Abstract DNA looping is a ubiquitous and critical feature of gene regulation. Although can be efficiently detected, tools to readily manipulate are limited. Here we develop CRISPR-based reagents for creation programmable loops. Cleavage-defective Cas9 proteins different specificity linked by heterodimerization or translational fusion create bivalent complexes able link two separate regions. After model-directed optimization, the validated using quantitative assay in E. coli . Looping...

Our recent studies have shown that CD44, a cell-surface protein with functions in many biologic processes, involved glucose metabolism of prostate cancer cells. However, the molecular mechanisms regulation need to be further elucidated. In present study, LNCaP cells infected lentivirus vector overexpressing CD44. The expression levels key enzymes known as PDK1 and PFKFB4 were determined using QRT-PCR western blot. PC3 knocked down shRNA respectively, then cell proliferation, invasion...

Genomic DNA is bound by many proteins that could potentially impede elongation of RNA polymerase (RNAP), but the factors determining magnitude transcriptional roadblocking in vivo are poorly understood. Through systematic experiments and modeling, we analyse how lac repressor (LacI) Escherichia coli cells controlled promoter firing rate, concentration affinity roadblocker protein, transcription-coupled repair protein Mfd, promoter-roadblock spacing. Increased readthrough roadblock at higher...

ABSTRACT This study presents the complete genome sequence of Anaerococcus sp . strain AH8042_DFU013_CI05, isolated from a diabetes-related foot ulcer at The Queen Elizabeth Hospital in Adelaide, Australia. comprises 1,752,963 bp circular chromosome and 14,073 plasmid, with G+C contents 32% 29%, respectively.

The basic helix–loop–helix (bHLH).PAS dimeric transcription factors have crucial roles in development, stress response, oxygen homeostasis and neurogenesis. Their target gene specificity depends part on partner protein choices, where dimerization with common Aryl hydrocarbon receptor nuclear translocator (Arnt) is an essential step towards forming active, DNA binding complexes. Using a new bacterial two-hybrid system that selects for loss of interactions, we identified 22 amino acids the...

Basic helix–loop–helix/Per–Arnt–Sim (bHLH/PAS) transcription factors function broadly in development, homeostasis and stress response. Active bHLH/PAS heterodimers consist of a ubiquitous signal-regulated subunit (e.g., hypoxia-inducible factors, HIF-1α/2α/3α; the aryl hydrocarbon receptor, AhR) or tissue-restricted NPAS1/3/4, Single Minded 1/2), paired with general partner protein, receptor nuclear translocator (Arnt Arnt2). We have investigated regulation neuron-enriched Arnt paralogue,...

Transcriptional interference (TI), where transcription from a promoter is inhibited by the activity of other promoters in its vicinity on same DNA, enables factors to regulate target indirectly, inducing or relieving TI controlling interfering promoter. For convergent promoters, stochastic simulations indicate that relief can be if repressor at has slow binding kinetics, making it either sensitive frequent dislodgement elongating RNA polymerases (RNAPs) promoter, able strong roadblock these...

The aryl hydrocarbon receptor (AhR) is a signal-regulated transcription factor, which canonically activated by the direct binding of xenobiotics. In addition, switching cells from adherent to suspension culture also activates AhR, representing nonxenobiotic, physiological activation AhR signaling. Here, we show that recruited target gene enhancers in both ligand [isopropyl-2-(1,3-dithietane-2-ylidene)-2-[<i>N</i>-(4-methylthiazol-2-yl)carbamoyl]acetate (YH439)]-treated and cells, suggesting...

Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature transcription, both sense and antisense, across all kingdoms life. Here, we discuss how transcription factor binding kinetics strongly influence ability to relieve or induce TI.

Enhancers are ubiquitous and critical gene-regulatory elements. However, quantitative understanding of the role DNA looping in regulation enhancer action specificity is limited. We used Escherichia coli NtrC enhancer-σ54 promoter system as an vivo model, finding that activation highly sensitive to enhancer-promoter (E-P) distance 300–6,000 bp range. loops formed by Lac repressor were able strongly regulate either positively or negatively, recapitulating targeting insulation. A single LacI...

