Coding potential of non-polyadenylated messenger RNA in mouse Friend cells.
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Animals↗
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Results for “non coding RNA”
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Bunyavirus nucleoprotein, N, and a non-structural protein, NSS, are coded by overlapping reading frames in the S RNA.
It has been shown previously, by sequence analysis of the S RNA segment of snowshoe hare (SSH) bunyavirus, that two overlapping open reading frames in the viral complementary sequence code for proteins with molecular weights of 26.8 X 10(3) and 10.5 X 10(3) respectively. In addition to the viral nucleocapsid (N) protein, which is coded by the S RNA, analyses of parental and reassortant bunyavirus-infected cell extracts have shown that the viral S RNA and M RNA species each code for non-structural proteins (NSS and NSM, respectively). In the present report, in vitro translation analyses of the S mRNA species recovered from virus-infected cells indicate that a single size class of mRNA directs the synthesis of N and NSS. Compositional analyses of selected tryptic peptides of N and NSS have provided proof that N is the product of the first open reading frame, and NSS the product of the second.
Bunyaviridae↗
Peptide coding capacity of polysomal and non-polysomal messenger RNA during growth of animal cells.
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Cell Line↗
Non-polyadenylated 22 s ribonucleoprotein particle is insensitive to translational inhibitor RNA of cryptobiotic gastrulae of Artemia salina.
A free cytoplasmic 22 S ribonucleoprotein particle exhibiting a major template activity in rabbit reticulocyte system has been identified in the cryptobiotic gastrulae of Artemia salina. This particle contains non-polyadenylated 9 S messenger RNA which codes primarily for a non-histone basic protein with an apparent molecular weight of 26 000 daltons. We have previously demonstrated the presence of a translational inhibitor RNA which is apparently responsible for transforming polyadenylated messenger (Slegers et al., FEBS Letters 80, 390-394, 1977). This inhibitor RNA was found to be completely ineffective on the template activity of non-polyadenylated 22 S messenger ribonucleoprotein, confirming the specificity of this regulatory RNA for polyadenylate sequences.
Animals↗
The organization of macronuclear rDNA molecules of four hypotrichous ciliated protozoans.
We have compared the structure of macronuclear DNA molecules that contain rRNA genes of four hypotricous ciliates, Stylonychia pustulata, Euplotes aediculatus, Oxytricha fallax and Oxytricha nova. The macronuclear rDNA, like all macronuclear DNA in hypotrichs, exists as achromosomal molecules of approximately single-gene size. The rDNA molecules have been cloned intact as recombinant plasmids and analyzed by restriction mapping and Southern hybridization. The sites of restriction enzymes BamHI, EcoRI, HindIII, PstI, PvuII and XhoI have similar but not identical patterns in Stylonychia and the two Oxytricha rDNAs. The restriction pattern of Euplotes rDNA is unlike those of the other three, with only one site of seventeen in the same position. Despite this divergence in nucleotide sequence, the overall structure of the rDNA molecules in the four hypotrichs is constant. The size of all the rDNA molecules is the same, 7.49 kb. Also, the positions of the regions coding for 19S and 25S rRNA are alike. The 25S coding region is at the 5' end of the DNA template strand (3' end of the RNA transcript), within 500 base pairs of the terminus of the DNA molecule. The 19S coding region is adjacent to the 25S region with less than 500 base pairs of spacer lying between the two genes. The largest non-coding sequence is at the 3' end of the DNA molecule adjoining the 19S RNA gene. The 3' non-coding regions show greater sequence divergence among the different rDNAs than do the coding regions. The similarity in size and organization of these molecules and the variability in the restriction patterns suggest that the gene structure is under tighter evolutionary constraint than is the primary nucleotide sequence.
Animals↗
Correction: Differential roles of coding and non-coding transcripts in obesity: insights from RNA-seq analysis of Macaca fascicularis hepatocytes.
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Published Erratum↗
Chicken lens delta-crystallin gene expression and methylation in several non-lens tissues.
RNA sequences coding for the most abundant chicken lens proteins, delta-crystallin, were detected at very low levels in day old post hatch chick lung, heart, kidney and liver, and in 6 day embryo headless bodies. The pattern of cytosine methylation within the CCGG sequences of the delta-crystallin genes was also examined and shown to vary in several non-lens tissues, from several stages of development. Embryonic neural retina, which expresses a higher level of delta-crystallin RNA than the above tissues, is no less methylated in the sites studied than the tissues which have no association with the eye, and is actually more heavily methylated than the kidney. Thus no obvious correlation was found between undermethylation and gene expression.
