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https://www.readbyqxmd.com/read/28890398/functional-characterization-of-pol-iii-u6-promoters-for-gene-knockdown-and-knockout-in-plutella-xylostella
#1
Yuping Huang, Yajun Wang, Baosheng Zeng, Zhaoxia Liu, Xuejiao Xu, Qian Meng, Yongping Huang, Guang Yang, Liette Vasseur, Geoff M Gurr, Minsheng You
RNA polymerase type III (Pol-III) promoters such as U6 are commonly used to express small RNAs, including short hairpin RNAs (shRNAs) and single guide RNAs (sgRNAs). Functional U6 promoters are widely used in CRISPR systems, and their characterization can facilitate genome editing of non-model organisms. In the present study, six U6 small nuclear RNA (snRNA) promoters containing two conserved elements of a proximal sequence element (PSEA) and a TATA box, were identified and characterized in the diamondback moth (Plutella xylostella) genome...
September 7, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28870864/counter-regulation-of-ecrg4-gene-expression-by-hypermethylation-dependent-inhibition-and-the-sp1-transcription-factor-dependent-stimulation-of-the-c2orf40-promoter
#2
Xitong Dang, Xiaorong Zeng, Raul Coimbra, Brian P Eliceiri, Andrew Baird
The human cytokine precursor ECRG4 has been associated with multiple physiological, developmental and pathophysiological processes involving cell proliferation, cell migration, innate immunity, inflammation, cancer progression and metastases. Although down-regulation of ECRG4 gene expression has been largely attributed to hypermethylation of CpG islands in the 5'untranslated region of the ECRG4 promoter, the mechanisms that underlie the dynamics of its regulation have never been systematically described. Here we show that the ECRG4 gene is widely expressed in human tissues and report that its core promoter lies between the -780 to +420 base pairs relative to the ATG start codon of the ECRG4 open reading frame...
September 1, 2017: Gene
https://www.readbyqxmd.com/read/28857320/identification-of-heteromolecular-binding-sites-in-transcription-factors-sp1-and-taf4-using-high-resolution-nmr-spectroscopy
#3
Emi Hibino, Rintaro Inoue, Masaaki Sugiyama, Jun Kuwahara, Katsumi Matsuzaki, Masaru Hoshino
The expression of eukaryotic genes is precisely controlled by interactions between general transcriptional factors and promoter-specific transcriptional activators. The fourth element of TATA-box binding protein-associated factor (TAF4), an essential subunit of the general transcription factor TFIID, serves as a coactivator for various promoter-specific transcriptional regulators. Interactions between TAF4 and site-specific transcriptional activators, such as Sp1, are important for regulating the expression levels of genes of interest...
August 31, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28847004/a-heterochromatin-dependent-transcription-machinery-drives-pirna-expression
#4
Peter Refsing Andersen, Laszlo Tirian, Milica Vunjak, Julius Brennecke
Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced is not understood. Here we show that, in Drosophila, transcription of PIWI-interacting RNA (piRNA) clusters-small RNA source loci in animal gonads-is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin...
September 7, 2017: Nature
https://www.readbyqxmd.com/read/28810828/suitable-reference-gene-for-quantitative-real-time-pcr-analysis-of-gene-expression-in-gonadal-tissues-of-minnow-puntius-sophore-under-high-temperature-stress
#5
Arabinda Mahanty, Gopal Krishna Purohit, Sasmita Mohanty, Nihar Ranjan Nayak, Bimal Prasanna Mohanty
BACKGROUND: High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poorly understood. Gonadal gene expression influence the gonadal development, physiology and the quality of egg/sperm produced in teleosts and the mechanistic understanding of spatio-temporal changes in the gonadal gene expression could be instrumental in controlling the fate of egg/sperm and the quality of seed produced...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28806956/mirnas-regulate-oxidative-stress-related-genes-via-binding-to-the-3-utr-and-tata-box-regions-a-new-hypothesis-for-cataract-pathogenesis
#6
Changrui Wu, Zhao Liu, Le Ma, Cheng Pei, Li Qin, Ning Gao, Jun Li, Yue Yin
BACKGROUND: Age-related cataracts are related to oxidative stress. However, the genome-wide screening of cataract related oxidative stress related genes are not thoroughly investigated. Our study aims to identify cataract regulated miRNA target genes that are related to oxidative stress and to propose a new possible mechanism for cataract formation. METHODS: Microarrays were used to determine the mRNA expression profiles of both transparent and cataractous lenses...
