• Through recognition of its binding proteins, m6A can regulate various aspects of mRNA metabolism and is essential for maintaining higher brain functions. (encyclopedia.pub)
  • Nuclear mRNA transcripts acquire a protein coat composed of cap- and RNA-binding proteins that allow nuclear export and dictate the functional program of cytoplasmic mRNAs ( Moore, 2005 ). (rupress.org)
  • Mechanically, m6A can be recognized by "reader" proteins or can directly modify RNA conformation, and it widely affects gene expression by mediating RNA stability, translation, splicing and export. (scienceopen.com)
  • The genetic information of life on Earth have been conserved in natural nucleotides-A, G, C, T(U) forming two exclusive sets of base pairs A-T(U) & G-C, that complementing to the fundamental processes of DNA replication & RNA transcription by several polymerases and translation to functional proteins via ribosomal reactions. (fortuneonline.org)
  • m 6 A recruits effector proteins that determine the fate of mRNAs through changes in splicing, cellular localization, stability, and translation efficiency. (molcells.org)
  • The m 6 A-modified RNAs then recruit m 6 A-binding proteins (readers) that guide these RNAs for RNA biogenesis processes such as pre-mRNA splicing, nuclear export, stabilization, degradation, and translation. (molcells.org)
  • The post-transcriptional modifications of mRNA, which include N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytidine (m5C), N7-methylguanosine (m7G), and N6,2-O-dimethyladenosine (m6Am) add a new layer to regulating mRNA metabolism and gene expression [ 2 ] . (encyclopedia.pub)
  • Given its diverse roles in mRNA metabolism and gene regulation, altered m6A profiles have been linked to various illnesses, including cancers and psychiatric disorders [ 4 ] . (encyclopedia.pub)
  • In addition to mRNA metabolism, a similar protein in yeast has been implicated in a variety of nuclear and cytoplasmic functions, including homologous recombination, meiosis, telomere maintenance, and microtubule assembly. (nih.gov)
  • The interacting complex contains the RNA binding motif protein 15/15B (RBM15/15B), vir-like m6A methyltransferase associated (VIRMA), zinc finger CCCH-type containing 13 (ZC3H13), and HAKAI which support the functioning and positioning of a writer complex. (encyclopedia.pub)
  • In addition, RNA modifications have been characterized not only in abundant non-coding RNA, such as transfer RNA (tRNA), ribosomal RNA (rRNA), and small nuclear RNA (snRNAs), but also in messenger RNA (mRNA) [ 2 ] . (encyclopedia.pub)
  • Different classes of RNA granules share some protein components and may use similar mechanisms to regulate mRNA translation/decay. (rupress.org)
  • The master kinase LKB1 is a key regulator of several cellular processes, including cell proliferation, cell polarity and cellular metabolism. (sdbonline.org)
  • The C-terminal domain of YTHDF2 selectively binds to m6A-containing mRNA whereas the N-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. (scienceopen.com)
  • Cellular 5'-3' mRNA exonuclease Xrn1 controls double-stranded RNA accumulation and anti-viral responses. (nih.gov)
  • In this review, we will focus on how the signal transduction pathways, which play key roles in diverse physiological and pathological conditions, coordinate cellular processes through m 6 A. Given that m 6 A also controls signaling pathways through RNA modification or acting as a ligand, understanding the crosstalk between signal transduction networks and m 6 A RNA processing will provide us insights into the complex biological systems. (molcells.org)
  • RNA modifications known as epitranscriptomics have emerged as a novel layer of transcriptomic regulation. (encyclopedia.pub)
  • Cytoplasmic RNA granules in germ cells (polar and germinal granules), somatic cells (stress granules and processing bodies), and neurons (neuronal granules) have emerged as important players in the posttranscriptional regulation of gene expression. (rupress.org)
  • Our findings therefore suggest that RNA decoration by m(6)A has a fundamental role in regulation of gene expression. (scienceopen.com)
  • Epigenetic modification of the transcribed RNA can be another layer of gene expression regulation. (molcells.org)
  • RBM15/15B mediate the binding of a writer complex to the U enriched region on mRNA and recruit writer complexes to specific sites [ 9 ] . (encyclopedia.pub)
  • Epitranscriptomics, also known as RNA modifications, refers to the study of post-transcriptional modifications of RNA molecules. (encyclopedia.pub)
  • N 6 -Methyladenosine (m 6 A) is a widespread, reversible chemical modification of RNA molecules, implicated in many aspects of RNA metabolism. (nature.com)
  • Pan, T. N 6 -methyl-Adenosine modification in messenger and long non-coding RNA. (nature.com)
  • Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. (scienceopen.com)
  • We review the relationship between different classes of these granules and discuss how spatial organization regulates messenger RNA translation/decay. (rupress.org)
  • Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1. (nih.gov)
