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a cis-acting acting element in the promoter

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https://www.readbyqxmd.com/read/28642136/a-novel-hepatitis-b-virus-derived-cis-acting-sequence-that-enhances-expression-of-transgenes-delivered-by-plasmid-vectors-in-eukaryote-cell-culture-systems
#1
Seoung-Ae Lee, Hong Kim, So-Young Lee, Bum-Joon Kim
We tested the effectiveness of a novel 13-bp hepatitis B virus (HBV)-derived cis-acting element (CAE) (ACCTCGACAAGGC), called the DT2 CAE, in augmenting transgene expression delivered by plasmid vectors in eukaryotic cells. The addition of the DT2 CAE just upstream of the start codon of several different target proteins (luciferase, EGFP, LHB, HBsAg, and MIF) in DNA plasmid constructs enhanced their translation in a posttranscriptional manner, irrespective of cell type (cell lines or primary cells) or promoter (CMV or HBV preS1 promoters), suggesting its feasibility for enhanced protein production in eukaryotic cell systems...
June 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28636266/marap2-4-a-waterlogging-responsive-erf-from-mentha-regulates-bidirectional-sugar-transporter-atsweet10-to-modulate-stress-response-in-arabidopsis
#2
Ujjal J Phukan, Gajendra Singh Jeena, Vineeta Tripathi, Rakesh Kumar Shukla
As waterlogging and successive events severely influence growth and development of economically important plants, we attempted to characterize the role of a waterlogging-responsive Group I (A-6) Ethylene response factor (MaRAP2-4) from Mentha arvensis. Waterlogging, ethylene and Methyl jasmonate rapidly induced the expression of MaRAP2-4. MaRAP2-4 interacted with multiple cis-elements like Dehydration response elements (DRE1/2), Anoxia/Jasmonic acid response element (JARE) and GCC box showing its involvement in multiple responses...
June 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28625133/recent-advances-in-targeting-the-hiv-1-tat-tar-complex
#3
Fardokht A Abulwerdi, Stuart F J Le Grice
Following seminal discoveries by Rosen and co-workers in 1985, the HIV-1 TAR has emerged as one of the most extensively studied regulatory elements of the HIV-1 genome. Located adjacent to the long terminal repeat promoter, this cis-acting motif, in conjunction with the viral Tat protein, plays a critical role in viral genomic RNA synthesis via modification of the transcription complex. As such, the Tat/TAR axis has been the subject of intense efforts aimed at developing therapeutic interventions, directed against both the protein and nucleic acid components...
June 15, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28624228/antisense-oligonucleotides-promote-exon-inclusion-and-correct-the-common-c-32-13t-g-gaa-splicing-variant-in-pompe-disease
#4
Erik van der Wal, Atze J Bergsma, Joon M Pijnenburg, Ans T van der Ploeg, W W M Pim Pijnappel
The most common variant causing Pompe disease is c.-32-13T>G (IVS1) in the acid α-glucosidase (GAA) gene, which weakens the splice acceptor of GAA exon 2 and induces partial and complete exon 2 skipping. It also allows a low level of leaky wild-type splicing, leading to a childhood/adult phenotype. We hypothesized that cis-acting splicing motifs may exist that could be blocked using antisense oligonucleotides (AONs) to promote exon inclusion. To test this, a screen was performed in patient-derived primary fibroblasts using a tiling array of U7 small nuclear RNA (snRNA)-based AONs...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28613112/a-model-for-evolution-and-regulation-of-nicotine-biosynthesis-regulon-in-tobacco
#5
Masataka Kajikawa, Nicolas Sierro, Takashi Hashimoto, Tsubasa Shoji
In tobacco, the defense alkaloid nicotine is produced in roots and accumulates mainly in leaves. Signaling mediated by jasmonates (JAs) induces the formation of nicotine via a series of structural genes that constitute a regulon and are coordinated by JA-responsive transcription factors of the ethylene response factor (ERF) family. Early steps in the pyrrolidine and pyridine biosynthesis pathways likely arose through duplication of the polyamine and nicotinamide adenine dinucleotide (NAD) biosynthetic pathways, respectively, followed by recruitment of duplicated primary metabolic genes into the nicotine biosynthesis regulon...
June 14, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28607146/epigenetic-transcriptional-memory-of-gal-genes-depends-on-growth-in-glucose-and-the-tup1-transcription-factor-in-saccharomyces-cerevisiae
#6
Varun Sood, Ivelisse Cajigas, Agustina D'Urso, William H Light, Jason H Brickner
Previously expressed inducible genes can remain poised for faster reactivation for multiple cell divisions, a conserved phenomenon called epigenetic transcriptional memory. The GAL genes in Saccharomyces cerevisiae show faster reactivation for up to seven generations after being repressed. During memory, previously produced Gal1 protein enhances the rate of reactivation of GAL1, GAL10, GAL2 and GAL7 These genes also interact with the nuclear pore complex (NPC) and localize to the nuclear periphery both when active and during memory...
