear. CCAAT/enhancer-binding protein α (C/ebpα) has been reported to be a key regulator of osteoclast cell lineage commitment, yet C/ebpα's roles in osteoclast terminal differentiation, activation and function and bone homeostasis, under physiological or pathological conditions, have not been studied because newborn C/ebpα null mice die within several hours after birth...
October 30, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29080249/concise-review-epigenetic-regulation-of-hematopoiesis-biological-insights-and-therapeutic-applications
#20
REVIEW
Chiara Antoniani, Oriana Romano, Annarita Miccio
Hematopoiesis is the process of blood cell formation starting from hematopoietic stem/progenitor cells (HSPCs). The understanding of regulatory networks involved in hematopoiesis and their impact on gene expression is crucial to decipher the molecular mechanisms that control hematopoietic development in physiological and pathological conditions, and to develop novel therapeutic strategies. An increasing number of epigenetic studies aim at defining, on a genome-wide scale, the cis-regulatory sequences (e.g., promoters and enhancers) used by human HSPCs and their lineage-restricted progeny at different stages of development...
October 28, 2017: Stem Cells Translational Medicine
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