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  • tRNA
  • Host factor involvement in BMV RNA replication is suggested by host-specific replication effects, biochemical studies, and cell biology studies as noted above and by the presence of multiple tRNA-related sequences and functions in the cis-acting replication signals on BMV RNAs ( 1 , 5 , 7 , 9 ). (pnas.org)
  • Among its related pathways are tRNA processing and Gene Expression . (genecards.org)
  • Genetic
  • Transcription - the transfer of DNA's genetic information through the synthesis of complementary molecules of messenger RNA - forms the basis of all cellular activities. (phys.org)
  • However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these genetic resources. (hindawi.com)
  • DDRT-PCR proved to be a fast approach to screen candidate genes from massive amounts of RNA-seq data and is a step forward towards better use of the available genetic resources generated by NGS technologies. (hindawi.com)
  • A variety of genetic variations in Avr genes, such as nucleotide substitution, insertion, deletion, frameshift, stop-codon mutation, truncation and copy number variation, are shown involved in the generation of novel types of virulent strains (Shan et al. (biomedcentral.com)
  • Genetic cross of strain P6497 and strain P7064 defined that the expression of P. sojae Avr1b is regulated by a trans-acting factor, and these two genes determine the Avr1b phenotype (Shan et al. (biomedcentral.com)
  • Changing genetic information through RNA editing. (columbia.edu)
  • For these factor characterizations we plan to employ a plethora of genetic and biochemical experiments which include tandem affinity purification of protein complexes, conditional gene silencing experiments and in vitro transcription assays. (grantome.com)
  • genomic
  • Development of a widely applicable regulated and tissue specific high level expression system for foreign genes in transgenic plants will have a profound impact on several currently ongoing plant biotechnology programs and on functional genomic studies. (allindianpatents.com)
  • Some of these direct the assembly of an RNA replication complex, which first synthesizes a negative-strand RNA replication intermediate and then uses this negative strand as a template for producing more positive-strand genomic RNAs. (pnas.org)
  • A third genomic RNA, RNA3, encodes the 3a cell-to-cell movement protein and the coat protein, which are required for BMV infection spread in its natural plant hosts but are dispensable for RNA replication ( 13 , 14 ). (pnas.org)
  • Recently, BRF2, a component of TFIIIB required for gene external RNA pol III transcription, was identified as an oncogene in squamous cell carcinomas of the lung through integrative genomic analysis. (biomedcentral.com)
  • Polymerase II
  • Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. (uniprot.org)
  • The Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. (uniprot.org)
  • In today's issue of the journal Nature, a team of researchers at the Gene Center of Ludwig-Maximilians-Universität (LMU) in Munich, led by Professor Patrick Cramer, provides the first detailed description of how the RNA polymerase II initiates gene transcription. (innovations-report.com)
  • What the LMU researchers in Cramer's group have now done is to determine the three-dimensional structure of the complex formed between RNA polymerase II and TFIIB from brewer's yeast. (innovations-report.com)
  • Eucaryotic transcription factors that stimulate RNA polymerase II by increasing the efficiency of elongation of specifically or randomly initiated RNA chains have been isolated and characterized. (pubmedcentralcanada.ca)
  • Horikoshi M, Sekimizu K, Hirashima S, Mitsuhashi Y, Natori S. Structural relationships of the three stimulatory factors of RNA polymerase II from Ehrlich ascites tumor cells. (pubmedcentralcanada.ca)
  • Overall, these experiments may uncover unique and essential factors or factor domains in a fundamentally important process, namely the recruitment of RNA polymerase II to DNA. (grantome.com)
  • The proposed studies of this application will explore mechanism and relevant factors of RNA polymerase II transcription in Trypanosoma brucei, a member of a group of parasites that cause major, devastating diseases in humans. (grantome.com)
  • expression
  • PPARA activates gene expression. (uniprot.org)
  • This transcription is the first step leading to gene expression. (phys.org)
  • lncRNAs can inhibit general protein-coding (pc) gene expression in trans ( a ) by preventing transcription factor (TF) activity (7SK lncRNA) or ( b ) by inhibiting RNAPII binding to DNA (B2 lncRNA). (beds.ac.uk)
  • However, several recent reports have demonstrated that while gene expressions obtained by digital gene expression (DGE) analysis were, for the most part, consistent with the results of the validation experiments, some discrepancies also occurred [ 1 - 3 ]. (hindawi.com)
  • Dunn, J.J., & Dubendorff, J. W. Use of T7 RNA polymerase to direct expression of cloned genes. (allindianpatents.com)
  • Differential expression of the oocyte and somatic 5 S RNA genes during Xenopus development can be explained by changes in transcription factor and histone interactions with the two types of gene. (biologists.org)
  • We report in this study that the endogenous small RNAs (sRNAs) are involved in the variation of expression of avirulence gene Avr1b in P. sojae . (biomedcentral.com)
  • These results indicate that the expression of RXLR effector genes are programmed by significantly enriched variations in their regulatory regions that lead to the variations in bidirectional transcription, which likely further affect production of endogenous sRNAs and silencing of homologous RXLR effector genes of Phytophthora pathogens. (biomedcentral.com)
  • We built a single Weighted Transcription Factor Co-expression Network (WTFCN) and TF sub-networks (based on the DO). (eurekaselect.com)
  • Non-coding RNAs are essential regulators of gene expression and transcription. (tech-strategy.org)
