• The canonical function of a bacterial sigma (σ) factor is to determine the gene specificity of the RNA polymerase (RNAP). (nih.gov)
  • The multisubunit RNA polymerase (RNAP) is the central enzyme responsible for RNA synthesis in bacteria. (nih.gov)
  • a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. (frontiersin.org)
  • The current study suggests that DksA is the glue that holds together two key components of bacterial gene expression -- a molecule called ppGpp and an enzyme called RNA polymerase. (infectioncontroltoday.com)
  • RNA polymerase carries out transcription, the first step in gene expression. (infectioncontroltoday.com)
  • Solving this structure meant that the researchers could at last determine just how DksA helped ppGpp hold fast to its target, RNA polymerase. (infectioncontroltoday.com)
  • DksA uses something scientists call the 'back door of gene expression,' a cavity on the RNA polymerase molecule called the secondary channel. (infectioncontroltoday.com)
  • Once there, the protein helps ppGpp stay bound to RNA polymerase. (infectioncontroltoday.com)
  • Studies of genes transcribed by RNA polymerase II (Pol II) have shown that open and closed chromatin structures are dynamically regulated through multiple mechanisms, including histone modifications, histone variant incorporation, and DNA methylation (reviewed in reference 17 ). (asm.org)
  • Genome-wide studies in Saccharomyces cerevisiae , for example, have revealed that promoters of most actively transcribed genes are depleted of nucleosomes and that histone density is inversely proportional to the transcription rate within coding regions, suggesting that nucleosomes are dynamically disassembled and reassembled at each passage of the polymerase ( 16 ). (asm.org)
  • 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)
  • For instance, H19 is the first lncRNA transcribed by RNA polymerase II and is expressed mainly in human embryonic cells. (jcancer.org)
  • Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for reverse transcription of RNA into complementary DNA. (sigmaaldrich.com)
  • Transcription begins when an enzyme called RNA polymerase (RNAP) latches onto the DNA ladder and pulls a small section apart lengthwise. (sciencedaily.com)
  • 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)
  • However, the order of events and the precise function of high-mobility group proteins during transcription initiation remain unclear. (nature.com)
  • Although HMG proteins do not possess intrinsic transcriptional activity, they are called architectural transcription factors because they modulate the transcription of their target genes by altering the chromatin structure at the promoter and/or enhancers 15 . (nature.com)
  • [ 10 ] CSB gene defects ( ERCC6 ) (at least 78 different mutations) result in altered expression of antiangiogenic and cell cycle genes and proteins, particularly p21, which can result in inhibition of cell cycle progression and growth. (medscape.com)
  • It leads straight to the active site, and presents a confined area where many proteins and antibiotics that control transcription may bind to carry out their business. (infectioncontroltoday.com)
  • Repressor proteins are coded for by regulatory genes. (proteopedia.org)
  • 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)
  • In the Nature study, Block and his colleagues tackled a fundamental principal of biology known as the central dogma, which states that in living organisms, genetic information flows from DNA to RNA to proteins. (sciencedaily.com)
  • A typical DNA ladder carries thousands of genes that encode thousands of proteins, which keep the organism alive and functioning. (sciencedaily.com)
  • Without it there would be no RNA messages, no proteins and no life. (sciencedaily.com)
  • Transcription factors help to regulate gene expression-turning genes on or off and dialing up or down their level of activity-often in partnership with the proteins that they bind. (mit.edu)
  • They anchor themselves and their partner proteins to DNA at binding sites in genetic regulatory sequences, bringing together the components that are needed to make gene expression happen. (mit.edu)
  • Transcription factors are a well-known family of proteins, but new research from Whitehead Institute Member Richard Young and colleagues shows that the picture we have had of them is incomplete. (mit.edu)
  • Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. (lu.se)
  • This set of genes is enriched in transcription factors, which modulate RNA expression. (sfari.org)
  • Once produced, it is largely unclear what circular RNAs do, although two are known to efficiently modulate the activity of microRNAs. (bcm.edu)