To determine the factors closely correlated with unhealthy psychological status of patients lung cancer and to ascertain whether psychology adversely affects their quality-of-life (QOL). Methods: Patients newly diagnosed between May 2013 December 2015 in Department Thoracic Surgery, Tianjin 4th Centre Hospital, Tianjin, China were enrolled this cross-sectional study. asked complete Symptom Checklist 90 (SCL-90) Quality Life Questionnaire (QLQ-C30) survey. From responses, correlation...

Antisense transcription is common in naturally occurring genomes and increasingly being used synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the of convergent genes can be mediated by antisense RNA effects transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between with untranslated intergenic spacers increasing length. After controlling RNA-mediated effects, which contributed about half observed total inhibition,...

The aryl hydrocarbon receptor (AhR) is traditionally defined as a transcription factor activated by exogenous polyaromatic and halogenated aromatic (PAH/HAH) ligands. Active AhR induces genes involved in xenobiotic metabolism, including cytochrome P4501A1, which function to metabolize activating However, recent studies implicate biological events that are apparently unrelated the response, implying endogenous activation mechanisms exist. Three zebrafish (Danio rerio) encode proteins...

We have previously found that TdT-interacting factor 1 (TdIF1) is a potential oncogene expressed in non-small cell lung cancer (NSCLC) and associated with poor prognosis. However, its exact mechanism still unclear. The lysine-specific demethylase (LSD1) crucial mediator of the epithelial–mesenchymal transition (EMT), an important process triggered during metastasis. Here, we confirm TdIF1 highly NSCLC related to lymph node metastasis through Cancer Genome Atlas (TCGA) analysis clinical...

Abstract Background Laminins are high-molecular weight (400 ~ 900 kDa) proteins in extracellular matrix, which serve as major component of the basal lamina, and play a crucial role promoting tumor cell migration. This study aimed at characterizing laminin cancer development, elucidating mechanism progression driven by laminin-Notch signaling bladder cancer. Methods 2D collagen/laminin culture system was established CCK-8/transwell assay conducted to evaluate proliferation/migration ability...

Convergent promoters exert transcriptional interference (TI) by several mechanisms including promoter occlusion, where elongating RNA polymerases (RNAPs) block access to a promoter. Here, we tested whether pausing of RNAPs obstructive DNA-bound proteins can enhance TI occlusion. Using the Lac repressor as 'roadblock' induce over target promoter, found only small increase in TI, with mathematical modelling suggesting that rapid termination stalled RNAP was limiting occlusion effect. As...

Abstract Motivation Exposure of mouse embryos to atrazine decreased histone tri-methylation at lysine 4 (H3K4me3) and increased expression alternatively spliced RNA in the third generation. Specificity protein (SP) family motifs were enriched promoters genes encoding differentially expressed alternative transcripts. Results H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) sperm, preimplantation embryo development male gonad primordial germ cells (PGCs) analysed identify paternal...

Genes are frequently regulated by interactions between proteins that bind to the DNA near gene and sites located far away, with intervening looped out. But it is not understood how efficient looping can occur when very apart. We develop a simple theoretical framework relates efficiency energetic cost benefit of looping, allowing prediction single or multiple nested loops at different distances. Measurements absolute loop efficiencies for Lac repressor λ CI using expression reporters in...

Lycium barbarum (Solanaceae) is a unique economic plant to China. The complete chloroplast (cp)genome was sequenced and assembled by using Illumina paired-end reads data. circular cp genome 155,656 bp in size, including pair of inverted repeat (IR) regions 25,451 bp, large single copy (LSC) region 86,554 small (SSC) 18,200 bp. Besides, 15 genes possess intron, while another three (clpP, rps12 ycf3) have couple introns. GC content entire L. genome, LSC, SSC IR are 37.8%, 35.9%, 32.3%, 43.2%,...

Abstract Proteins that can bring together separate DNA sites, either on the same or different molecules, are critical for a variety of DNA-based processes. However, there no general and technically simple assays to detect proteins capable looping in vivo nor quantitate their efficiency. Here, we develop quantitative assay DNA-looping Escherichia coli requires only basic cloning techniques LacZ assay. The is based loop assistance, where two binding sites candidate protein inserted internally...