• Separate phylogenetic analyses, with data partitioned according to genes, produced some conflicting results. (unboundmedicine.com)
  • Though separated from one another within the cell, nuclear genes and those of mitochondria and chloroplasts can affect each other in a number of ways. (wikipedia.org)
  • Nuclear genes play major roles in the expression of chloroplast genes and mitochondrial genes. (wikipedia.org)
  • The remaining mitochondrial proteins, metabolic enzymes, DNA and RNA polymerases, ribosomal proteins, and mtDNA regulatory factors are all encoded by nuclear genes. (wikipedia.org)
  • The majority of proteins in a cell are the product of messenger RNA transcribed from nuclear genes, including most of the proteins of the organelles, which are produced in the cytoplasm like all nuclear gene products and then transported to the organelle. (wikipedia.org)
  • Nuclear respiratory factor (NRF-1) fuses to respiratory encoding genes proteins, to the rate-limiting enzyme in biosynthesis, and to elements of replication and transcription of mitochondrial DNA, or mtDNA. (wikipedia.org)
  • Later, a reclassification based on multigene phylogeny of the sequences of several protein-coding genes including actin ( ACT1 ), largest subunit and second-largest subunit of the RNA polymerase II gene ( RPB1 and RPB2 ), the second subunit of mitochondrial cytochrome oxidase ( COX2 ), along with the D1/D2 region of the LSU rRNA gene provided sound support for the proposal the genus Nakazawaea (Tsui et al. (researchsquare.com)
  • RNA polymerase II is recruited to the promoters of protein-coding genes in living cells. (wikiversity.org)
  • Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. (biorxiv.org)
  • In the vast majority of eukaryotes, OXPHOS is operated by genes encoded by two genomes - most in the nuclear genome (nDNA) and 37 in the short circular mitochondrial genome (mtDNA). (biorxiv.org)
  • This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
  • Therefore, the principal limitation of this group of methods is the incapacity to address splicing, fusion genes, or RNA editing-related research questions. (biomedcentral.com)
  • Chimeric mRNAs fused by two previously separate genes located on different genomic loci may allow a limited number of genes to encode a substantially large number of mRNAs and proteins. (biomedcentral.com)
  • For instance, RNA polymerase I transcribes genes that encode structural components of the ribosome . (microbiologynote.com)
  • RNA polymerase II is responsible for transcribing protein-coding genes, producing messenger RNAs (mRNAs) that carry the genetic information to the site of protein synthesis . (microbiologynote.com)
  • To accomplish this, eukaryotes utilize three different RNA polymerases, each responsible for transcribing a specific subset of genes. (microbiologynote.com)
  • RNA Pol I primarily operates within the nucleolus, where it transcribes specific genes responsible for producing three essential ribosomal RNA (rRNA) molecules. (microbiologynote.com)
  • It transcribes protein-coding genes to produce precursor messenger RNA (pre-mRNA). (microbiologynote.com)
  • Additionally, RNA Pol II is involved in transcribing genes that encode small nucleolar RNAs (snoRNAs) involved in rRNA processing and small nuclear RNAs (snRNAs) involved in mRNA processing, with the exception of U6 snRNA. (microbiologynote.com)
  • Located within the nucleoplasm, RNA Pol III transcribes genes that encode diverse RNA molecules. (microbiologynote.com)
  • Additionally, RNA Pol III transcribes the genes responsible for producing the 5S rRNA, U6 snRNA, and the 7S RNA associated with the signal recognition particle (SRP). (microbiologynote.com)
  • A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes ( atp1 , atp6 and matR ) were recently transferred from Cuscuta to Plantago . (biomedcentral.com)
  • Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. (biomedcentral.com)
  • The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. (biomedcentral.com)
  • This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. (biomedcentral.com)
  • The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests that transferred genes may be evolutionarily important in generating mitochondrial genetic diversity. (biomedcentral.com)
  • The neuroprotective effects of conditioned medium (CM) of hESCs (H9), wt hiPSCs (WTC-11) and the ALS iPSCs, on MN apoptosis and viability, formation and maintenance of neurites, mitochondrial activity and expression of inflammatory genes, were examined. (springer.com)
  • In the model with pathogenic SOD1 mutation, ALS iPSC-CM attenuated all examined hallmarks of ALS pathology, rescued human ALS-MNs from denervation and death, restored mitochondrial health, and reduced the expression of inflammatory genes. (springer.com)
