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Artificial transcriptional factor

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https://www.readbyqxmd.com/read/29451902/an-artificial-mirna-system-reveals-that-relative-contribution-of-translational-inhibition-to-mirna-mediated-regulation-depends-on-environmental-and-developmental-factors-in-arabidopsis-thaliana
#1
Patrick von Born, Marti Bernardo-Faura, Ignacio Rubio-Somoza
Development and fitness of any organism rely on properly controlled gene expression. This is especially true for plants, as their development is determined by both internal and external cues. MicroRNAs (miRNAs) are embedded in the genetic cascades that integrate and translate those cues into developmental programs. miRNAs negatively regulate their target genes mainly post-transcriptionally through two co-existing mechanisms; mRNA cleavage and translational inhibition. Despite our increasing knowledge about the genetic and biochemical processes involved in those concurrent mechanisms, little is known about their relative contributions to the overall miRNA-mediated regulation...
2018: PloS One
https://www.readbyqxmd.com/read/29448919/jasmonic-acid-facilitates-flower-opening-and-floral-organ-development-through-the-upregulated-expression-of-slmyb21-transcription-factor-in-tomato
#2
Tomoko Niwa, Takamasa Suzuki, Yumiko Takebayashi, Rie Ishiguro, Tetsuya Higashiyama, Hitoshi Sakakibara, Sumie Ishiguro
Plants coordinate the timing of flower opening with pollen and gynoecium maturation to achieve successful pollination. However, little is known about how the coordination is executed. We found that flower bud development was paused immediately before flower opening in a jasmonic acid (JA)-insensitive tomato mutant, jai1-1. Phytohormone measurement and RNA analysis in flower buds revealed that newly synthesised JA peaked at two days before flower opening and the expression of a transcription factor gene SlMYB21 delayed in jai1-1...
February 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29444635/diel-pattern-of-circadian-clock-and-storage-protein-gene-expression-in-leaves-and-during-seed-filling-in-cowpea-vigna-unguiculata
#3
Julia Weiss, Marta I Terry, Marina Martos-Fuentes, Lisa Letourneux, Victoria Ruiz-Hernández, Juan A Fernández, Marcos Egea-Cortines
BACKGROUND: Cowpea (Vigna unguiculata) is an important source of protein supply for animal and human nutrition. The major storage globulins VICILIN and LEGUMIN (LEG) are synthesized from several genes including LEGA, LEGB, LEGJ and CVC (CONVICILIN). The current hypothesis is that the plant circadian core clock genes are conserved in a wide array of species and that primary metabolism is to a large extent controlled by the plant circadian clock. Our aim was to investigate a possible link between gene expression of storage proteins and the circadian clock...
February 14, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29427065/rice-tocopherol-deficiency-1-encodes-a-homogentisate-phytyltransferase-essential-for-tocopherol-biosynthesis-and-plant-development-in-rice
#4
Yunhui Zhang, Kai Liu, Xiaomei Zhu, Yan Wu, Suobing Zhang, Haiyuan Chen, Jing Ling, Yingjie Wang, Xianwen Fang
RTD1 encodes a homogentisate phytyltransferase catalyzing a key step in rice tocopherol biosynthesis, confers cold tolerance and regulates rice development by affecting the accumulation of DELLA protein SLENDER RICE1. Tocopherols are one of the most important lipid-soluble antioxidants having indispensable roles in living organisms. The physiological functions of tocopherols have been comprehensively characterized in animals and artificial membranes. However, genetic and molecular functions of tocopherols in plants are less understood...
February 9, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29408646/utrophin-up-regulation-by-artificial-transcription-factors-induces-muscle-rescue-and-impacts-the-neuromuscular-junction-in-mdx-mice
#5
Cinzia Pisani, Georgios Strimpakos, Francesca Gabanella, Maria Grazia Di Certo, Annalisa Onori, Cinzia Severini, Siro Luvisetto, Stefano Farioli-Vecchioli, Irene Carrozzo, Antonio Esposito, Tamara Canu, Elisabetta Mattei, Nicoletta Corbi, Claudio Passananti
Up-regulation of the dystrophin-related gene utrophin represents a promising therapeutic strategy for the treatment of Duchenne Muscular Dystrophy (DMD). In order to re-program the utrophin expression level in muscle, we engineered artificial zinc finger transcription factors (ZF-ATFs) that target the utrophin "A" promoter. We have previously shown that the ZF-ATF "Jazz", either by transgenic manipulation or by systemic adeno-associated viral delivery, induces significant rescue of muscle function in dystrophic "mdx" mice...
