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https://www.readbyqxmd.com/read/28639194/rnaa-induced-by-tata-box-targeting-micrornas
#1
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
#2
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
#3
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
#4
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...
June 17, 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
#5
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...
June 13, 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
#6
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
#7
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
#8
Juan Wang, Shasha Zhao, Wei He, Yun Wei, Yang Zhang, Henry Pegg, Paul Shore, Stefan Ge Roberts, Wensheng Deng
RNA polymerase II 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 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...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28537238/-divergence-of-paralogous-growth-hormone-encoding-genes-and-their-promoters-in-salmonidae
#9
D N Kamenskaya, M V Pankova, D M Atopkin, V A Brykov
In many fish species, including salmonids, the growth-hormone is encoded by two duplicated paralogous genes, gh1 and gh2. Both genes were already in place at the time of divergence of species in this group. A comparison of the entire sequence of these genes of salmonids has shown that their conserved regions are associated with exons, while their most variable regions correspond to introns. Introns C and D include putative regulatory elements (sites Pit-1, CRE, and ERE), that are also conserved. In chars, the degree of polymorphism of gh2 gene is 2-3 times as large as that in gh1 gene...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28529265/comparative-transcriptomic-analysis-identifies-reprogramming-and-differentiation-genes-differentially-expressed-in-uipscs-and-escs
#10
Liang Shi, Yazhou Cui, Xiaoyan Zhou, Jing Luan, Linli Wang, Jinxiang Han
Embryonic stem cells (ESCs) technology has garnered worldwide attention for its therapeutic applications in vivo. Researchers have previously shown that non-viral induced pluripotent stem cells (iPSCs) can be generated from urine. As a potential alternative, Urinary iPSCs (UiPSCs) are highly similar to embryonic stem cells (ESCs) in many aspects such as morphology, expression of pluripotency markers and the capacity to develop into three germ layers in vitro and in vivo. However, the degree of gene expression similarity between iPSCs and ESCs has not been completely elucidated...
May 20, 2017: Bioscience Trends
https://www.readbyqxmd.com/read/28520978/ldb1-mediated-enhancer-looping-can-be-established-independent-of-mediator-and-cohesin
#11
Ivan Krivega, Ann Dean
Mechanistic studies in erythroid cells indicate that LDB1, as part of a GATA1/TAL1/LMO2 complex, brings erythroid-expressed genes into proximity with enhancers for transcription activation. The role of co-activators in establishing this long-range interaction is poorly understood. Here we tested the contributions of the RNA Pol II pre-initiation complex (PIC), mediator and cohesin to establishment of locus control region (LCR)/β-globin proximity. CRISPR/Cas9 editing of the β-globin promoter to eliminate the RNA Pol II PIC by deleting the TATA-box resulted in loss of transcription, but enhancer-promoter interaction was unaffected...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28498449/bioinformatic-analysis-of-the-effects-and-mechanisms-of-decitabine-and-cytarabine-on-acute-myeloid-leukemia
#12
Shiyong Zhou, Pengfei Liu, Huilai Zhang
Acute myeloid leukemia (AML) is a frequently occurring malignant disease of the blood and may result from a variety of genetic disorders. The present study aimed to identify the underlying mechanisms associated with the therapeutic effects of decitabine and cytarabine on AML, using microarray analysis. The microarray datasets GSE40442 and GSE40870 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially methylated sites were identified in AML cells treated with decitabine compared with those treated with cytarabine via the Linear Models for Microarray Data package, following data pre‑processing...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28483054/a-novel-class-i-chitinase-from-hippophae-rhamnoides-indications-for-participating-in-ice-cbf-cold-stress-signaling-pathway
#13
Prakriti Kashyap, Renu Deswal
Plant chitinases are the members of PR (Pathogenesis related) proteins family and protect plants from biotic and abiotic stress. A novel chitinase HrCHI1 (Accession number JQ289153) of 954bp ORF encoding 317 amino acids protein was cloned, expressed and characterized from seabuckthorn, a cold/freeze tolerant shrub. The 3D structure (predicted with I-TASSER server) showed highest homology with Oryza sativa class I chitinase (PDB 2dkvA). Putative promoter region (obtained by genome walking) showed GCC box, E-boxes, the binding site for bHLH proteins and DRE elements, the CBF (C-repeat binding factor) binding site besides TATA and CAAT boxes...
June 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28411686/mechanism-underlying-berberine-s-effects-on-hsp70-tnf%C3%AE-under-heat-stress-correlation-with-the-tata-boxes
#14
Jing-Fei Jiang, Fan Lei, Zhi-Yi Yuan, Yu-Gang Wang, Xin-Pei Wang, Xiao-Jin Yan, Xuan Yu, Dong-Ming Xing, Li-Jun DU
Heat stress can stimulate an increase in body temperature, which is correlated with increased expression of heat shock protein 70 (HSP70) and tumor necrosis factor α (TNFα). The exact mechanism underlying the HSP70 and TNFα induction is unclear. Berberine (BBR) can significantly inhibit the temperature rise caused by heat stress, but the mechanism responsible for the BBR effect on HSP70 and TNFα signaling has not been investigated. The aim of the present study was to explore the relationship between the expression of HSP70 and TNFα and the effects of BBR under heat conditions, using in vivo and in vitro models...