June 12, 2017: Genetics
https://www.readbyqxmd.com/read/28594957/distinctive-features-and-differential-regulation-of-the-drts-genes-of-arabidopsis-thaliana
#7
Antonio Maniga, Stefania Ghisaura, Lara Perrotta, Maria Giovanna Marche, Rino Cella, Diego Albani
In plants and protists, dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are part of a bifunctional enzyme (DRTS) that allows efficient recycling of the dihydrofolate resulting from TS activity. Arabidopsis thaliana possesses three DRTS genes, called AtDRTS1, AtDRTS2 and AtDRTS3, that are located downstream of three members of the sec14-like SFH gene family. In this study, a characterization of the AtDRTS genes identified alternatively spliced transcripts coding for AtDRTS isoforms which may account for monofunctional DHFR enzymes supporting pathways unrelated to DNA synthesis...
2017: PloS One
https://www.readbyqxmd.com/read/28584068/genomic-insights-into-the-evolution-of-the-nicotine-biosynthesis-pathway-in-tobacco
#8
Masataka Kajikawa, Nicolas Sierro, Haruhiko Kawaguchi, Nicolas Bakaher, Nikolai V Ivanov, Takashi Hashimoto, Tsubasa Shoji
In tobacco (Nicotiana tabacum), nicotine is the predominant alkaloid. It is produced in the roots and accumulated mainly in the leaves. Jasmonates play a central signaling role in damage-induced nicotine formation. The genome sequence of tobacco provides us an almost complete inventory of structural and regulatory genes involved in nicotine pathway. Phylogenetic and expression analyses revealed a series of structural genes of the nicotine pathway, forming a regulon, under the control of jasmonate-responsive ETHYLENE RESPONSE FACTOR (ERF) transcription factors...
June 2017: Plant Physiology
https://www.readbyqxmd.com/read/28559488/viral-dna-replication-orientation-and-hnrnps-regulate-transcription-of-the-human-papillomavirus-18-late-promoter
#9
Xiaohong Wang, Haibin Liu, Hui Ge, Masahiko Ajiro, Nishi R Sharma, Craig Meyers, Pavel Morozov, Thomas Tuschl, Amar Klar, Donald Court, Zhi-Ming Zheng
The life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Although expression of viral early genes is initiated immediately upon virus infection of undifferentiated basal cells, viral DNA amplification and late gene expression occur only in the mid to upper strata of the keratinocytes undergoing terminal differentiation. In this report, we show that the relative activity of HPV18 TATA-less late promoter P811 depends on its orientation relative to that of the origin (Ori) of viral DNA replication and is sensitive to the eukaryotic DNA polymerase inhibitor aphidicolin...
May 30, 2017: MBio
https://www.readbyqxmd.com/read/28549169/regulatory-dynamics-of-11p13-suggest-a-role-for-ehf-in-modifying-cf-lung-disease-severity
#10
Lindsay R Stolzenburg, Rui Yang, Jenny L Kerschner, Sara Fossum, Matthew Xu, Andrew Hoffmann, Kay-Marie Lamar, Sujana Ghosh, Sarah Wachtel, Shih-Hsing Leir, Ann Harris
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28545024/an-unusual-intragenic-promoter-of-piwil2-contributes-to-aberrant-activation-of-oncogenic-pl2l60
#11
Shan-Shan Liu, Ning Liu, Meng-Yao Liu, Lei Sun, Wu-Yan Xia, Hong-Min Lu, Yu-Jie Fu, Guo-Liang Yang, Juan-Jie Bo, Xiao-Xing Liu, Haizhong Feng, Hailong Wu, Lin-Feng Li, Jian-Xin Gao
PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28527335/dissection-of-cis-regulatory-element-architecture-of-the-rice-oleosin-gene-promoters-to-assess-abscisic-acid-responsiveness-in-suspension-cultured-rice-cells
#12
Sol Kim, Soo-Bin Lee, Chae-Seong Han, Mi-Na Lim, Sung-Eun Lee, In Sun Yoon, Yong-Sic Hwang
Oleosins are the most abundant proteins in the monolipid layer surrounding neutral storage lipids that form oil bodies in plants. Several lines of evidence indicate that they are physiologically important for the maintenance of oil body structure and for mobilization of the lipids stored inside. Rice has six oleosin genes in its genome, the expression of all of which was found to be responsive to abscisic acid (ABA) in our examination of mature embryo and aleurone tissues. The 5'-flanking region of OsOle5 was initially characterized for its responsiveness to ABA through a transient expression assay system using the protoplasts from suspension-cultured rice cells...
May 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28508170/viral-vector-based-evaluation-of-regulatory-regions-in-the-neuron-specific-enolase-nse-promoter-in-mouse-cerebellum-in-vivo
#13
Yoichiro Shinohara, Toshinori Ohtani, Ayumu Konno, Hirokazu Hirai
We investigated the neuron-specific enolase (NSE) promoter in terms of its promoter strength and neuronal specificity in the cerebellum in vivo. The 1.8 kb rat NSE promoter was divided into three regions, A (0.8 kb), B (0.7 kb), and C (0.3 kb), starting from the 5' side. Then, we made various deletion constructs and assessed them by virally expressing GFP under the control of one of the deleted promoters. Removing region A reduced GFP expression to ~6% of that of the original 1.8 kb promoter. Further deletion of region B (presence of region C alone) did not influence the promoter strength, but removing region B from the original 1...