January 30, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29393635/pip-hogu-an-artificial-assembly-with-cooperative-dna-recognition-capable-of-mimicking-transcription-factor-pairs
#6
Zutao Yu, Chuanxin Guo, Yulei Wei, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Cooperation between pairs of transcription factors (TFs) has been widely demonstrated to play a pivotal role in the spatiotemporal regulation of gene expression, but blocking cooperative TF pair-DNA interactions synergistically has been challenging. To achieve this, we designed programmable DNA binder pyrrole-imidazole polyamides conjugated to host-guest assemblies (Pip-HoGu) to mimic the cooperation between natural TF pairs. By incorporating cyclodextrin (Cyd)-adamantane (Ada), we synthesized Ada1 (PIP1-Ada) and Cyd1 (PIP2-Cyd), which were evaluated using Tm, EMSA, competitive, and SPR assays and molecular dynamics studies...
February 2, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29390151/high-co2-hypoxia-responsive-transcription-factor-network-involved-in-persimmon-fruit-deastringency
#7
Qing-Gang Zhu, Zi-Yuan Gong, Miao-Miao Wang, Xian Li, Donald Grierson, Xue-Ren Yin, Kun-Song Chen
Plant responses to anaerobic environments are regulated by ethylene response factors (ERFs) in both vegetative and productive organs, but the roles of other transcription factors (TFs) in hypoxia responses are poorly understood. Here, eight TFs (DkbHLH1, DkMYB9/10/11, DkRH2-1, DkGT3-1, DkAN1-1, DkHSF1) were shown to be strongly up-regulated by AHCA (artificial high CO2 atmosphere, 1 % O2 and 95 % CO2). Dual-luciferase assay indicated some TFs were activators of previously characterized DkERFs, including DkMYB10 for the DkERF9 promoter, DkERF18/19 and DkMYB6 for the DkERF19 promoter, DkERF21/22 for the DkERF10 promoter...
January 30, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29389011/reprogramming-cell-fate-with-artificial-transcription-factors
#8
REVIEW
Evan A Heiderscheit, Asuka Eguchi, Mackenzie C Spurgat, Aseem Z Ansari
Transcription factors (TFs) reprogram cell states by exerting control over gene regulatory networks and the epigenetic landscape of a cell. Artificial transcription factors (ATFs) are designer regulatory proteins comprised of modular units that can be customized to overcome challenges faced by natural TFs in establishing and maintaining desired cell states. Decades of research on DNA-binding proteins and synthetic molecules has provided a molecular toolkit for ATF design and the construction of genome-scale libraries of ATFs capable of phenotypic manipulation and reprogramming of cell states...
February 1, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29344646/engineered-zinc-finger-transcription-factors-inhibit-the-replication-and-transcription-of-hbv-in%C3%A2-vitro-and-in%C3%A2-vivo
#9
Wei Luo, Junxia Wang, Dengfeng Xu, Huili Bai, Yangli Zhang, Yuhong Zhang, Xiaosong Li
In the present study, an artificial zinc-finger transcription factor eukaryotic expression vector specifically recognizing and binding to the hepatitis B virus (HBV) enhancer (Enh) was constructed, which inhibited the replication and expression of HBV DNA. The HBV EnhI‑specific pcDNA3.1‑artificial transcription factor (ATF) vector was successfully constructed, and then transformed or injected into HepG2.2.15 cells and HBV transgenic mice, respectively. The results demonstrated that the HBV EnhI (1,070‑1,234 bp)‑specific ATF significantly inhibited the replication and transcription of HBV DNA in vivo and in vitro...
January 17, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29338732/transcriptional-profile-and-epstein-barr-virus-infection-status-of-laser-cut-immune-infiltrates-from-the-brain-of-patients-with-progressive-multiple-sclerosis
#10
Caterina Veroni, Barbara Serafini, Barbara Rosicarelli, Corrado Fagnani, Francesca Aloisi
BACKGROUND: It is debated whether multiple sclerosis (MS) might result from an immunopathological response toward an active Epstein-Barr virus (EBV) infection brought into the central nervous system (CNS) by immigrating B cells. Based on this model, a relationship should exist between the local immune milieu and EBV infection status in the MS brain. To test this hypothesis, we analyzed expression of viral and cellular genes in brain-infiltrating immune cells. METHODS: Twenty-three postmortem snap-frozen brain tissue blocks from 11 patients with progressive MS were selected based on good RNA quality and prominent immune cell infiltration...