  • Trans-splicing is a special form of RNA processing where exons from two different primary RNA transcripts are joined end to end and ligated. (wikipedia.org)
  • The capped splice leader is trans-spliced onto each gene to generate monocistronic capped and polyadenylated transcripts. (wikipedia.org)
  • Whole-transcriptome sequencing (RNA-seq) technology has emerged as a revolutionary platform for genome-wide quantification of mRNA transcripts. (biomedcentral.com)
  • Some of them are for non-coding RNA transcripts longer than 200 nucleotides, called long non-coding RNAs (lncRNAs) [ 1 , 2 ]. (jcancer.org)
  • Altered gene expression patterns were observed in 133 RNA transcripts with at least a 2 fold change. (cdc.gov)
  • Six var gene transcripts best distinguished severe from uncomplicated malaria, including UpsA and 2 CIDRα1 domains. (bvsalud.org)
  • Var gene transcripts in Papua New Guinean children with severe malaria were similar to those reported from Africa. (bvsalud.org)
  • As a result of the sense strand undergoing transcription, a pre-mRNA is formed that complements the sense strand. (wikipedia.org)
  • Intergenic trans-splicing is characterized by the splicing together of exons formed form the pre-mRNA of two different genes, resulting in trans-genic mRNA. (wikipedia.org)
  • Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy. (biomedcentral.com)
  • In total, these results indicate that inhibition or slowing of canonical pre-mRNA processing events shifts the steady-state output of protein-coding genes towards circular RNAs, which likely helps explain why and how circular RNAs show tissue-specific expression profiles. (bcm.edu)
  • In particular, we are interested in determining how cellular cues can alter the ratio of linear mRNA to circular RNA for a given gene. (bcm.edu)
  • To date, it is well known that lncRNAs participate in chromatin modifications and transcriptional and translational regulation of protein-encoding genes or regulate protein function and activity through specific binding [ 3 - 5 ]. (jcancer.org)
  • that is, they inhibit the transcription of messenger RNA from their target genes. (proteopedia.org)
  • 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)
  • 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 also suggest tests that could discriminate between a variety of feedforward regulation architectures of the target genes by OCT4, SOX2 and NANOG. (lu.se)
  • This study shows that CRISPRi mediates precise transcriptional pausing, which can be followed by transcription termination. (nature.com)
  • Whether alterations in the expression pattern of these genes, particularly transcriptional factors, is associated with carcinogenic potential of TCA needs to be elucidated. (cdc.gov)
  • 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)
  • RNA-seq offers several advantages over microarrays or RT-qPCR for detecting differentially expressed genes (DEGs). (biomedcentral.com)
  • The dissociable sigma (σ) factor subunit directs the RNAP to different sets of genes to allow their expression in response to various cellular needs. (nih.gov)
  • Finally, it seems appropriate to consider the "sodium channel syndrome" (mutations in the gene of the α subunit of the sodium channel, SCN5A gene) as a single clinical entity that may manifest in a wide range of phenotypes, to thus have a better insight on these cardiac syndromes and potential outcomes for their clinical treatment. (bvsalud.org)
  • The PEP enzyme recognizes the -10 and -35 cis -elements, similar to those found in bacterial promoters whereas the NEP enzyme recognizes the YRTA-motif, which can also be found upstream of several genes with PEP promoters indicating that these genes can be transcribed by both polymerases ( Pfannschmidt and Liere, 2005 ). (frontiersin.org)
  • Patrick Cramer is carrying out research on the enzyme that transcribes the DNA code to enable a protein to be synthesized from a gene. (mpg.de)
  • The RNAP enzyme then builds a new, complementary strand of RNA by chemically copying each base in one of the exposed DNA strands. (sciencedaily.com)
  • But that has left open the question of whether the RNAP enzyme actually climbs up the DNA ladder one rung at a time, or does it move instead in chunks--for example, does it add three bases of RNA, then jump along and add another three bases. (sciencedaily.com)
  • Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene. (jax.org)
  • These syndromes arise from mutations of genes critical for nucleotide-excision repair and RNA transcription. (medscape.com)
  • [ 9 ] At least 30 known CSA mutations have been characterized to date, primarily mutations in group 8 excision-repair cross-complementation gene ( ERCC8 ) on band 5q12. (medscape.com)