  • Studies of CD3 y transcriptional control revealed parallels with elements regulating HIV-1 gene expression, including a stem loop structure similar to HIV TAR. (biomedcentral.com)
  • Using a multistep selection and screening process, we have isolated yeast mutants in multiple complementation groups that inhibit BMV-directed gene expression. (pnas.org)
  • Together, these results show that BMV RNA replication in yeast depends on multiple host genes, some of which directly or indirectly affect the regulated expression and accumulation of 2a. (pnas.org)
  • Moreover, a thorough understanding of trypanosome gene expression will help to control the parasite in the long term. (grantome.com)
  • nucleolar
  • This size cut-off distinguishes lncRNAs from small RNAs such as microRNAs, piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and small interfering RNAs (siRNAs) and arises from RNA preparation methods that capture RNA molecules above this size. (beds.ac.uk)
  • nucleotide
  • One example is the 331 nucleotide 7SK lncRNA, which represses transcription elongation by preventing the PTEFβ transcription factor from phosphorylating the RNAPII carboxy-terminal domain (CTD) [ 14 ] (Figure 1 a). (beds.ac.uk)
  • Here, we identified fragments of 18 genes that are responsive to salt stress in R. trigyna using differential-display reverse transcription PCR (DDRT-PCR) followed by local BLAST searches against the RNA-seq data to identify the same or longer nucleotide sequences. (hindawi.com)
  • synthesis
  • While the major steps in RNA synthesis have been known for several decades, scientists have only recently begun to decipher the detailed molecular steps of the complex transcription process. (phys.org)
  • Therefore, gene transcription and protein synthesis must be carried out with great precision. (innovations-report.com)
  • The replication complex of each virus assembles on specific membrane sites in the infected cell ( 3 - 5 ), and such association with cell membranes appears particularly important for positive-strand RNA synthesis ( 6 ). (pnas.org)
  • BMV 1a and 2a interact ( 10 - 12 ) and in vivo colocalize on the endoplasmic reticulum at the sites of BMV RNA synthesis ( 5 ). (pnas.org)
  • Since SL RNA is consumed in trans splicing, parasite viability crucially depends on continuously strong SL RNA synthesis. (grantome.com)
  • vitro
  • ERβ-AGO2 association was confirmed in vitro and in vivo in both the nucleus and cytoplasm and is shown to be RNA-mediated. (beds.ac.uk)
  • Cooper JA, Moss B. In vitro translation of immediate early, early, and late classes of RNA from vaccinia virus-infected cells. (pubmedcentralcanada.ca)
  • A potential molecular mechanism to explain the developmental switch that turns off oocyte 5 S DNA transcription has been experimentally reconstructed in vitro and more recently tested in vivo. (biologists.org)
  • replication
  • Several lines of evidence suggest that multiple steps in positive-strand RNA virus RNA replication depend on specific host factors. (pnas.org)
  • BMV encodes two RNA replication factors, 1a and 2a, containing three domains conserved throughout the large alphavirus-like superfamily of animal and plant viruses ( 9 ). (pnas.org)
  • effector
  • Finally, ErbB2-potentiated RNA Pol I transcription could be stimulated by ligand and was not substantially repressed by inhibition of PI3-K and MEK/ERK (extracellular signal regulated kinase), the main ErbB2 effector signaling pathways. (aacrjournals.org)
  • Expanded analysis showed that up to 31% of the P. sojae RXLR effector genes were associated with sRNAs. (biomedcentral.com)
  • Factors
  • Interactions between transcription factors and specific DNA sequences. (memorize.com)
  • Both factors and histones bind 5 S RNA genes with specificity. (biologists.org)
  • A decline in transcription factor abundance, differential binding of transcription factors to oocyte and somatic 5 S genes, and increased competition with the histones for association with DNA during early embryogenesis, can account for the developmental decision to selectively repress the oocyte genes, while retaining the somatic genes in the transcriptionally active state. (biologists.org)
  • Central to this mechanism is the specific association of both transcription factors and histones with 5 S RNA genes. (biologists.org)
  • How the interplay of histones and transcription factors is thought to affect transcription, and how their respective contributions might change during development from an oocyte, to an embryo and eventually to a somatic cell is the focus of this review. (biologists.org)
  • pathways
  • The transcriptome is dramatically altered in fl3 mutants, in which the downregulated genes are primarily enriched in pathways related to translation, ribosome, misfolded protein responses, and nutrient reservoir activity. (plantcell.org)
  • lncRNAs
  • Long non-protein-coding RNAs (lncRNAs) are proposed to be the largest transcript class in the mouse and human transcriptomes. (beds.ac.uk)
  • lncRNAs work in cis when their effects are restricted to the chromosome from which they are transcribed, and work in trans when they affect genes on other chromosomes. (beds.ac.uk)
  • mechanisms
  • In addition, the genes identified in the present study are promising candidates for further elucidation of the salt tolerance mechanisms in R. trigyna . (hindawi.com)
  • microRNAs
  • The objective of this study was to investigate if this protective effect is reflected in the attenuation of the transcription of microRNAs known to induce apoptosis and cell death by gene silencing. (arvojournals.org)
  • isolation
  • One week later, the animals were sacrificed, lenses isolated and promptly processed for RNA isolation and subsequent preparation of cDNAs by reverse transcriptase reaction. (arvojournals.org)
  • interacts
  • Microbial infection) Interacts with influenza A virus (IAV) RNA polymerase subunits PA, PB1 and PB2, and nucleocapsid NP (PubMed:21900157, PubMed:26864902). (genecards.org)