May 15, 2017: Cerebellum
https://www.readbyqxmd.com/read/28499417/genome-wide-characterization-and-expression-analyses-of-superoxide-dismutase-sod-genes-in-gossypium-hirsutum
#14
Wei Wang, Xiaopei Zhang, Fenni Deng, Rui Yuan, Fafu Shen
BACKGROUND: Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton. RESULTS: In the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum)...
May 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28487507/transcriptional-regulation-of-foxp3-requires-integrated-activation-of-both-promoter-and-cns-regions-in-tumor-induced-cd8-treg-cells
#15
Sreeparna Chakraborty, Abir K Panda, Sayantan Bose, Dia Roy, Kirti Kajal, Deblina Guha, Gaurisankar Sa
T-regulatory cells are an upsurge in the tumor microenvironment and induce immune-evasion. CD4(+) Treg cells are well characterized whereas the role of CD8(+) Tregs in cancer has recently started to crease attention. Here, we report an augmentation CD8(+)FOXP3(+) Tregs in breast tumor microenvironment. FOXP3, the lineage-specific transcription factor, is a dominant regulator of Treg cell development and function. FOXP3 is induced preferentially by divergent signaling in CD4(+) Treg cells. But how FOXP3 is induced and maintained in tumor-CD8(+) Tregs is the Cinderella of the investigation...
May 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28480497/expression-analysis-of-genes-encoding-double-b-box-zinc-finger-proteins-in-maize
#16
Wenlan Li, Jingchao Wang, Qi Sun, Wencai Li, Yanli Yu, Meng Zhao, Zhaodong Meng
The B-box proteins play key roles in plant development. The double B-box (DBB) family is one of the subfamily of the B-box family, with two B-box domains and without a CCT domain. In this study, 12 maize double B-box genes (ZmDBBs) were identified through a genome-wide survey. Phylogenetic analysis of DBB proteins from maize, rice, Sorghum bicolor, Arabidopsis, and poplar classified them into five major clades. Gene duplication analysis indicated that segmental duplications made a large contribution to the expansion of ZmDBBs...
May 8, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28457869/satellite-repeats-identify-x-chromatin-for-dosage-compensation-in-drosophila-melanogaster-males
#17
Sonal S Joshi, Victoria H Meller
A common feature of sex chromosomes is coordinated regulation of X-linked genes in one sex. Drosophila melanogaster males have one X chromosome, whereas females have two. The resulting imbalance in gene dosage is corrected by increased expression from the single X chromosome of males, a process known as dosage compensation. In flies, compensation involves recruitment of the male-specific lethal (MSL) complex to X-linked genes and modification of chromatin to increase expression. The extraordinary selectivity of the MSL complex for the X chromosome has never been explained...
May 22, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28445829/the-role-of-peu-mir164-and-its-target-penac-genes-in-response-to-abiotic-stress-in-populus-euphratica
#18
Xin Lu, Hui Dun, Conglong Lian, Xiaofei Zhang, Weilun Yin, Xinli Xia
Plant miR164 family is highly conserved and miR164 members regulate conserved targets belonging to NAC transcription factors. Our previous studies have revealed that peu-miR164a-e and its target gene POPTR_0007s08420 participate in abiotic stress response in Populus euphratica according to deep sequencing and degradome sequencing. In this study, miR164 family comprises six members that generate two mature products (miR164a-e and miR164f) and target seven NAC genes in P. euphratica. Co-expression in Nicotiana benthamiana and 5' RACE confirmed that peu-miR164 directs PeNAC070, PeNAC012 and PeNAC028 mRNAs cleavage...
June 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28407294/altered-tert-promoter-and-other-genomic-regulatory-elements-occurrence-and-impact
#19
Barbara Heidenreich, Rajiv Kumar
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome...
April 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28389698/evolution-of-the-duplicated-intracellular-lipid-binding-protein-genes-of-teleost-fishes
#20
REVIEW
Ananda B Venkatachalam, Manoj B Parmar, Jonathan M Wright
Increasing organismal complexity during the evolution of life has been attributed to the duplication of genes and entire genomes. More recently, theoretical models have been proposed that postulate the fate of duplicated genes, among them the duplication-degeneration-complementation (DDC) model. In the DDC model, the common fate of a duplicated gene is lost from the genome owing to nonfunctionalization. Duplicated genes are retained in the genome either by subfunctionalization, where the functions of the ancestral gene are sub-divided between the sister duplicate genes, or by neofunctionalization, where one of the duplicate genes acquires a new function...
April 7, 2017: Molecular Genetics and Genomics: MGG
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