Downstream polymerase factor. Medical search. Frequent questions

The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. (ias.ac.in)
Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. (ias.ac.in)
For some genes, the abundance of the circular RNA exceeds that of the associated linear mRNA by a factor of 10, raising the interesting possibility that the function of some protein-coding genes may actually be to produce circular noncoding RNAs, not proteins. (bcm.edu)
Using RNAi screening in Drosophila cells, we identified many hnRNPs, SR proteins, core spliceosome, and transcription termination factors that control the outputs of reporter and endogenous genes. (bcm.edu)
Upon inhibiting RNA polymerase II termination, circular RNA levels were similarly increased due to readthrough transcripts extending into downstream genes and being subjected to backsplicing. (bcm.edu)
In addition to regulating each other through feedback loops, these genes also regulate downstream target genes involved in the maintenance and differentiation of embryonic stem cells. (lu.se)
With a kinetic modeling approach we ascribe function to the observed OCT4-SOX2-NANOG network by making plausible assumptions about the interactions between the transcription factors at the gene promoter binding sites and RNA polymerase (RNAP), at each of the three genes as well as the target genes. (lu.se)
The switch stabilizes the expression levels of the three genes, and through their regulatory roles on the downstream target genes, leads to a binary decision: When OCT4, SOX2 and NANOG are expressed and the switch is ON, the self-renewal genes are ON and the differentiation genes are OFF. (lu.se)
We show that this is a genome-wide feature of highly expressed genes, by identifying a domain of ∼700 bp with high CpG content downstream of the transcription start site, correlating with high levels of transcription. (nih.gov)
Finally, using electrophoretic mobility shift assay, we have identified YYl-related factors that bind to two other transcription initiators in cellular genes. (princeton.edu)
Central to this response is the activation of the light-inducible promoter, PcarQRS, and the transcription of three downstream genes, carQ, carR and carS. (aber.ac.uk)
A focused analysis of transcription factors that directly interact with the predicted DENV-NS5 interacting proteins was performed, followed by the identification of downstream genes that are differentially expressed after dengue infection using previously published RNA-seq data. (springernature.com)
The promoter is a DNA sequence upstream of the 5′-flanking region of the structural gene and is capable of specifically recognizing and binding RNA polymerase, which regulates the expression of downstream genes by binding to specific recognition sites of transcription factors [ 10 ]. (biomedcentral.com)
Genes are transcribed by enzymes called RNA polymerases that generate a single-stranded RNA identical in sequence (with the exception of U in place of T) to one of the strands of the double-stranded DNA. (basicmedicalkey.com)
Eukaryotic genes are transcribed in the nucleus by three different RNA polymerases , each principally responsible for one of the major classes of RNA. (basicmedicalkey.com)

An additional study found that the proximal promoter is one of many thousand direct targets of transcription factor, Myc, in vivo. (wikipedia.org)
Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. (nih.gov)
TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. (biorxiv.org)
Although the TATA-Binding Protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-Associated Factor (TAF) subunits recognize downstream promoter elements, act as co-activators, and interact with nucleosomes. (biorxiv.org)
Here we show that transcription induces stable TAF binding to downstream promoter DNA, independent of upstream contacts, TBP, or other basal transcription factors. (biorxiv.org)
This transcription-dependent TAF complex promotes subsequent activator-independent transcription, and promoter response to TAF mutations in vivo correlates with the level of downstream, rather than overall, Taf1 crosslinking. (biorxiv.org)
Reference: DNA replication-related elements cooperate to enhance promoter activity of the drosophila DNA polymerase alpha 73-kDa subunit gene. (neb.com)
An analysis was carried out on the promoter region of the Drosophila DNA polymerase alpha 73-kDa subunit gene and the factor(s) activating the promoter. (neb.com)
Within this region, we found three sequences identical or similar to the DNA replication-related element (DRE), 5'-TATCGATA, which is known as a common promoter-activating element for the Drosophila DNA polymerase alpha 180-kDa subunit gene and the proliferating cell nuclear antigen gene. (neb.com)
The results indicate that the three DREF-binding sites cooperate to enhance promoter activity of the DNA polymerase alpha 73-kDa subunit gene. (neb.com)
Other transcription factors and RNA polymerase then assemble on the promoter to form a pre-initiation complex (PIC). (stemcelldaily.com)
Each RNA polymerase requires the assistance of several other proteins or protein complexes, called general (or basal) transcription factors, which must assemble into a complex on the promoter in order for RNA polymerase to bind and start transcription. (stemcelldaily.com)
These include upstream and downstream promoter-proximal elements, enhancers, repressers, and silencers, which modulate the rate of specific initiation by RNA polymerase II. (princeton.edu)
We have recently shown that the adeno-associated virus type 2 P5 promoter +1 region (P5 + 1 element) binds transcription factor YY1 (ref. 5). (princeton.edu)
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. (umn.edu)
During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. (umn.edu)
The structures show the 3D topology of the σ S factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. (umn.edu)
Initiation by yeast RNA polymerase II at the adenoviral major late promoter in vitro. (cornell.edu)