  • This finding suggests a role for this σ 54 in gene regulation that extends beyond its known function as an RNAP gene specificity factor. (nih.gov)
  • Chromatin-mediated regulation of transcription involves DNA methylation and histone modifications. (nature.com)
  • These data suggest that FECR1 circular RNA acts as an upstream regulator to control breast cancer tumor growth by coordinating the regulation of DNA methylating and demethylating enzymes. (biomedcentral.com)
  • This suggests a mechanism by which the regulation of protein synthesis can produce a defined program of gene expression at the RNA level. (sfari.org)
  • The epigenetic regulation of spatiotemporal gene expression is crucial for human development. (researchgate.net)
  • Regulation of nucleosome density is therefore an important mechanism to enable the transcription machinery to access the DNA. (asm.org)
  • This rethinking of how transcription factors work may lead to a better understanding of gene regulation, and may provide new targets for RNA-based therapeutics. (mit.edu)
  • The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. (frontiersin.org)
  • In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. (frontiersin.org)
  • Further, substantial amount of RNA may be required if a large number of genes need to be tested. (biomedcentral.com)
  • The gradual conversion from endosymbiont to organelle during the course of evolution has clearly been accompanied by a dramatic reduction in genome size as the chloroplasts lost most of their genes to the nucleus. (frontiersin.org)
  • With the exception of the first and last exons of genes, every other exon in the genome has splicing signals at its 5' and 3' ends and theoretically can circularize. (bcm.edu)
  • Tat increases the transcription of HIV's RNA genome by binding to the virus' RNA and then recruiting cellular machinery to it. (mit.edu)
  • It is usually found in eukaryotes and mediated by the spliceosome, although some bacteria and archaea also have "half-genes" for tRNAs. (wikipedia.org)
  • The findings, reported in the current issue of the journal Cell , suggest that bacteria rely on a key protein in order to properly regulate gene expression -- a process fundamental to cell survival. (infectioncontroltoday.com)
  • In recent work, Artsimovitch and her colleagues discovered that ppGpp regulates gene expression by controlling amino acid production in bacteria. (infectioncontroltoday.com)
  • Using ppGpp-based compounds to shut down gene expression in harmful bacteria could help curb the spread of infections. (infectioncontroltoday.com)
  • Each repressor targets a specific co-regulated group of genes by recognizing a specific sequence of DNA, called the operator in bacteria . (proteopedia.org)
  • A hallmark feature of the σ 54 -RNAP is the obligatory requirement for an activator ATPase to allow transcription initiation. (nih.gov)
  • Different activator ATPases couple diverse environmental cues to the σ 54 -RNAP to mediate adaptive changes in gene expression. (nih.gov)
  • RNAP continues moving down the DNA strand until the gene is fully copied. (sciencedaily.com)
  • Background: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. (researchgate.net)
  • Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. (biomedcentral.com)
  • IMPORTANCE RNA synthesis is the first step of gene expression. (nih.gov)
  • Decreased DNA and RNA synthesis, increased sister chromatid exchanges, and increased chromosomal breaks may occur. (medscape.com)
  • Genetic alterations in the tuberous sclerosis complex (TSC) genes, key mediators of protein synthesis, are strongly associated with autism spectrum disorders. (sfari.org)
  • In addition, they discovered a set of genes that exhibit an unusually high increase in the efficiency of protein synthesis in the mutant mice. (sfari.org)
  • The First Strand cDNA Synthesis Kit is used for the synthesis of the first strand cDNA as the starting reaction for two-step RT PCR.The kit includes Reverse Transcriptase AMV for first strand synthesis, two different primers, our PCR Nucleotide Mix, and Control Neo pa RNA. (sigmaaldrich.com)
  • The lac repressor, and the group of genes it controls, which is called an operon , were the first such gene regulatory system to be discovered. (proteopedia.org)
  • 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)
  • The regulatory elements required for this cell-specific gene expression are likely located within its proximal promoter. (molvis.org)
  • Stochastic models of gene transcription with upstream drives: exact solution and sample path characterization. (crossref.org)