March 2017: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/28410879/determination-of-reference-genes-that-are-independent-of-feeding-rhythms-for-circadian-studies-of-mouse-metabolic-tissues
#15
Reiko Nakao, Hiroki Okauchi, Chiaki Hashimoto, Naoyuki Wada, Katsutaka Oishi
Real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis is a popular method for the measurement of mRNA expression level and is a critical tool for basic research. The identification of suitable reference genes that are stable and not affected by experimental conditions is a critical step in the accurate normalization of RT-PCR. On the other hand, the levels of numerous transcripts exhibit circadian oscillation in various peripheral tissues and it is thought to be regulated by feeding rhythms in addition to the molecular circadian clock...
April 5, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28402630/benzoisoquinolinediones-as-potent-and-selective-inhibitors-of-brpf2-and-taf1-taf1l-bromodomains
#16
Léa Bouché, Clara D Christ, Stephan Siegel, Amaury E Fernández-Montalván, Simon J Holton, Oleg Fedorov, Antonius Ter Laak, Tatsuo Sugawara, Detlef Stöckigt, Cynthia Tallant, James Bennett, Octovia Monteiro, Laura Díaz-Sáez, Paulina Siejka, Julia Meier, Vera Pütter, Jörg Weiske, Susanne Müller, Kilian V M Huber, Ingo V Hartung, Bernard Haendler
Bromodomains (BD) are readers of lysine acetylation marks present in numerous proteins associated with chromatin. Here we describe a dual inhibitor of the bromodomain and PHD finger (BRPF) family member BRPF2 and the TATA box binding protein-associated factors TAF1 and TAF1L. These proteins are found in large chromatin complexes and play important roles in transcription regulation. The substituted benzoisoquinolinedione series was identified by high-throughput screening, and subsequent structure-activity relationship optimization allowed generation of low nanomolar BRPF2 BD inhibitors with strong selectivity against BRPF1 and BRPF3 BDs...
May 11, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28388414/transcription-impacts-the-efficiency-of-mrna-translation-via-co-transcriptional-n6-adenosine-methylation
#17
Boris Slobodin, Ruiqi Han, Vittorio Calderone, Joachim A F Oude Vrielink, Fabricio Loayza-Puch, Ran Elkon, Reuven Agami
Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. Here, we sought for a possible connection between transcription and translation. Employing an unbiased screen of multiple human promoters, we identified a positive effect of TATA box on translation and a general coupling between mRNA expression and translational efficiency...
April 6, 2017: Cell
https://www.readbyqxmd.com/read/28385923/phenotype-of-mutations-in-the-promoter-region-of-the-%C3%AE-globin-gene
#18
Paloma Ropero, Sara Erquiaga, Beatriz Arrizabalaga, Germán Pérez, Silvia de la Iglesia, María José Torrejón, Celia Gil, Cela Elena, María Tenorio, Jorge M Nieto, Félix de la Fuente-Gonzalo, Ana Villegas, Fernando-Ataúlfo González Fernández, Rafael Martínez
BACKGROUND: β(+)-Thalassaemia is characterised by reduced production of β chains, which decrease can be caused by mutations in the promoter region (CACCC or TATA box), and is classified as mild or silent depending on the extent of β-globin chain reduction. In both cases, homozygotes or compound heterozygotes for these mutations usually have thalassaemia intermedia. Frequently the diagnosis is made in adulthood or even in old age. A total of 37 alterations in the promoter region have been described so far...
April 6, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28383698/bidirectional-terminators-in-saccharomyces-cerevisiae-prevent-cryptic-transcription-from-invading-neighboring-genes
#19
Nicole Uwimana, Pierre Collin, Célia Jeronimo, Benjamin Haibe-Kains, François Robert
Transcription can be quite disruptive for chromatin so cells have evolved mechanisms to preserve chromatin integrity during transcription, thereby preventing the emergence of cryptic transcripts from spurious promoter sequences. How these transcripts are regulated and processed remains poorly characterized. Notably, very little is known about the termination of cryptic transcripts. Here, we used RNA-Seq to identify and characterize cryptic transcripts in Spt6 mutant cells (spt6-1004) in Saccharomyces cerevisiae...
April 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28371478/transcriptional-regulation-of-voltage-gated-ca-2-channels
#20
REVIEW
R González-Ramírez, R Felix
The transcriptional regulation of voltage-gated Ca(2+) (CaV ) channels is an emerging research area that promises to improve our understanding of how many relevant physiological events are shaped in the central nervous system, the skeletal muscle and other tissues. Interestingly, a picture of how transcription of CaV channel subunit genes is controlled is evolving with the identification of the promoter regions required for tissue-specific expression and the identification of transcription factors that control their expression...
March 31, 2017: Acta Physiologica
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