January 16, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29335877/development-of-cyclic-amp-receptor-protein-based-artificial-transcription-factor-for-intensifying-gene-expression
#11
Peng Zhao, Wenjuan Wang, Pingfang Tian
Vector-dependent gene overexpression typically relies on an efficient operon and sufficient RNA polymerases (RNAPs). The lac (lactose) operon is a paradigm of transcription control, and cyclic AMP receptor protein (CRP) is a global regulator capable of recruiting RNAPs. However, the gap between lac operon and CRP has not been well bridged. In this work, CRP was fused to lac repressor protein (lacI) to form an artificial transcription factor (ATF) with the expectation that when LacI acted on the lacO-positioned upstream of gene of interest, the LacI-tethered CRP would trap RNAPs and thus improve the expression of PuuC, an aldehyde dehydrogenase catalyzing 3-hydroxypropionaldehyde (3-HPA) to 3-hydroxypropionic acid (3-HP) in Klebsiella pneumoniae...
January 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29323152/unravelling-the-effects-of-mechanical-physiological-conditioning-on-cardiac-adipose-tissue-derived-progenitor-cells-in-vitro-and-in-silico
#12
Aida Llucià-Valldeperas, Ramon Bragós, Carolina Soler-Botija, Santiago Roura, Carolina Gálvez-Montón, Cristina Prat-Vidal, Isaac Perea-Gil, Antoni Bayes-Genis
Mechanical conditioning is incompletely characterized for stimulating therapeutic cells within the physiological range. We sought to unravel the mechanism of action underlying mechanical conditioning of adipose tissue-derived progenitor cells (ATDPCs), both in vitro and in silico. Cardiac ATDPCs, grown on 3 different patterned surfaces, were mechanically stretched for 7 days at 1 Hz. A custom-designed, magnet-based, mechanical stimulator device was developed to apply ~10% mechanical stretching to monolayer cell cultures...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29298679/sequence-motif-finder-using-memetic-algorithm
#13
Jader M Caldonazzo Garbelini, André Y Kashiwabara, Danilo S Sanches
BACKGROUND: De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important role in understanding the mechanisms of gene regulation and helps to develop new drugs. RESULTS: We here present Memetic Framework for Motif Discovery (MFMD), an algorithm that uses semi-greedy constructive heuristics as a local optimizer. In addition, we used a hybridization of the classic genetic algorithm as a global optimizer to refine the solutions initially found...
January 3, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29277612/conditional-constitutive-expression-system-of-a-drug-protein-in-vivo-by-positive-feedback-loop-using-an-inducer-independent-artificial-transcription-factor
#14
Eun-Bin Lee, Ho-Dong Lim, Sung-Hwan You, Dae-Eun Cheong, Geun-Joong Kim
Bacterial-mediated drug delivery is a potential and promising strategy for the specific treatment of cancer with therapeutic molecules, especially with genetically encoded proteins. These proteins must be tightly regulated due to cytotoxicity and thus are usually expressed under the control of the PBAD and TetA/TetR promoters in vivo. Since protein expression from these systems is triggered by exogenous inducer, periodic intravenous injection of inducer is necessary. However, these treatments can result in non-homogenous and/or inefficient expression of therapeutic proteins in vivo due to impeded diffusion and dilution of the inducer further from the injection site...
December 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29274293/activation-of-klf4-expression-by-small-activating-rna-promotes-migration-and-invasion-in-colorectal-epithelial-cells
#15
Qinqin Zhou, Dejun Fan, Kejun Huang, Xiuting Chen, Yufeng Chen, Qingyun Mai
RNA activation mediated by small double-stranded RNAs targeting promoter sequence named small activating RNAs (saRNAs), is one of the mechanisms for gene activation. Artificial regulation of gene expression through RNA activation doesn't affect the alteration of the genomic DNA sequences or exogenous plasmid DNA, therefore it is a relative manageable approach for gene perturbation. KLF4 is a member of zinc-finger transcription factors and its functions in colorectal cells are still controversial. In order to elucidate the functions of KLF4, we synthesized saRNAs that target the promoter regions of KLF4 and transfected into varied colorectal epithelial cell lines...