  • Specific signal sequences, AREs for example[ 17 ], can affect the rate at which the poly-adenosine tail is shortened. (berkeley.edu)
  • Among the hundreds of known RNA modifications, N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes. (encyclopedia.pub)
  • Although chemical modifications of RNA have been described for a half-century, only recently with the advancement of technology have we started to elucidate their functions [ 1 ] . (encyclopedia.pub)
  • Klungland, A. & Dahl, J.A. Dynamic RNA modifications in disease. (nature.com)
  • An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. (scienceopen.com)
  • N 6 -methyladenosine modulates messenger RNA translation efficiency. (nature.com)
  • The MACOM complex does not have catalytic activity, but it is necessary for efficient m 6 A methylation by recruiting RNA substrates and stabilizing the MAC-MACOM complex in the nucleus and nuclear speckles. (molcells.org)
  • Human-derived hepatic cell lines are a valuable alternative to primary hepatocytes for drug metabolism, transport and toxicity studies. (cancerindex.org)
  • Little quantitative information exists as to either how many transcript copies of particular genes are m 6 A modified ('m 6 A levels') or the relationship of m 6 A modification(s) to alternative RNA isoforms. (nature.com)
  • Under the association of specific co-factors, writers show spatiotemporal N6-methyltransferase activity. (scienceopen.com)
  • The subcellular localization of messenger RNA (mRNA) precisely controls where protein products are synthesized and where they function. (bvsalud.org)
  • However, obtaining an mRNA's subcellular localization through wet-lab experiments is time-consuming and expensive, and many existing mRNA subcellular localization prediction algorithms need to be improved. (bvsalud.org)
  • MicroRNAs (miRNAs) comprise a group of small non-coding RNAs 18~25 nucleotides (nt) in length that posttranscriptionally regulate gene expression via binding to the 3′-untranslated regions (3′-UTRs) of target gene mRNA [ 1 , 2 ]. (biomedcentral.com)
  • This specific binding between miRNA and target mRNA leads to the repression of protein synthesis and the subsequent degradation of the targeted mRNA [ 11 ] (Fig. 1 ). (biomedcentral.com)
  • The DEAD (Asp-Glu-Ala-Asp)-box helicase family is the largest helicase family in eukaryotes and functions in nearly all aspects of eukaryotic RNA metabolism [ 1 , 2 ]. (biomedcentral.com)
  • Briefly, RNA polymerase II transcribes miRNA genes, leading to the formation of long precursor transcripts named primary miRNAs (pri-miRNAs), which have stem-loop structures consisting of hundreds of nucleotides. (biomedcentral.com)
  • The long-distance transport of messenger RNAs (mRNAs) has been shown to be important for several developmental processes in plants. (researchgate.net)
  • A popular method for identifying travelling mRNAs is to perform RNA-Seq on grafted plants. (researchgate.net)
  • The m 6 A modification in coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m 6 A around the stop codons and within the 3′ untranslated regions is generally negatively correlated with the abundance of associated mRNAs. (biomedcentral.com)
  • Long non-coding RNAs (lncRNAs) are a type of non-coding RNA with a length that exceeds 200 nucleotides. (frontiersin.org)
  • Does a transcript get translated, stored, decayed or transported to a specific subcellular location? (biomedcentral.com)
  • In this Review, we discuss the chemical properties and design of effective reagents for RNA 2′-OH acylation, highlighting the unique problem of 2′-OH reactivity in the presence of water. (nature.com)
  • Histochemical localization of immunoreactive substances using labeled antibodies as reagents. (lookformedical.com)
  • To provide a more intuitive understanding of the role of DDX3X in cancer, we summarized its functions and specific mechanisms in various types of cancer and presented its involvement in cancer-related signalling pathways. (biomedcentral.com)
  • Houseley, J. & Tollervey, D. The many pathways of RNA degradation. (nature.com)
  • Traditionally, most of these methods involved the chemical modification of RNA structure using solid-state synthesis or enzymatic transformations. (nature.com)
  • However, over the past 15 years, the direct functionalization of RNA by selective acylation of the 2′-hydroxyl (2′-OH) group has emerged as a powerful alternative that enables the simple modification of both synthetic and transcribed RNAs. (nature.com)
  • Based on its function in RNA metabolism, DDX3X has a major effect on many biological processes. (biomedcentral.com)
  • In this review, we first describe its functions in RNA metabolism and other biological processes. (biomedcentral.com)
  • RNA is a versatile biomolecule with a broad range of biological functions that go far beyond its initially described role as a simple information carrier. (nature.com)
  • Understanding how the force affects the opening and closing of a single base pair, which is a basic step for RNA folding and unfolding and a fundamental behavior in some important biological activities, is crucial to understanding the mechanism of RNA folding and unfolding under mechanical force. (bvsalud.org)