  • However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. (biomedcentral.com)
  • the smaller Y chromosome carries genes that initiate male sex differentiation, as well as a few other genes. (msdmanuals.com)
  • In the eukaryotic cell nucleus, chromatin is the physiological template of all DNA-dependent processes including transcription. (nature.com)
  • The histone chaperone FACT (facilitates chromatin transcription) is a heterodimeric complex, consisting of SUPT16 and SSRP1 (Spt16 and Pob3 in yeast) that is responsible for the deposition of H2A/H2B-dimers onto DNA 11 , 12 . (nature.com)
  • Using a CRISPR Cas9-guided immunoprecipitation assay, we identify a circular RNA in the FLI1 promoter chromatin complex, consisting of FLI1 exons 4-2-3, referred to as FECR1.Overexpression of FECR1 enhances invasiveness of MDA-MB231 breast cancer cells. (biomedcentral.com)
  • Histone modifications and chromatin-associated protein complexes are crucially involved in the control of gene expression, supervising cell fate decisions and differentiation. (researchgate.net)
  • Chromatin also regulates Pol I transcription, although its mechanistic details are less understood. (asm.org)
  • Spliced leader (SL) trans-splicing is used by certain microorganisms, notably protists of the Kinetoplastae class to express genes. (wikipedia.org)
  • We investigated the expression of genes of interest using quantitative reverse transcription PCR. (molvis.org)
  • By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. (lu.se)
  • Whereas "normal" (cis-)splicing processes a single molecule, trans-splicing generates a single RNA transcript from multiple separate pre-mRNAs. (wikipedia.org)
  • A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)
  • Using this CasIP assay, we identified FECR1, a FLI1 exonic circular RNA that binds to the FLI1 promoter and epigenetically activates FLI1 in breast cancer cells. (biomedcentral.com)
  • In contrast, in the case of ''true'' bivalency, virtually all cells in the population carry both marks simultaneously at the promoter in question, leading to low, if any, expression for that gene in all cells. (researchgate.net)
  • We also demonstrated that the −657 to +411 DCT promoter fragment efficiently directs RB cell-specific transcription of the luciferase reporter gene in cell lines. (molvis.org)
  • instead, it binds RNA from a region called an arginine-rich motif (ARM) that is unstructured but has a high affinity for RNA. (mit.edu)
  • When the ARM binds to HIV RNA, the two molecules form a more stable structure together. (mit.edu)
  • Deep sequencing has revealed thousands of eukaryotic protein-coding genes that defy the central dogma, producing circular noncoding RNAs rather than linear messenger RNAs. (bcm.edu)
  • The Block team focused on a crucial step in the central dogma, a process known as "transcription," where each gene is copied from DNA onto RNA. (sciencedaily.com)
  • A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq. (crossref.org)
  • We reviewed published microarray and RNA sequencing studies in which gene expression profiles were compared between human RB and normal retina tissues. (molvis.org)
  • In Cockayne syndrome II, the defective CS group B protein, an SNF2-family DNA-dependent ATPase, is implicated in transcription elongation, transcription coupled repair, and DNA base excision repair. (medscape.com)
  • In Ascaris, the spliced leader sequence is needed to the RNA gene can be transcribed. (wikipedia.org)
  • Although mechanistically simple, this step occurs in a highly selective manner, as the sequence of the repeats can drastically alter the efficiency of circular RNA production. (bcm.edu)
  • Almost any sequence can now be efficiently circularized in eukaryotic cells, which has enabled us (and others) to begin to ask how circular RNAs function. (bcm.edu)
  • Biotin labeled cRNA transcript was synthesized using cDNA, fragmented and hybridized to HuGeneFL GeneChip probe arrays representing more than 6800 human genes and expressed sequence tags. (cdc.gov)
  • When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. (biomedcentral.com)
  • Explore the normal functions of human genes and the health implications of genetic changes. (medlineplus.gov)
  • Total RNA was used for the preparation of double standard cDNA. (cdc.gov)
  • GXD's primary emphasis is on endogenous gene expression during development. (jax.org)
  • The RNA recognition motif protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development. (uni-halle.de)
  • A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU). (uni-halle.de)
  • The 23rd pair, the sex chromosomes (X and Y), determines a person's sex as well as containing other functional genes. (msdmanuals.com)
