• Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)
  • One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. (mdpi.com)
  • In addition, cells can produce more than 300 different protein variants from AARS genes through alternative splicing of their mRNAs or post-translational protein fragmentation. (fascea.pics)
  • Ribonucleic acid (RNA) has multiple roles in cellular functions, from coding genes to non-coding regulatory activities. (biomedcentral.com)
  • These mutations occur in genes that provide instructions for making molecules called transfer RNAs. (medlineplus.gov)
  • Our genome-wide chromatin immunoprecipitation experiments revealed that Gß1 colocalized and interacted with RNA polymerase II on fibrotic genes in an angiotensin II-dependent manner. (bvsalud.org)
  • Serine and arginine-rich (SR) proteins are RNA-binding proteins (RBPs) known as constitutive and alternative splicing regulators. (molcells.org)
  • One such important family of regulatory RBPs is the Serine-Arginine (SR) family of proteins. (molcells.org)
  • Regulatory non-coding RNAs and RNA-binding proteins (RBPs) are important research areas in gene regulation and RNA biology. (rochester.edu)
  • Our laboratory is interested in the understanding of pathophysiological function and molecular mechanism of new non-coding RNAs (and RBPs) and new modes of gene regulation in c. (rochester.edu)
  • An essential branched-chain aliphatic amino acid found in many proteins . (lookformedical.com)
  • An unnatural amino acid that is used experimentally to study protein structure and function. (lookformedical.com)
  • Furthermore, they have specific amino acid binding sites ready to interact with other proteins. (fascea.pics)
  • The amino acid sequence for this part of the protein resembled that of a human cytokine, EMAP II, which recruits circulating immune cells in tissues to promote inflammation. (fascea.pics)
  • A cDNA clone encoding a protein consisting of 189 amino acid residues including a sodefrin sequence was isolated from a Cynops pyrrhogaster abdominal gland cDNA library. (wiley.com)
  • This clone encoded a precursor protein of 192 amino acid residues, including a sodefrin-like peptide sequence with substitutions of two amino acid residues. (wiley.com)
  • Diverse SR proteins play partially overlapping but distinct roles in transcription-coupled splicing and mRNA processing in the nucleus. (molcells.org)
  • In addition, shuttling SR proteins act as adaptors for mRNA export and as regulators for translation in the cytoplasm. (molcells.org)
  • Depletion of Gß1 led to derepression of the fibrotic response at the mRNA and protein levels under basal conditions and an enhanced fibrotic response after sustained stimulation of the angiotensin II type I receptor. (bvsalud.org)
  • For some amino acids there are two variants with a separate enzyme for use in protein translation, which takes place in the mitochondria. (fascea.pics)
  • F o For as long as living things have been building proteins based on the code of messenger RNA molecules, there have been aminoacyl-tRNA synthetases. (fascea.pics)
  • The company that Schimmel co-founded aTyr Pharma in San Diego, AARS proteins envision themselves as an entirely new class of drugs, distinct from small molecules or other biologics. (fascea.pics)
  • As splicing is linked to transcriptional and post-transcriptional steps, SR proteins are implicated in the regulation of multiple aspects of the gene expression program. (molcells.org)
  • In this mini-review, the essential functions of SR proteins in splicing regulation, with a focus on their roles as RNA binders in the ribonucleoprotein complex (RNP) will be summarized. (molcells.org)
  • The results all together confirm the role of sense/antisense RNA-based regulation of gene expression, expanding the sense/antisense atlas of S. cerevisiae . (biomedcentral.com)
  • This mini-review will summarize the roles of SR proteins as RNA binders, regulators, and connectors from transcription in the nucleus to translation in the cytoplasm. (molcells.org)
  • While other proteins have taken on supporting roles, the number and variety of byproducts found in AARS are remarkable, Schimmel says. (fascea.pics)