Animals↗
Functional properties of strychnine-sensitive glycine receptors expressed in Xenopus oocytes injected with a single mRNA.
Mature rat spinal cord cDNA libraries constructed in lambda gt10 and lambda ZAPII were screened with an oligonucleotide probe (39 mer), and 4 clones that possess DNA-inserts encoding a glycine receptor subunit were obtained. The cloned cDNAs were used to reconstruct the nucleotide sequence of the full-length open reading frame consisting of 1350 base pairs (bp) as well as the 5'-(184 bp) and 3'-(591 bp) non-coding regions. Synthetic RNA transcribed in vitro from the glycine receptor cDNA induced Xenopus oocytes to synthesize functional glycine receptor that generated large Cl- currents. The electrophysiological properties of the wild-type receptor and some mutant receptors produced by site-directed mutagenesis were analyzed.
Acetylcholine↗
Abbreviated 3' non-coding region in duck alpha D globin messenger RNA defines evolutionarily conserved sequences.
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Animals↗
Nucleotide sequence of a cloned cDNA copy of TMV (cowpea strain) RNA, including the assembly origin, the coat protein cistron, and the 3' non-coding region.
The cloned cDNA derived from the 3' end of cowpea strain (Cc) RNA of tobacco mosaic virus (TMV) has been sequenced. Substantial sequence information of 1,060 nucleotides from the 3' end of the RNA reveals some interesting features: (1) the coat protein cistron corresponds to residues 210-701 from the 3' end. Some errors in the amino acid sequence previously reported have been corrected and the revised total length of the coat protein is 162 amino acid residues. The capping site of the coat protein mRNA is at residue 711 from the 3' end of genome RNA. (2) The assembly origin of reconstitution is positioned within the coat protein cistron at residue 369-461 which can be formed into a highly base-paired hairpin loop structure. The sequence, GAXGUUG, in the loop region and a triplet-repeated purine base tract surrounding the loop are found. These structural features are common to assembly origins of both Cc and vulgare strains. (3) We find the sequence highly homologous to, but distinct from, the genuine assembly origin. It will be called the pseudo-assembly origin, which is located in the corresponding region to the assembly origin of the vulgare strain, outside the coat protein cistron. There is also the sequence, GAXGUUG, in the middle of the region. (4) In the 5' flanking region of the coat protein cistron, a long reading frame, probably of 30 K protein, is found. The coding region is terminated in the coat protein cistron and thus the 30 K protein and the coat protein cistrons overlap. (5) The 3' non-coding region is 209 residues long and can be folded into a possible tRNA-like structure. Surprisingly, we find that the 3' terminal sequence of Cc RNA is not very similar to that of vulgare RNA but extensively homologous to that of turnip yellow mosaic virus (TYMV) RNA.
Amino Acid Sequence↗
ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription.
The regulation of transcription by RNA polymerase II (RNAPII) underpins all cellular processes and is perturbed in thousands of diseases. In humans, RNAPII transcribes ∼20000 protein-coding genes and engages in apparently futile non-coding transcription at thousands of other sites. Despite being so ubiquitous, this transcription is usually attenuated soon after initiation and the resulting products are immediately degraded by the nuclear exosome. We and others have recently described a new complex, "Restrictor", which appears to control such unproductive transcription. Underpinned by the RNA binding protein, ZC3H4, Restrictor curtails unproductive/pervasive transcription genome-wide. Here, we discuss these recent discoveries and speculate on some of the many unknowns regarding Restrictor function and mechanism.
Humans↗
Epigenetic alterations induced by ionizing radiation: pathways to cancer and prognostic strategies.
PURPOSE: Ionizing radiation (IR) is widely used not only in cancer diagnosis and therapy, but its biological effects also extend beyond radiation-induced lethal lesions, e.g., specifically DNA double-strand breaks (DNA-DSBs). This review aims to summarize current evidence on IR-induced epigenetic alterations and to integrate mechanistic insights from radiation chemistry and radiation biology that link DNA damage to long-term epigenetic dysregulation. RESULTS: Experimental and clinical studies collectively show that IR induces persistent epigenetic reprogramming, including global and gene-specific DNA methylation changes, radiation-responsive histone modifications, chromatin remodeling, and dysregulation of non-coding RNAs. Aberrant RNA methylation, including modifications like N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanine (m7G), and N3-methylcytosine (m3C), is closely linked to tumorigenesis and progression. Due to its tumor-specific properties, RNA methylation markers, specifically m6A, m5C, m1A, m7G, and m3C, emerge as valuable markers in liquid biopsy. Radiation chemistry studies indicate that epigenetically modified bases, for example, m5C, are preferential targets of radiation-induced oxidative damage, thereby promoting mutational hotspots and genomic instability. By altering DNA repair, apoptosis, immune responses, and cellular differentiation, these epigenetic changes promote carcinogenesis, radioresistance, and tissue toxicity. CONCLUSION: IR-induced epigenetic alterations represent a critical interface between initial DNA damage and long-term biological outcomes. Improved understanding of radiation-associated epigenetic signatures may enhance risk assessment, inform prognostic stratification, and support the development of epigenetic-targeted strategies to optimize radiotherapy and reduce adverse effects.