Functionally, it binds to RNA Polymerase II. (wikipedia.org)
All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
Specific sequences on DNA, called promoters , determine where the RNA polymerase binds and how frequently it initiates transcription. (basicmedicalkey.com)

To identify upstream regulators or downstream effectors of CDK8, a dominant modifier genetic screen was performed in Drosophila based on the defects in vein patterning caused by specific depletion or overexpression of CDK8 or CycC in developing wing imaginal discs. (sdbonline.org)
The chromosome 7q31 breakpoint was mapped to a position 205 kb downstream of the FOXP2 locus and 22 kb upstream of the MDFIC gene (Fig. 1a ). (biomedcentral.com)
Activation of yeast RNA polymerase II transcription by a thymidine-rich upstream element in vitro. (cornell.edu)

Mitochondrial regulation of apoptosis further downstream was investigated, showing changes in the mitochondrial membrane potential, cytochrome c release into the cytoplasm, and enhanced activation of cleaved caspase-3 and Poly ADP-ribose polymerase (PARP). (hindawi.com)
This TF induction was dependent on signal transducer and activator of transcription-6 signaling and poly ADP ribose polymerase activity. (haematologica.org)

This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. (osti.gov)
In vitro synthesis of RNA requires a purified DNA plasmid, purified RNA polymerase, metal-ion enzyme cofactors, and raw-material nucleotides. (bioprocessintl.com)
Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides that function as regulatory factors in many human diseases, including cancer. (jcancer.org)
A poly-A polymerase then adds about 200 adenine nucleotides to form the poly-A tail. (stemcelldaily.com)
As RNA polymerase repetitively adds nucleotides to the 3′-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. (umn.edu)

In Caenorhabditis elegans , RNA-dependent RNA polymerases (RdRPs) are used for the small RNA-guided production of additional small RNAs 8 that are complementary to terminally modified mRNA fragments 9 . (nature.com)
Polyadenylation is essential for the stability of the transcript, preventing the mRNA from being the target of posttranscriptional gene silencing (PTGS) via RNA-dependent RNA polymerase 6 (RDR6) in plants ( Luo and Chen, 2007 ). (frontiersin.org)
RNAs and proteins can also engage in more transient interactions, for example during co-transcriptional regulation of RNA polymerases or during post-transcriptional regulation of (pre-)mRNA life cycles. (fu-berlin.de)
Transcription is the process of copying genetic information from DNA into RNA, especially mRNA, by the enzyme RNA polymerase. (stemcelldaily.com)
It is the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase. (stemcelldaily.com)
A cleavage and polyadenylation specificity factor (CPSF) recognizes a polyadenylation signal (AAUAAA) on the pre-mRNA and cleaves it downstream of this signal. (stemcelldaily.com)
In bacteria , a single RNA polymerase produces the primary transcript precursors for all three major classes of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). (basicmedicalkey.com)
Further analyses of the LHA and VMH confirmed pathological changes in these regions including effects on SIRT1 downstream targets and reduced mRNA levels of orexin (hypocretin), prodynorphin and melanin-concentrating hormone (MCH) in the LHA and of brain-derived neurotrophic factor (BDNF) in the VMH. (lu.se)

Accurate determination of ccfDNA is necessary to ensure good quality and quantity for downstream analysis using next-generation sequencing or polymerase chain reaction techniques. (technologynetworks.com)
Methods: NOD2 and miRNA expression in stimulated HCT116 cells were assessed by quantitative reverse transcription-polymerase chain reaction. (elsevierpure.com)
To confirm their findings, they performed droplet digital polymerase chain reaction (PCR) analysis of all 26 tissue samples tested with exome sequencing and 13 additional samples. (medscape.com)