  • Compared side by side, cyclosporine (CsA), a mitochondrial membrane blocker that prevents the leakage of mitochondrial DNA, failed to avert the death of ALS-MNs, although CsA and ALS iPSC-CM equally stabilized MN mitochondria and attenuated inflammatory genes. (springer.com)
  • [6] Or, transcription factories are present and the euchromatin is brought within the nearest transcription factory and A1BG messenger RNA (mRNA) is transcribed. (wikiversity.org)
  • mRNA extraction and reverse transcription polymerase chain reaction Total RNA was extracted using Trizol reagent. (wee1signaling.com)
  • Biochemical methods included analysis of mitochondrial function and mitochondrial biogenesis, as well as mRNA and protein expression of mitochondrial biogenesis signaling molecules, including silent information regulator 1 (SIRT1), peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α), nuclear respiratory factor 1 (NRF1) and mitochondrial transcription factor A (TFAM). (thno.org)
  • Finally, a separate domain (residues 1-96) of protein N388 may be involved in mRNA binding that results in translational regulation of T4 DNA polymerase (Pavlov & Karam, 1994). (embl.de)
  • The pre-mRNA molecules produced by RNA Pol II undergo various modifications, such as splicing and capping, before they are transported out of the nucleus for translation into proteins. (microbiologynote.com)
  • Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit 6 (mtATP6). (unboundmedicine.com)
  • METHODS: Two cohorts of 20-week-old and 52-week-old wild-type (WT) C57BL/6J and NOD2 knockout (Nod2-KO) mice were treated with broad-spectrum antibiotics and fecal samples were collected to investigate temporal dynamics of the intestinal microbiota (bacteria and fungi) using 16S ribosomal RNA and internal transcribed spacer 1 sequencing. (bvsalud.org)
  • Specific interactions of the polymerase complex with host proteins may be determining factors in both of these characteristics and play important roles in the viral life cycle. (nih.gov)
  • To investigate this question, we performed a comprehensive proteomic analysis of human host proteins associated with the polymerase of the well-characterized H5N1 Vietnam/1203/04 isolate. (nih.gov)
  • The most intriguing and novel finding was the large number of mitochondrial proteins (∼20%) that associated with the PA subunit. (nih.gov)
  • These proteins mediate molecular transport across the mitochondrial membrane or regulate membrane potential and may in concert with the identified mitochondrion-associated apoptosis inducing factor (AIFM1) have roles in the induction of apoptosis upon association with PA. (nih.gov)
  • The nuclear genome encodes the remaining mitochondrial proteins, which are then transported into the mitochondria. (wikipedia.org)
  • Nuclear cells such as platelets do not possess nuclear DNA and therefore must have alternative sources for the RNA that they need to generate proteins. (wikipedia.org)
  • Chimeric RNAs and proteins are identical to those produced from a chromosomal rearrangement found in human endometrial stromal tumours[ 5 ]. (biomedcentral.com)
  • Most mitochondrial proteins synthesized in the cytosol. (rahulgladwin.com)
  • These include the proteins involved in mitochondrial DNA (mtDNA) replication, which, if defective, can produce mtDNA mutations leading to mitochondrial dysfunction and disease [ 2 ]. (biomedcentral.com)
  • Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. (embl.de)
  • Our data show that PBMCs are a promising source to monitor HD progression and highlights nDNA damage and diverging mitochondrial and nuclear genome responses representing early cellular impairments in HD. (nature.com)
  • The diagram describes the eukaryotic preinitiation complex which includes the general transcription factors and RNA Polymerase II. (wikiversity.org)
  • Alpha-amanitin, produced by Amanita phalloides: inhibits eukaryotic polymerase II. (rahulgladwin.com)
  • Among the 16 DNA polymerases identified in the eukaryotic cell so far, only DNA polymerase γ (pol γ) is known to function in mitochondria [ 3 - 5 ]. (biomedcentral.com)
  • Eukaryotic transcription is a complex process that allows eukaryotic cells to convert genetic information stored in DNA into RNA molecules, which can be transported and used for various cellular functions. (microbiologynote.com)
  • Eukaryotic transcription produces different types of RNA molecules with diverse functions. (microbiologynote.com)
  • In summary, eukaryotic transcription is a vital process that enables cells to convert DNA information into functional RNA molecules. (microbiologynote.com)
  • These enzymes are responsible for transcribing various types of RNA molecules within the nucleus of eukaryotic cells . (microbiologynote.com)
  • Operating within the nucleoplasm, RNA Pol II takes on a central role in eukaryotic transcription. (microbiologynote.com)