August 14, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28806616/parvovirus-b19-integration-into-human-cd36-erythroid-progenitor-cells
#7
Tyler Janovitz, Susan Wong, Neal S Young, Thiago Oliveira, Erik Falck-Pedersen
The pathogenic autonomous human parvovirus B19 (B19V) productively infects erythroid progenitor cells (EPCs). Functional similarities between B19V nonstructural protein (NS1), a DNA binding endonuclease, and the Rep proteins of Adeno-Associated Virus (AAV) led us to hypothesize that NS1 may facilitate targeted nicking of the human genome and B19 vDNA integration. We adapted an integration capture sequencing protocol (IC-Seq) to screen B19V infected human CD36+ EPCs for viral integrants, and discovered 40,000 unique B19V integration events distributed throughout the human genome...
August 11, 2017: Virology
https://www.readbyqxmd.com/read/28774347/microrna-dysregulation-in-polyglutamine-toxicity-of-tata-box%C3%A2-binding-protein-is-mediated-through-stat1-in-mouse-neuronal-cells
#8
Reema Roshan, Ashwani Choudhary, Aksheev Bhambri, Bhawani Bakshi, Tanay Ghosh, Beena Pillai
BACKGROUND: Polyglutamine diseases constitute a class of neurodegenerative disorders associated with expansion of the cytosine-adenine-guanine (CAG) triplet, in protein coding genes. Expansion of a polyglutamine tract in the N-terminal of TBP is the causal mutation in SCA17. Brain sections of patients with spinocerebellar ataxia 17 (SCA17), a type of neurodegenerative disease, have been reported to contain protein aggregates of TATA-binding protein (TBP). It is also implicated in other neurodegenerative diseases like Huntington's disease, since the protein aggregates formed in such diseases also contain TBP...
August 3, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28716709/isolation-and-characterization-of-the-5-flanking-region-of-the-human-pdxk-gene
#9
ShuoHao Huang, ZhengQing Liu, ZhenQiao Ma, JianYun Zhang, LongQuan Huang
Pyridoxal kinase is a key enzyme for the biosynthesis of pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the catalytically active form of vitamin B6, and acts as a cofactor in >140 different enzyme reactions. It is still unknown how the kinase synthesis is regulated in the cells, and nothing has been reported about the gene promoter. In the present study, based on the bioinformatics analysis of the 5'-flanking region of the human PDXK gene, we cloned the promoter region by PCR. Through the construction of a series of luciferase expression vectors containing the human PDXK promoter region, we characterized the promoter in terms of its structure and function...
July 14, 2017: Gene
https://www.readbyqxmd.com/read/28689656/body-temperature-cycles-control-rhythmic-alternative-splicing-in-mammals
#10
Marco Preußner, Gesine Goldammer, Alexander Neumann, Tom Haltenhof, Pia Rautenstrauch, Michaela Müller-McNicoll, Florian Heyd
The core body temperature of all mammals oscillates with the time of the day. However, direct molecular consequences of small, physiological changes in body temperature remain largely elusive. Here we show that body temperature cycles drive rhythmic SR protein phosphorylation to control an alternative splicing (AS) program. A temperature change of 1°C is sufficient to induce a concerted splicing switch in a large group of functionally related genes, rendering this splicing-based thermometer much more sensitive than previously described temperature-sensing mechanisms...