  • Plant DCL4 is involved in the biogenesis of either functional endogenous or exogenous (i.e. viral) short interfering (si)RNAs, thus playing crucial antiviral roles. (biomedcentral.com)
  • The transfer RNAs associated with progressive external ophthalmoplegia are present in mitochondria and help assemble the proteins that carry out the steps of oxidative phosphorylation. (medlineplus.gov)
  • The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. (bvsalud.org)
  • Recent global analyses of SR-RNA interaction maps have advanced our understanding of SR-regulated gene expression. (molcells.org)
  • The long-term objective of our laboratory is to identify novel RNA-based molecular mechanisms that control gene expression and conduct pathophysiological function in cardiac system, as well as to develop novel therapeutic approaches for the prevention or treatment of human cardiovascular diseases. (rochester.edu)
  • He received his Ph.D. degree in the laboratory of Dr. En-Duo Wang in Biochemistry and Molecular Biology from Shanghai Institute of Biochemistry and Cell Biology of Chinese Academy of Science in 2008, where he studied the structural and functional interplay of transfer RNA (tRNA) and tRNA synthetase in bacteria, yeast and human. (rochester.edu)
  • A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis. (lookformedical.com)
  • Given their essential role in protein synthesis, they occur regularly and are unlikely to disappear from a viable genome. (fascea.pics)
  • For example, if the AARS of a pathogen is different enough from that of humans, an antibiotic could be developed that disrupts protein synthesis in the infectious agent. (fascea.pics)
  • Many AARS have been linked to human diseases caused not by defects in protein assembly but by these other non-canonical functions. (fascea.pics)
  • The discovery of new functions for these ancient proteins was "a big surprise," he says. (fascea.pics)
  • Plant Dicer-like proteins (DCLs) are RNase III, double-stranded RNA (dsRNA)-specific endonucleases with specialized functions in producing short (s)RNAs of 21- to 24-nucleotides (nt), including micro (mi)RNAs and short interfering (si)RNAs of endogenous or viral origin. (biomedcentral.com)
  • Twenty alpha-amino acids are the subunits which are polymerized to form proteins . (lookformedical.com)
  • The latter function is associated with the ability of RNA to form double-stranded (ds) or ds-like secondary structures. (biomedcentral.com)
  • The simplest form of RNA silencing, widely known as RNA interference (RNAi), is conserved in diverse eukaryotic species, including the fungal kingdom, but has been lost in the model budding yeast, Saccharomyces cerevisiae [ 15 ]. (biomedcentral.com)
  • These led to the conclusion that DCL4 and DCL2 act redundantly and one of the two alone is sufficient to perceive dsRNA of viral origin, process it into siRNA of viral origin (vsiRNAs) and initiate the plant RNA silencing-based antiviral defense [ 14 ]. (biomedcentral.com)
  • We recently discovered a new type of stress-responsive, protein-directed human RNA switch that regulates expression of vascular endothelial growth factor-A in human monocytic cells (Ray, PS, et al. (rochester.edu)
  • Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. (lookformedical.com)
  • Transfer RNAs help assemble protein building blocks (amino acids) into functioning proteins. (medlineplus.gov)
  • Nucleic acids (DNA & RNA) are the building blocks of genetic material. (bankofbiology.com)
  • In this study we expressed plant DCL4 in Saccharomyces cerevisiae , an RNAi-depleted organism, in which we could highlight the role of dicing as neither Argonautes nor RNA-dependent RNA polymerase is present. (biomedcentral.com)
  • In general, RRM domains recognize RNA, whereas RS domains participate in diverse protein-protein and protein-RNA interactions. (molcells.org)
  • J. Singh, T. Litfin, K. Paliwal, J. Singh, A. K. Hanumanthappa, and Y. Zhou, "SPOT-1D-Single: Improving the single-sequence-based prediction of protein secondary structure, back-bone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning. (sparks-lab.org)