  • Fig. 5: Acylation protects RNA from degradation. (nature.com)
  • Lipid metabolism refers to the synthesis and degradation of lipids in cells and involves the breakdown or storage of fats for energy and the synthesis of structural and functional lipids. (frontiersin.org)
  • We have addressed this issue by designing fusions of Cas9 and guide RNA tra. (researchgate.net)
  • Not all guide RNAs can cleave the DNA efficiently remains a major challenge to CRISPR/Cas9-mediated genome engineering. (bvsalud.org)
  • Therefore, understanding how the Cas9 complex successfully and efficiently identifies specific functional targets through base-pairing has great implications for such applications. (bvsalud.org)
  • Fig. 3: Overview of functional groups introduced into RNA using acylation chemistry. (nature.com)
  • Research in both animal models and humans has begun to unravel the profound complexity of lncRNAs and demonstrated that lncRNAs exert direct effects on glucose and lipid metabolism both in vivo and in vitro . (frontiersin.org)
  • The DEAD-box helicase family member DDX3X (DBX, DDX3) functions in nearly all stages of RNA metabolism and participates in the progression of many diseases, including virus infection, inflammation, intellectual disabilities and cancer. (biomedcentral.com)
  • Tumor specific expression, expression at the earliest stages of tumor development, and direct exposure to blood, suggest that TVMs are ideal biomarkers for both ovarian cancer diagnosis and targeted immunotherapy. (nih.gov)
  • In this review, we describe the function of DDX3X in RNA metabolism, cellular stress response, innate immune response, metabolic stress response in pancreatic β cells and embryo development. (biomedcentral.com)
  • We elaborate on how RNA 2′-OH acylation is being exploited to develop selective chemical probes that enable interrogation of RNA structure and function, and describe new developments and applications in the field. (nature.com)
  • The development of chemical methods to control, manipulate and modify RNA has the potential to yield new insights into its many functions and properties. (nature.com)
  • The National Institute of Neurological Disorders and Stroke (NINDS) is interested in those specific applications which include the Morris K. Udall Centers of Excellence, or other Parkinson's research centers, in the pursuit of those research objectives focused on Parkinson's Disease (PD) or related parkinsonisms. (nih.gov)
  • Data table showing topics related to specific cancers and associated disorders. (cancerindex.org)
  • In this review, we mainly discuss the structure, localization and functions of DDX3X. (biomedcentral.com)
  • Many more non-coding RNAs reside in the genome, and most of them have unknown functions ( 1 ). (frontiersin.org)
  • The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability. (lookformedical.com)
  • Mechanical force has been widely used to study RNA folding and unfolding. (bvsalud.org)
  • The analysis of sequencing data from 27 different organs/tissues of Arabidopsis also proved that most miRNAs are widely expressed, whereas a fraction of miRNAs exhibit tissue-specific expression patterns [ 16 ]. (biomedcentral.com)
  • Fig. 7: Reversible acylation for controlling RNA activity. (nature.com)
  • Aberrant lipid metabolism is associated with higher concentrations of plasma lipids, including low-density lipoprotein (LDL), cholesterol, very-low-density lipoprotein, and triglycerides, and involved in such diseases as atherosclerosis ( 8 ). (frontiersin.org)
  • The present review provides an update on lncRNA-mediated metabolism and highlights the role of lncRNAs in various diseases that involve glucose and lipid metabolism. (frontiersin.org)
  • In higher plants, long-distance RNA transport via the phloem is crucial for communication between distant plant tissues to align development with stress responses and reproduction. (researchgate.net)
  • Harcourt, E. M., Kietrys, A. M. & Kool, E. T. Chemical and structural effects of base modifications in messenger RNA. (nature.com)
  • The 10-nt seed sequence at the 3' end of the guide RNA is critical to target recognition and cleavage. (bvsalud.org)
  • lncRNAs are found in every branch of life, displaying a high degree of tissue- and cell-specific distribution ( 9 ). (frontiersin.org)
  • Lin, C. & Yang, L. Long noncoding RNA in cancer: wiring signaling circuitry. (nature.com)
  • Several recent studies suggest that specific RNAs are among the potential long-distance information transmitters. (researchgate.net)
  • In this work, we investigated the opening and closing process of an RNA base pair under mechanical force with constant-force stretching molecular dynamics simulations. (bvsalud.org)
  • Nop9 recognizes structured and single-stranded RNA elements of pre-ribosomal RNA. (nih.gov)
  • RNA velocity of single cells. (nature.com)
  • Specific scientific projects of interest include the use of clinico-pathological correlations to study mechanisms of pathogenesis in PD or other parkinsonian conditions, characterization of the pathological features of these conditions, and the collection of patient data on their associated symptoms. (nih.gov)