Bacteria transcribe their genomes with the help of multi-subunit RNA polymerases (RNAPs), which comprise two large β and β' subunits that form the active site, two regulatory α subunits and an ω subunit that supports RNAP assembly. (fu-berlin.de)
Pausing and termination can be further modulated by elongation factors, such as N-utilization substances A and G. Some regulatory factors or RNAs can stably insulate RNAP from the destabilizing effects of terminators over long distances (processive anti-termination). (fu-berlin.de)
In these processes, transcript-borne regulatory RNAs alone or in conjunction with protein factors assemble on the surface of RNAP and accompany the enzyme during further transcription by an RNA looping mechanism, rendering the elongation complex resistant to pause and/or termination signals downstream of the original modification site. (fu-berlin.de)

We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations. (biorxiv.org)
We identify an important role for DDX5 in G 1 -S-phase progression where it directly regulates DNA replication factor expression by promoting the recruitment of RNA polymerase II to E2F-regulated gene promoters. (aacrjournals.org)
Most promoters for RNA polymerase II also have a conserved sequence called the TATA box, which is recognized by a subunit of the transcription factor TFIID. (stemcelldaily.com)

At the heart of the replisome lie the replicative DNA polymerases which catalyse synthesis of daughter DNA strands with astonishing accuracy and efficiency. (figshare.com)
RNA synthesis is terminated intrinsically, when the elongation complex transcribes a stable RNA hairpin followed by a uridine-rich stretch, or with the aid of transcription termination factor ρ. (fu-berlin.de)
Huang YH, Said N, Loll B, Wahl MC (2019) Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis. (fu-berlin.de)
Elongation involves the synthesis of RNA by RNA polymerase along the DNA template. (stemcelldaily.com)
RNA synthesis occurs in the 5' → 3' direction with the RNA polymerase catalyzing a nucleophilic attack by the 3-OH of the growing RNA chain on the alpha-phosphorus atom on an incoming ribonucleoside 5-triphosphate. (stemcelldaily.com)
RNA polymerases differ from DNA polymerases in that they can initiate the synthesis of new strands in the absence of a primer. (basicmedicalkey.com)

RNA-based processive anti-termination is exemplified by the polymerase utilization ( put ) signal of phage HK022. (fu-berlin.de)
Krupp F, Said N, Huang YH, Loll B, Bürger J, Mielke T, Spahn CMT, Wahl MC (2019) Structural basis for the action of an all-purpose transcription anti-termination factor. (fu-berlin.de)
Termination occurs when RNA polymerase reaches a termination signal on the DNA template and releases the RNA transcript. (stemcelldaily.com)
Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. (ox.ac.uk)
Both RNA polymerase I and II (Pol I and Pol II) in budding yeast employ a functionally homologous "torpedo-like" mechanism to promote transcriptional termination. (ox.ac.uk)
This is followed by the combined actions of Rat1p and Sen1p to degrade the Pol I-associated nascent transcript that consequently promote termination in the downstream rDNA spacer sequence. (ox.ac.uk)
Our data suggest that the previously defined in vitro Pol I termination mechanism involving the action of the Reb1p DNA-binding factor to "road-block" Pol I transcription close to the termination region may have overlooked more complex in vivo molecular processes. (ox.ac.uk)
A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. (cornell.edu)

Positive Orientation General Transcription Factor IIF (GTF2F2) is further downstream directed in the same orientation. (wikipedia.org)

We demonstrate that this selective regulation of RNA polymerase II phosphorylation state exists within human cells, consistent with in vitro assays. (rcsb.org)
REGULATION of eukaryotic messenger RNA transcription is governed by DNA sequence elements that serve as binding sites for sequence-specific transcription factors 1-3 . (princeton.edu)
Although the TATA element-binding factor TFIID has been purified and cloned from several organisms and has provided invaluable insight into the process of transcription initiation and its regulation, little is known about factors that interact at the +1 region. (princeton.edu)
2008. Plasmodium gene regulation: far more to factor in. . (cornell.edu)

The transcript is cleaved at an internal site before RNA polymerase II finishes transcribing. (stemcelldaily.com)