  • We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
  • By revealing the fundamental mechanisms by which circular RNAs are generated, we have developed plasmid and viral-based methods for ectopically expressing circular RNAs. (bcm.edu)
  • Currently, there are three basic types of tests to determine if an individual has been infected with SARS-CoV-2: viral nucleic acid (RNA) detection, viral antigen detection, and detection of antibodies to the virus. (medscape.com)
  • Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. (biomedcentral.com)
  • Twenty-two of the pairs, chromosome numbers 1 to 22, the autosomes, are normally homologous (identical in size, shape, and position and number of genes). (msdmanuals.com)
  • Each gene has a specific location (locus), which is typically the same on each of the 2 homologous chromosomes. (msdmanuals.com)
  • Here we show that bivalent domains and chromosome architecture for bivalent genes are dynamically regulated during the cell cycle in human pluripotent cells. (researchgate.net)
  • The genes that occupy the same locus on each chromosome of a pair (one inherited from the mother and one from the father) are called alleles. (msdmanuals.com)
  • A chromosome contains many genes. (msdmanuals.com)
  • The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. (biomedcentral.com)
  • We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). (biomedcentral.com)
  • A comprehensive understanding of gene expression in human RB is essential for the development of safe and effective new therapies. (molvis.org)
  • Young, Oksuz and Henninger got their biggest clue that researchers might be overlooking something from the human immunodeficiency virus (HIV), which produces a transcription factor-like protein called Tat. (mit.edu)
  • Studies have been conducted in our laboratory to determine whether exposure to TCA causes alterations in expression of cancer related genes in cultured human cells. (cdc.gov)
  • pendent of those associated with cretory ducts, columnar epithelia the KRAS gene is more frequent- other key mechanistic characteris- lining the gastrointestinal tract and ly mutated in human cancer, which tics of IARC Group 1 carcinogens. (who.int)
  • to other RNAs may initiate epige- cleus pathways. (who.int)
  • We are continuing to elucidate the mechanism by which circular RNAs are produced. (bcm.edu)
  • 80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. (mdpi.com)
  • Surprisingly, when spliceosome components were depleted or inhibited pharmacologically, the steady-state levels of circular RNAs increased while expression of their associated linear mRNAs concomitantly decreased. (bcm.edu)
  • All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. (biomedcentral.com)
  • As one of the most widely used tools for transcriptome profiling, quantification of differential gene expression has played a pivotal role in the identification of pathway and gene-network interactions [ 1 - 3 ]. (biomedcentral.com)
  • The differential gene expression data analysis was performed using GeneChip 4.0 software. (cdc.gov)
  • Here we show that high-mobility group AT-hook 2 protein (HMGA2) induces DNA nicks at the transcription start site, which are required by the histone chaperone FACT complex to incorporate nucleosomes containing the histone variant H2A.X. Further, phosphorylation of H2A.X at S139 (γ-H2AX) is required for repair-mediated DNA demethylation and transcription activation. (nature.com)
  • Further investigation into how the common organism Escherichia coli regulates gene expression has given scientists new ideas for designing antibiotics that might drastically reduce a bacterium's ability to resist drugs. (infectioncontroltoday.com)
  • Thus, FLI1 drives tumor metastasis not only through the canonical oncoprotein pathway, but also by using epigenetic mechanisms mediated by its exonic circular RNA. (biomedcentral.com)
  • At least 28 genes are involved in the nucleotide excision repair pathway, which is involved in protection against UV-induced DNA damage. (medscape.com)
  • Genic trans-splicing allows variability in RNA diversity and increases proteome complexity. (wikipedia.org)
  • DNA is often compared to a twisted ladder consisting of two strands connected by molecular rungs called "bases," which are known by the abbreviations A, T, G and C. Lengthier DNA sequences code for genes, which contain explicit instructions for building a specific protein. (sciencedaily.com)
  • Burst-Like Transcription of Mutant and Wildtype MYH7-Alleles as Possible Origin of Cell-to-Cell Contractile Imbalance in Hypertrophic Cardiomyopathy. (crossref.org)