  • Each of these eukaryotic RNA polymerases is composed of a large complex of 12 or more subunits. (microbiologynote.com)
  • RNA polymerase II holoenzyme complex may also have to search for one or more transcription start sites. (wikiversity.org)
  • All RNA-seq library preparation methods are globally relying on the same molecular steps, such as reverse transcription (RT), fragmentation, indexing, and amplification. (biomedcentral.com)
  • First strand cDNA was synthesized from 2 ug of total RNA using the Reverse Transcription System Kit. (wee1signaling.com)
  • When dNTPs and in vitro synthesized R2Bm RNA are added to the integrase reaction mixtures, reverse transcription occurs and is dependent upon the presence of the rDNA target site. (nih.gov)
  • Initiation marks the beginning of transcription, where RNA polymerase, the enzyme responsible for transcription, recognizes specific DNA sequences known as promoters and binds to them. (microbiologynote.com)
  • This process continues until the RNA polymerase reaches a termination signal, which signals the end of transcription. (microbiologynote.com)
  • Quadriceps muscle biopsy samples from 48 patients with CFS were processed to detect enterovirus RNA by two stage, reverse transcription, nested polymerase chain reaction (RT-NPCR), using enterovirus group specific primer sets. (bmj.com)
  • However, enteroviruses have been implicated in the pathogenesis of chronic myocarditis and dilated cardiomyopathy, and the recent application of the reverse transcription, nested polymerase chain reaction (RT-NPCR), including nucleotide sequencing of PCR products, has unequivocally demonstrated coxsackie B3-like RNA in endomyocardial biopsies from such cases. (bmj.com)
  • Nevertheless, we found decreased level of factors associated with mitochondrial biogenesis and an associated dampening of the mitochondrial DNA damage frequency in HD, implying an early defect in mitochondrial activity. (nature.com)
  • Mitochondrial biogenesis serves a crucial role in maintaining mitochondrial homeostasis and salubrious properties of resveratrol (RSV) has been well-defined. (thno.org)
  • However, the molecular mechanisms governing mitochondrial biogenesis in developmental fluoride neurotoxicity remain unclear and the related therapeutic dietary agent is lacking. (thno.org)
  • Both in vivo and in vitro experiments showed that sodium fluoride (NaF) caused mitochondrial dysfunction and impaired mitochondrial biogenesis. (thno.org)
  • Also, NaF elevated SIRT1 levels and suppressed SIRT1 deacetylase activity along with decreased levels of PGC-1α, NRF1 and TFAM, suggestive of dysregulation of mitochondrial biogenesis signaling molecules. (thno.org)
  • Moreover, enhancement of mitochondrial biogenesis by TFAM overexpression alleviated NaF-induced neuronal death through improving mitochondrial function in vitro . (thno.org)
  • Further in vivo and in vitro studies identified RSV, the strongest specific SIRT1 activator, improved mitochondrial biogenesis and subsequent mitochondrial function to protect against developmental fluoride neurotoxicity via activating SIRT1-dependent PGC-1α/NRF1/TFAM signaling pathway. (thno.org)
  • Noteworthy, epidemiological data indicated intimate correlations between disturbed circulating levels of mitochondrial biogenesis signaling molecules and fluoride-caused intellectual loss in children. (thno.org)
  • Our data suggest the pivotal role of impaired mitochondrial biogenesis in developmental fluoride neurotoxicity and the underlying SIRT1 signaling dysfunction in such neurotoxic process, which emphasizes RSV as a potential therapeutic dietary agent for relieving developmental fluoride neurotoxicity. (thno.org)
  • The results of separate analyses from RPB1 and RPB2 are in agreement with the combined analyses that resolve a paraphyletic Clavicipitaceae comprising three well-supported clades (i.e. (unboundmedicine.com)
  • The mitochondrial genome (mtDNA) is replicated separately from the host genome. (wikipedia.org)
  • To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. (biorxiv.org)
  • Except for CAG sizing, mitochondrial and nuclear DNA (mtDNA and nDNA) parameters have not yet proven to be representative biomarkers for disease and future therapy. (nature.com)
  • DNA polymerase γ ( POLG ) is the only known mitochondrial DNA (mtDNA) polymerase. (biomedcentral.com)
  • The additional accuracy is accounted for by a separate enzyme system that repairs the mismatched base pairs remaining after replication. (online-sciences.com)
  • Many mutations map to the polymerase and exonuclease domains of the enzyme and produce a broad clinical spectrum. (biomedcentral.com)
  • it appears that sequences within the 250-nt long 3'-untrans- lated region of R2Bm RNA are recognized by the enzyme and, together with 5-10 residues in the primer end of the 28 S rDNA, permit chain synthesis (18). (nih.gov)
  • DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. (catsboard.com)
  • Here we identified some chimeric mRNAs in pigs and analyzed the expression of them across individuals and breeds using RNA-sequencing data. (biomedcentral.com)
  • The present study identified 669 putative chimeric mRNAs in pigs, of which 251 chimeric candidates were detected in a set of RNA-sequencing data. (biomedcentral.com)
  • This study was conducted to determine whether elevated hydrostatic pressure alters mitochondrial structure, triggers release of the dynamin-related guanosine triphosphatase (GTPase) optic atrophy type 1 (OPA1) or cytochrome C from mitochondria, alters OPA1 gene expression, and can directly induce apoptotic cell death in cultured retinal ganglion cell (RGC)-5 cells. (molvis.org)
  • Mitochondrial fission, characterized by the conversion of tubular fused mitochondria into isolated small organelles, was triggered after three days exposure to elevated hydrostatic pressure. (molvis.org)
  • The HD cellular phenotype is reminiscent of mitochondrial dysfunction. (nature.com)
  • However, a low amount of a chimeric RNA ( JAZF1-JJAZ1 ) was detected in normal endometrial tissues, joining the JAZF1 gene on chromosome band 7p15 to the JJAZ1/SUZ12 gene on chromosome band 17q21[ 5 ]. (biomedcentral.com)
  • Given the absence of any detectable rearranged DNA in cells producing chimeric RNAs, the obvious explanation is the rearrangement at the RNA level. (biomedcentral.com)
  • We used RNA-seq to look for chimeric RNAs that map to both MmuPV1 and host genomes. (nih.gov)
  • [ 7 ] Sofosbuvir inhibits the HCV NS5B RNA-dependent RNA polymerase, which is also required for replication. (medscape.com)
  • the complex series of events that assure replication of long terminal repeats, including in- ternal primer binding sites on the RNA template, priming by tRNAs, and template switching, is unnecessary. (nih.gov)
  • This gene codes for the cytosolic isozyme, which is involved in the malate-aspartate shuttle, which allows malate to cross past the mitochondrial membrane and be converted to oxaloacetate to perform further cellular functions. (wikipedia.org)
  • Elevated hydrostatic pressure triggered mitochondrial changes including mitochondrial fission and abnormal cristae depletion, alteration of OPA1 gene expression, and release of OPA1 and cytochrome C into the cytoplasm before the onset of apoptotic cell death in differentiated RGC-5 cells. (molvis.org)
  • Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. (biomedcentral.com)
  • Mutations in the POLG gene have emerged as one of the most common causes of inherited mitochondrial disease in children and adults. (biomedcentral.com)
  • Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. (biomedcentral.com)
  • DNA polymerase ε removes the primers of Okazaki fragments on the lagging strand. (online-sciences.com)
  • It synthesizes transfer RNA (tRNA), which plays a vital role in protein synthesis by bringing specific amino acids to the ribosome. (microbiologynote.com)
  • Because mitochondrial changes have been identified in association with neuronal death in other models of central nervous system disease [ 2 , 3 ], it is possible that glaucomatous optic neuropathy may also involve mitochondrial changes. (molvis.org)
  • These factors may have also contributed to the regulation of mitochondrial functions. (wikipedia.org)
  • [ 7 ] More specifically, sofosbuvir is a nucleotide prodrug in that it undergoes intracellular metabolism to form an active urine analog to be incorporated into HCV RNA, where it behaves as a chain terminator. (medscape.com)
  • This function is performed by DNA- directed DNA-polymerases ( EC 2.7.7.7 ) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. (embl.de)
  • Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. (embl.de)
  • Elongation is the stage where RNA polymerase moves along the DNA template, synthesizing an RNA molecule that is complementary to the DNA sequence. (microbiologynote.com)
  • Through a series of stages, including initiation, elongation, and termination, RNA polymerases produce different types of RNA molecules with diverse cellular functions. (microbiologynote.com)
  • In this study, we set out to generate a method for affordable, efficient, and accurate bulk RNA profiling of a large number of samples that combines the high-throughput capacity of single-cell transcriptomics and the high performance of standard RNA-seq. (biomedcentral.com)
  • Depletion of FAHD1 has been associated with impaired mitochondrial respiration 13 , 16 and associated with a reversible type of cellular senescence phenotype 14 that is linked to intermediate potential shortcomings in the electron transport system. (jove.com)