Quantitative real-time polymerase chain reactions were used to assess levels of SIRT1-3 and downstream targets in post mortem brain tissue from HD patients and control cases as well as after selective hypothalamic expression of mutant huntingtin (HTT) using recombinant adeno-associated viral vectors in mice. (lu.se)

Further analysis of two overlapping deficiency lines and mutant alleles led to identification of genetic interactions between the CDK8-CycC pair and the components of the Decapentaplegic (Dpp, the Drosophila homolog of TGFβ, or Transforming Growth Factor-β) signaling pathway. (sdbonline.org)
Genetic analysis strongly implied that CarR is an antisigma factor that sequesters CarQ in a transcriptionally inactive complex. (aber.ac.uk)
These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. (biomedcentral.com)
Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination. (biomedcentral.com)
Variations in the response to dental treatments may be due to several factors, including genetic variability. (bvsalud.org)
1,2 The variations in the response to treatment may be due to several factors such as illness, differences in pharmacokinetics and pharmacodynamics of drugs, environmental factors and genetic factors. (bvsalud.org)
1,3 Whereas genetic factors may contribute to the effectiveness and safety of a drug, pharmacogenomics has been recently discussed. (bvsalud.org)

It was observed that CDK8-CycC positively regulates transcription activated by Mad (Mothers against dpp) , the primary transcription factor downstream of the Dpp/TGFβ signaling pathway . (sdbonline.org)
Interferon regulatory factor 8 regulates RANTES gene transcription in cooperation with interferon regulatory factor-1, NF-kappaB, and PU.1. (cornell.edu)

Signaling intensification through epithelial growth factor receptor (EGFR), mitogenactivated protein kinase (MAPK) pathway, Phosphatidylinositol 3-kinase (PI3K) pathway and overactivation of the translation initiation complex (TIC) has been previously characterized in RCC cell lines and tumor samples. (usp.br)

In the third chapter, a novel PrimPol binding protein, polymerase delta-interacting protein 2 (PolDIP2), is identified and characterised as a stimulatory factor for PrimPol's primer extension activities. (figshare.com)
The TATA box is recognized by a transcription factor called TATA-binding protein (TBP), which is part of a larger complex called TFIID. (stemcelldaily.com)
Sequence analysis predicted that CarQ is a member of the ECF (extracytoplasmic function) subfamily of RNA polymerase sigma factors, and that CarR is an inner membrane protein. (aber.ac.uk)
Synergistic activation of interleukin-12 p35 gene transcription by interferon regulatory factor-1 and interferon consensus sequence-binding protein. (cornell.edu)

The first presented article consists of a review of the AEP superfamily, functionally repositioning the group under the category of primase-polymerases. (figshare.com)

both E2F1 and c-Myc are stimulating factors of H19 expression, and the H19 lncRNA functions as a downstream effector of c-Myc and E2F1 in tumor development and progression [ 11 ]. (jcancer.org)

Purity among commercially available polymerase enzymes is variable, and some enzymes are stabilized with bovine serum albumin (BSA). (bioprocessintl.com)

We identified an element 2 kb downstream of this breakpoint with epigenetic characteristics of an enhancer. (biomedcentral.com)
Identification of functional enhancer elements downstream of the inversion breakpoint. (biomedcentral.com)

The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt. (osti.gov)

Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. (nih.gov)
Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. (nih.gov)
Interchangeable RNA polymerase I and II enhancers. (cornell.edu)

Transcription factor TFIID (or TATA-binding. (genexplain.com)

RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. (nih.gov)

Transcription initiation sites were newly identified in the region downstream of the previously determined sites. (neb.com)

Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. (ias.ac.in)

There was also no translocation of apoptosis-inducing factor (AIF) from mitochondria to the nucleus in apoptotic keratinocytes, indicating Tan IIA-induced apoptosis occurs mainly through the caspase pathway. (hindawi.com)

The RNA polymerase transcribes one strand, the antisense (-) strand, of the DNA template. (stemcelldaily.com)

The α 2 ββ'ω core enzyme cooperates with transcription factors and responds to signals on DNA templates and nascent RNAs to achieve full functionality in vivo . (fu-berlin.de)

The non-coding regions downstream of coding sequences (CDS) is usually termed terminators. (frontiersin.org)