  • J. Singh, K. Paliwal, T Zhang, J. Singh, T Litfin, Y. Zhou, "Improved RNA Secondary Structure and Tertiary Base-pairing Prediction Using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning. (sparks-lab.org)
  • The tRNA Leu(UUR) molecule is present in cellular structures called mitochondria. (medlineplus.gov)
  • A cell biologist, Alexandra manages grants in the areas of chromosome and nuclear structures, motor proteins, cytoskeletal filaments, and intracellular transport. (nih.gov)
  • A. Kumar, J. Singh, K. Paliwal, J. Singh, Y. Zhou, "Single-sequence and profile-based Prediction of RNA solvent accessibility using dilated convolution neural network. (sparks-lab.org)
  • Transfer RNAs help assemble protein building blocks (amino acids) into functioning proteins. (medlineplus.gov)
  • During protein assembly, this molecule attaches to the amino acid leucine (Leu) and inserts it into the appropriate locations in the growing protein. (medlineplus.gov)
  • The A3243G mutation reduces the ability of tRNA Leu(UUR) to add leucine to proteins that are being assembled, which slows protein production. (medlineplus.gov)
  • This mutation impairs the ability of mitochondria to make proteins, use oxygen, and produce energy. (medlineplus.gov)
  • The mutation, A3302G located at the acceptor arm of tRNA-Leu, caused the dysfunction via reducing the mitochondrial copy number [ 10 ]. (biomedcentral.com)
  • With the help of computers, protein pockets prediction can save manpower and fin. (biomedcentral.com)
  • Q. Yuan, J. Chen, H. Zhao, Y. Zhou, and Y. Yang, "Structure-aware protein-protein interaction site prediction using deep graph convolutional network. (sparks-lab.org)
  • J. Singh, K. Paliwal, J. Singh, Y. Zhou, "RNA Backbone Torsion and Pseudotorsion Angle Prediction using Dilated Convolutional Neural Networks. (sparks-lab.org)
  • Success will represent an unprecedented level of control over nanoscale motion, building an engineering capacity that will eventually be used to design protein nanoassemblies capable of sophisticated intracellular therapeutic functions such as genome repair. (nih.gov)
  • P. Xiong, R. Wu, J. Zhan, and Y. Zhou, "Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement. (sparks-lab.org)
  • However, up-regulation of PTPN12 and miR-146b-3p mimic suppressed ERBB2 protein expression but induced its gene expression. (degruyter.com)
  • Q. Chen, K. Liu, R. Yu, B. Zhou, P. Huang, Z. Cao, Y. Zhou, and J. Wang, "From "dark matter" to "star": Insight into the regulation mechanisms of plant functional long non-coding RNAs. (sparks-lab.org)
  • Some tRNAs contain a fifth stem-loop named extra arm, which is located in the RNA sequence between the anticodon stem and the T stem [ 5 ]. (biomedcentral.com)
  • The MT-TL1 gene provides instructions for making a molecule called a transfer RNA (tRNA), which is a chemical cousin of DNA. (medlineplus.gov)
  • The MT-TL1 gene provides instructions for making a specific form of tRNA that is designated as tRNA Leu(UUR) . (medlineplus.gov)
  • Levels of Brf1 and Pol III (RNA polymerase III-dependent) gene transcription in HCC patients with alcohol consumption are higher than the cases of non-HCC with or without alcohol intake. (oncotarget.com)
  • Within mitochondria, tRNA Leu(UUR) is involved in the assembly of proteins that carry out a series of chemical steps called oxidative phosphorylation. (medlineplus.gov)
  • Protein complex identification from protein-protein interaction (PPI) networks is crucial for understanding cellular organization principles and functional mechanisms. (biomedcentral.com)
  • The m 6 A modification is recognized by the reader proteins, such as YTH-domain family proteins and specific RNA binding proteins (RBPs), which mediate the downstream effects of m 6 A methylation [ 4 ]. (biomedcentral.com)
  • MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. (biomedcentral.com)
  • S. Liang, Z. Li, J. Zhan, and Y. Zhou, "De novo protein design by an energy function based on series expansion in distance and orientation dependence. (sparks-lab.org)