  • In simulating the RNA cis-splicing mechanism, a cDNA is thought to be generated by trans-splicing when it is aligned to multiple non-contiguous genomic loci and the fusion junction obeys canonical GU-AG splice site. (biomedcentral.com)
  • Thus, the initial product is a branched chain in which the cDNA copy of the R2Bm RNA is covalently linked to the 28 S rDNA and hydrogen bonded to the RNA. (nih.gov)
  • Experiments with in vitro synthe- sized R2Bm RNA containing varying numbers of terminal As indicate that the efficiency of cDNA synthesis decreases as the terminus changes from 4 to 1 to 8 As (17, 18). (nih.gov)
  • DNA polymerases utilize one deoxyribonucleoside triphosphate as a source of the deoxyribonucleoside monophosphate for the growing DNA strand by the removal of pyrophosphate. (online-sciences.com)
  • The RNA-primed synthesis of DNA demonstrating the template function of the complementary strand parental DNA . (online-sciences.com)
  • Once bound, RNA polymerase begins to unwind the DNA double helix and initiate the synthesis of a complementary RNA strand. (microbiologynote.com)
  • Furthermore, Bcl-2 family such as mitochondrial pro‑apoptotic Bax, anti-apoptotic Bcl-xl and Bid were regulated by Manu A, triggering the mitochondrial apoptotic pathway. (spandidos-publications.com)
  • StAR mediates the transfer of cholesterol from the outer to the inner mitochondrial membrane, where cholesterol is then converted by cytochrome P450 scc to pregnenolone, the precursor for all steroids. (jneurosci.org)
  • Cardiac mitochondrial aconitase activity decreased after DE exposure in both strains. (nih.gov)
  • DNA polymerases require the presence of a primer (i.e. oligonucleotide of RNA with free 3´ hydroxyl group), a template (i.e single-stranded DNA), and deoxyribonucleotides (d ATP , d CTP, d GTP, and d TTP) in order to function. (online-sciences.com)
  • Unravelling this history will probably require sequencing multiple mitochondrial and nuclear genomes from Plantago . (biomedcentral.com)
  • Hexokinase II (HKII), the predominant isoform overexpressed in cancer cells, has dual functions of promoting glycolysis as well as inhibiting mitochondrial-mediated apoptosis. (oncotarget.com)
  • Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. (embl.de)
  • The assay is based on the cleavage of WST 1 to formazan dye by cellular mitochondrial dehydrogenases. (wee1signaling.com)
  • For those circumstances in which the holoenzyme is built onto the euchromatin, it is necessary to consider the holoenzyme components and the likely sequence of binding, RNA polymerase II entrance upon the scene and subsequent action. (wikiversity.org)
  • B ) Schematic of HOE-1 protein showing the mitochondrial targeting sequence (MTS) and nuclear localization signals (NLS). (elifesciences.org)
  • Additionally, non-coding RNAs, which make up the majority of the transcriptional output in cells, play crucial roles in various cellular processes. (microbiologynote.com)
  • To detect and characterise enterovirus RNA in skeletal muscle from patients with chronic fatigue syndrome (CFS) and to compare efficiency of muscle energy metabolism in enterovirus positive and negative CFS patients. (bmj.com)
  • This reduces both the RNA-seq cost and preparation time by allowing the generation of a single sequencing library that contains multiple distinct samples/cells [ 1 ]. (biomedcentral.com)
  • Finally, we show that active RNA polymerase II is found in distinct domains in the nucleus that constitute a subset of the total Comr stained chromatin. (biologists.com)
  • A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. (embl.de)
  • Through its activity, RNA Pol I ensures the synthesis of crucial components of the ribosome, the cellular machinery responsible for protein synthesis. (microbiologynote.com)
  • In somatic tissues, the diversity of methylation patterns are only recently emerging but they are often associated with the RNA-directed DNA methylation (RdDM) pathway. (salk.edu)
  • Ledipasvir and sofosbuvir have separate mechanisms of action. (medscape.com)
  • RNA is required for optimal activity. (nih.gov)
  • 12 In contrast, several groups have been unable to find enteroviral RNA in muscle from patients with inflammatory myopathies by RT-PCR, 13- 15 while PCR studies on muscle from CFS patients have given conflicting 16, 17 or negative 18 results. (bmj.com)
  • Mitochondrial structural changes were also assessed by electron microscopy and three-dimenstional (3D) electron microscope tomography. (molvis.org)
  • Electron microscopy confirmed the fission and noted no changes to mitochondrial architecture, nor outer membrane rupture. (molvis.org)
  • This method is capable of studying the mutation rate of many microbial species and can be applied to problems ranging from the generation of high-fidelity polymerases to measuring the frequency of antibiotic resistance emergence. (bvsalud.org)