December 23, 2017: Cell Biology International
https://www.readbyqxmd.com/read/29246684/control-the-intracellular-nf-%C3%AE%C2%BAb-activity-by-a-sensor-consisting-of-mirna-and-decoy
#16
Danyang Wang, Huanhuan Tang, Xinhui Xu, Wei Dai, Jian Wu, Jinke Wang
Many diseases are associated with the abnormal activation of NF-κB and its signaling pathway. NF-κB has become an important target for disease treatment and development of new drugs. Many various NF-κB inhibitors were therefore developed; however, they have difficulties to become clinical drugs due to their adverse side effects resulted from the affected normal physiological functions of this transcription factor. To overcome this limitation, this study construct a transgenic vector that can express an artificial miRNA targeting NF-κB RelA under the control of a NF-κB-specific promoter...
December 12, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29242230/paracrine-brassinosteroid-signaling-at-the-stem-cell-niche-controls-cellular-regeneration
#17
Fidel Lozano-Elena, Ainoa Planas-Riverola, Josep Vilarrasa-Blasi, Rebecca Schwab, Ana I Caño-Delgado
Stem cell regeneration is crucial for both cell turnover and tissue healing in multicellular organisms. In Arabidopsis roots, a reduced group of cells known as the quiescent center (QC) acts as a cell reservoir for surrounding stem cells during both normal growth and in response to external damage. Although cells of the QC have a very low mitotic activity, plant hormones such as brassinosteroids (BR) can promote QC divisions. Here, we used a tissue-specific strategy to investigate the spatial signaling requirements of BR-mediated QC divisions...
December 14, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29235474/engineering-cell-signaling-using-tunable-crispr-cpf1-based-transcription-factors
#18
Yuchen Liu, Jinghong Han, Zhicong Chen, Hanwei Wu, Hongsong Dong, Guohui Nie
The catalytically dead Cpf1 endonuclease from Acidaminococcus sp. BV3L6 (dAsCpf1) has been used to construct effective transcriptional repressors in bacteria and plants. However, it is still unclear if dAsCpf1 can function in human cells as a transcriptional regulator or a signal conductor. Here, we repurpose the dAsCpf1 system in human cells for a variety of functions, including the activation or repression of gene transcription. Moreover, we construct programmable ligand-controlled dAsCpf1 systems either by coupling crRNAs with engineered riboswitches or by fusing dAsCpf1 proteins with G protein-coupled receptors...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29213259/characterization-of-a-suppressive-cis-acting-element-in-the-epstein-barr-virus-lmp1-promoter
#19
Masahiro Yoshida, Takayuki Murata, Keiji Ashio, Yohei Narita, Takahiro Watanabe, H M Abdullah Al Masud, Yoshitaka Sato, Fumi Goshima, Hiroshi Kimura
Latent membrane protein 1 (LMP1) is a major oncogene encoded by Epstein-Barr virus (EBV) and is essential for immortalization of B cells by the virus. Previous studies suggested that several transcription factors, such as PU.1, RBP-Jκ, NFκB, EBF1, AP-2 and STAT, are involved in LMP1 induction; however, the means by which the oncogene is negatively regulated remains unclear. Here, we introduced short mutations into the proximal LMP1 promoter that includes recognition sites for the E-box and Ikaros transcription factors in the context of EBV-bacterial artificial chromosome...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29188374/characterization-of-a-gene-regulatory-network-underlying-astringency-loss-in-persimmon-fruit
#20
Soichiro Nishiyama, Noriyuki Onoue, Atsushi Kono, Akihiko Sato, Keizo Yonemori, Ryutaro Tao
Transcriptome analysis of a persimmon population segregating for an astringency trait in fruit suggested central roles for a limited number of transcriptional regulators in the loss of proanthocyanidin accumulation. Persimmon (Diospyros kaki; 2n = 6x = 90) accumulates a large amount of proanthocyanidins (PAs) in its fruit, resulting in an astringent taste. Persimmon cultivars are classified into four types based on the nature of astringency loss and the amount of PAs at maturity. Pollination constant and non-astringent (PCNA)-type cultivars stop accumulating PAs in the early stages of fruit development and their fruit can be consumed when still firm without the need for artificial deastringency treatments...
November 29, 2017: Planta
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