August 3, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28680479/a-novel-sugarcane-bacilliform-virus-promoter-confers-gene-expression-preferentially-in-the-vascular-bundle-and-storage-parenchyma-of-the-sugarcane-culm
#11
San-Ji Gao, Mona B Damaj, Jong-Won Park, Xiao-Bin Wu, Sheng-Ren Sun, Ru-Kai Chen, T Erik Mirkov
BACKGROUND: Saccharum species such as sugarcane and energy cane are key players in the expanding bioeconomy for sugars, bioenergy, and production of high-value proteins. Genomic tools such as culm-regulated promoters would be of great value in terms of improving biomass characteristics through enhanced carbon metabolism for sugar accumulation and/or fiber content for biofuel feedstock. Unlike the situation in dicots, monocot promoters currently used are limited and mostly derived from highly expressed constitutive plant genes and viruses...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28672841/clinicopathological-phenotype-and-genetics-of-x-linked-dystonia-parkinsonism-xdp-dyt3-lubag
#12
REVIEW
Toshitaka Kawarai, Ryoma Morigaki, Ryuji Kaji, Satoshi Goto
X-linked dystonia-parkinsonism (XDP; OMIM314250), also referred to as DYT3 dystonia or "Lubag" disease, was first described as an endemic disease in the Philippine island of Panay. XDP is an adult-onset movement disorder characterized by progressive and severe dystonia followed by overt parkinsonism in the later years of life. Among the primary monogenic dystonias, XDP has been identified as a transcriptional dysregulation syndrome with impaired expression of the TAF1 (TATA box-binding protein associated factor 1) gene, which is a critical component of the cellular transcription machinery...
June 26, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28639194/rnaa-induced-by-tata-box-targeting-micrornas
#13
Yijun Zhang, Hui Zhang
Recent studies reveal that some nuclear microRNAs (miRNA) and synthesized siRNAs target gene promoters to activate gene transcription (RNAa). Interestingly, our group identified a novel HIV-1-encoded miRNA, miR-H3, which targets specifically the core promoter TATA box of HIV-1 and activates viral gene expression. Depletion of miR-H3 significantly impaired the replication of HIV-1. miR-H3 mimics could activate viruses from CD4(+) T cells isolated from patients receiving suppressive highly active antiretroviral therapy, which is very intriguing for reducing HIV-1 latent reservoir...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28639192/endogenous-mirnaa-mirna-mediated-gene-upregulation
#14
Vera Huang
The phenomenon of RNA activation (RNAa) was initially discovered by Li and colleagues about a decade ago. Subsequently, gene activation by exogenously expressed small activating RNA has been demonstrated in different cellular contexts by a number of laboratories. Conceivably, endogenously expressed microRNAs may also utilize RNA activation as a cellular mechanism for gene regulation, which may be dysregulated in disease states such as cancer. RNA activation can be applied to gain-of-function studies and holds great promise for disease intervention...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28639191/promoter-targeted-small-activating-rnas-alter-nucleosome-positioning
#15
Bin Wang, Yunzhang Hu
Epigenetic modification of target promoters has been identified as a mechanism underlying RNA activation (RNAa) induced by promoter-targeting small activating RNAs (saRNAs), but it is unclear how the chromosomal environment influences gene expression. In a study of the activation of the OCT4, SOX2, and NANOG genes by saRNAs, we found that saRNA targeting induced nucleosome-depleted region (NDRs) and the accumulation of RNA polymerase II (RNAPII) near or at the saRNA target sites. Additionally, promoters containing certain cis-regulatory elements such as the TATA box and CpG islands (CGIs) appeared to be more susceptible to RNAa...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28634074/distinct-regulation-of-activity-dependent-transcription-of-immediate-early-genes-in-cultured-rat-cortical-neurons
#16
Mamoru Fukuchi, Tomofumi Sanabe, Toshifumi Watanabe, Takane Kubota, Akiko Tabuchi, Masaaki Tsuda
The activity-regulated expression of immediate early genes (IEGs) contributes to long-lasting neuronal functions underlying long-term memory. However, their response properties following neuronal activity are unique and remain poorly understood. To address this knowledge gap, here we further investigated the response properties of two representative IEGs, c-fos and brain-derived neurotrophic factor (Bdnf). Treatment of cultured cortical cells with KCl produces a depolarization process that results in the increase of intracellular calcium concentration in a KCl concentration-dependent manner...