2917366 . RA Buratowski S., Hahn S., Guarente L., Sharp P. A. RT Five Intermediate Complexes in Transcription Initiation by RNA Polymerase II RL Cell 56:549-561 (1989). (genexplain.com)

Liu, B , Zuo, Y & Steitz, TA 2016, ' Structures of E. coli σ S -transcription initiation complexes provide new insights into polymerase mechanism ', Proceedings of the National Academy of Sciences of the United States of America , vol. 113, no. 15, pp. 4051-4056. (umn.edu)

Footprinting analysis using the recombinant DRE-binding factor (DREF) or Kc cell nuclear extract demonstrated that DREF can bind to all three DRE-related sites. (neb.com)

This study was designed to determine whether miRNAs regulate NOD2 expression as well as downstream nuclear factor kappaB activation and inflammatory responses in colonic epithelial HCT116 cells. (elsevierpure.com)

Moreover, enriched CpG levels correlate with increased RNA polymerase II elongation rates in vivo. (nih.gov)

In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. (osti.gov)
Chapter 4 focusses on the development and use of a gel-based fluorescent primase assay to assess PrimPol's ability to reprime downstream of DNA damage lesions and secondary structures. (figshare.com)
Here we report the crystal structures of E. coli transcription initiation complexes (TICs) containing the stressresponsive σ S factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ S -TIC) at about 3.9-Å resolution. (umn.edu)

Interferon regulatory factor 1 is an essential and direct transcriptional activator for interferon {gamma}-induced RANTES/CCl5 expression in macrophages. (cornell.edu)

We applied an assay that measures the stability of maintenance of an episomal plasmid in human tissue culture cells to screen for new DNA replication factors. (aacrjournals.org)

Within SEC two elongation factors, positive transcription elongation factor b (P-TEFb) and elongation factor for RNA polymerase II 2 (ELL2) are key components. (biomedcentral.com)

Hodgson, David A. / Light-induced carotenogenesis in Myxococcus xanthus functional characterization of the ECF sigma factor CarQ and antisigma factor CarR . (aber.ac.uk)

Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors OCT4, SOX2 and NANOG. (lu.se)
Identification of cis-acting elements bound by specific transcription factors can reveal transcriptional regulatory mechanisms and gene expression patterns involved in environmental adaptation processes [ 11 ]. (biomedcentral.com)

Using in vitro transcription run-off assays, we present biochemical evidence that CarQ functions as a bacterial sigma factor and is responsible for transcription initiation at PcarQRS. (aber.ac.uk)

However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. (osti.gov)
The dengue virus (DENV) possesses an RNA-dependent RNA polymerase (NS5) that replicates its RNA genome besides capping the nascent RNA to enhance stability. (springernature.com)

In contrast to monocytes, human macrophages did not show increased tissue factor expression upon stimulation with lipopolysaccharide and interferon-γ. (haematologica.org)

These results support a model in which, instead of a global enhancement of downstream enzymatic activities, proline isomerases selectively boost the activity of a subset of CTD regulatory factors specific for cis-proline. (rcsb.org)

These considerations suggest that other currently unknown factors that recruit or enhance positive feedback mechanisms are crucial for stable epigenetic changes. (nature.com)

Eukaryotes have three types of RNA polymerases (I, II and III), each responsible for transcribing different types of RNA. (stemcelldaily.com)

Anatomy9

Organisms18

Chemicals and Drugs121

Analytical, Diagnostic and Therapeutic Techniques and Equipment35

Phenomena and Processes76

Disciplines and Occupations1

Information Science4

Health Care4

Genes15

Promoter18

Binds3

Upstream3

Poly ADP ribose2

Nucleotides5

MRNA8

Chain reaction3

RNAP3

Promoters3

Synthesis6

Termination8

Further downstream1

Regulation4

Transcript1

Quantitative1

Genetic7

Regulates2

Kinase1

Protein4

Functionally1

Effector1

Enzymes1

Enhancer2

Extracytoplasmic1

Enhancers3

TFIID1

Caenorhabditis1

Initiation sites1

Differentially expressed1

Nucleus1

Strand1

Core enzyme1

Regions1

19891

Mechanism1

Bind1

Activation1

Vivo1

Structures3

Activator1

Assay1

Elongation factors1

Functional1

Transcriptional2

Vitro1

Nascent2

Expression1

Regulatory factors1

Recruit1

Eukaryotes1