August 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28627437/molecular-characterization-and-functional-analysis-of-ppar%C3%AE-promoter-in-yellow-catfish-pelteobagrus-fulvidraco
#17
Wen-Jing You, Yao-Fang Fan, Yi-Huan Xu, Kun Wu, Xiao-Ying Tan
Peroxisome proliferator-activated receptor α (PPARα) is a ligand-activated transcription factor that plays critical roles in the regulation of many important physiological processes. In the present study, the 1686-bp PPARα promoter for yellow catfish Pelteobagrus fulvidraco was first cloned and characterized. The transcription start site (TSS) of PPARα gene was mapped using RLM-5'RACE method. The luciferase vectors were constructed and transiently transfected into HepG2 cells and HEK293 cells, respectively, for functional analysis of promoters...
September 5, 2017: Gene
https://www.readbyqxmd.com/read/28614407/genome-wide-identification-and-characterization-of-micrornas-differentially-expressed-in-fibers-in-a-cotton-phytochrome-a1-rnai-line
#18
Qing Miao, Peng Deng, Sukumar Saha, Johnie N Jenkins, Chuan-Yu Hsu, Ibrokhim Y Abdurakhmonov, Zabardast T Buriev, Alan Pepper, Din-Pow Ma
Cotton fiber is an important commodity throughout the world. Fiber property determines fiber quality and commercial values. Previous studies showed that silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with simultaneous improvements in fiber quality (longer, stronger and finer fiber) and other key agronomic traits. Characterization of the altered molecular processes in these RNAi genotypes and its wild-type controls is a great interest to better understand the PHYA1 RNAi phenotypes...
2017: PloS One
https://www.readbyqxmd.com/read/28559903/expression-of-cddhn4-a-novel-ysk2-type-dehydrin-gene-from-bermudagrass-responses-to-drought-stress-through-the-aba-dependent-signal-pathway
#19
Aimin Lv, Nana Fan, Jianping Xie, Shili Yuan, Yuan An, Peng Zhou
Dehydrin improves plant resistance to many abiotic stresses. In this study, the expression profiles of a dehydrin gene, CdDHN4, were estimated under various stresses and abscisic acid (ABA) treatments in two bermudagrasses (Cynodon dactylon L.): Tifway (drought-tolerant) and C299 (drought-sensitive). The expression of CdDHN4 was up-regulated by high temperatures, low temperatures, drought, salt and ABA. The sensitivity of CdDHN4 to ABA and the expression of CdDHN4 under drought conditions were higher in Tifway than in C299...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28539359/a-transcription-factor-iia-binding-site-differentially-regulates-rna-polymerase-ii-mediated-transcription-in-a-promoter-context-dependent-manner
#20
Juan Wang, Shasha Zhao, Wei He, Yun Wei, Yang Zhang, Henry Pegg, Paul Shore, Stefan G E Roberts, Wensheng Deng
RNA polymerase II (pol II) is required for the transcription of all protein-coding genes and as such represents a major enzyme whose activity is tightly regulated. Transcriptional initiation therefore requires numerous general transcriptional factors and cofactors that associate with pol II at the core promoter to form a pre-initiation complex. Transcription factor IIA (TFIIA) is a general cofactor that binds TFIID and stabilizes the TFIID-DNA complex during transcription initiation. Previous studies showed that TFIIA can make contact with the DNA sequence upstream or downstream of the TATA box, and that the region bound by TFIIA could overlap with the elements recognized by another factor, TFIIB, at adenovirus major late core promoter...
July 14, 2017: Journal of Biological Chemistry
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