Ionizing radiation↗
Chromatin structure along the ribosomal DNA of Dictyostelium. Regional differences and changes accompanying cell differentiation.
The ribosomal genes of Dictyostelium discoideum are extrachromosomal palindromic DNA molecules situated in the nucleolus. Each molecule comprises ribosomal RNA coding regions and non-transcribed spacer regions. We used both biochemical and electron microscopic approaches to investigate the structure of transcribing and non-transcribing chromatin. Nucleoli from exponentially growing cells were digested with micrococcal nuclease, and the resulting DNA fragments were separated by gel electrophoresis and transferred to DBM paper. They were hybridized with cloned EcoRI fragments derived from different parts of the ribosomal gene. Probes of the coding region showed a smear, while probes of the non-transcribed regions gave pronounced banding patterns more complex than typical nucleosome repeats, but not due solely to sequence-specific cutting by micrococcal nuclease. The DNA of the coding region was digested more quickly than that of the non-transcribed ones. When nucleoli were digested with restriction enzymes, sites within the coding region were accessible and sites in the non-transcribed region were protected. The structure of ribosomal chromatin in differentiating cells, in which the rate of ribosomal RNA synthesis is reduced, was examined using essentially the same methods. The coding region, probed by hybridization to micrococcal digests, then showed a typical DNA repeat pattern indicating that this region had become condensed into nucleosomes, and its accessibility to restriction enzymes was very much reduced. On electron micrographs of lysed nucleoli from exponentially growing cells, two types of chromatin were observed, one with a beaded nucleosomal appearance, the other with putative RNA polymerase molecules attached to fibres indistinguishable from free DNA adsorbed to the same grid. The combined results suggest that whereas regions that are not transcribed are packaged with proteins that protect them from nuclease digestion, actively transcribing ribosomal genes are associated with few macromolecular constituents apart from those required for transcription and its regulation.
Cell Nucleolus↗
An unusually long non-coding region in rat lens alpha-crystallin messenger RNA.
Most of the mRNA sequence coding for the alpha A2 chain of the ocular lens protein alpha-crystallin from rat, has been determined by sequencing cloned DNA copies of this mRNA. The 892-base pair cDNA sequence encompasses all but 52 N-terminal amino acids of the alpha A2 chain. It lacks the sequence characteristic for the 22 extra amino acids inserted in the alpha A2 -like chain, named alpha AIns. A stretch of 583 nuceotides, representing more than 50% of the entire mRNA sequence, is located 3' wards of the alpha A2 coding sequence. It contains the characteristic AAUAAA signal involved in poly(A) -addition and represents an unexpectedly long non-coding region. Examination of the total cytoplasmic poly(A) RNA of rat lens by filter-hybridization and subsequent translation of the electrophoretically separated mRNA fractions shows that the alpha A2 chain is encoded by mRNA species which are distinct from the alpha AIns encoding mRNA. No evidence is obtained for an extensive size heterogeneity in the 3' untranslated regions of these two different rat lens mRNAs.
Animals↗
In vitro synthesis of the gene coding for the glycoprotein E1 of Sindbis virus.
Ds cDNA of the 42S virionic RNA of Sindbis Virus has been synthesized and cloned in the plasmid pBR 322. Restriction map analysis and hybridization studies show that two clones cover the 3' end non coding region of the RNA, the whole membrane glycoprotein E1 and a peptide of MW 6,000 daltons. The use of these clones in experiments of gene expression in mammalian cell is discussed.
Base Sequence↗
Nucleotide sequence of the 3' non-coding region and N gene of the S RNA of a serologically distinct tospovirus.
A tomato spotted wilt-like virus (TSWV-I) is a distinct member of the Tospovirus genus of the Bunyaviridae and is distinguished from the typical TSWV by having a serologically distinct nucleoprotein (N). A cDNA clone extending from the 3' terminus of the viral RNA through the entire N open reading frame (ORF) was sequenced. The TSWV-I N ORF is capable of encoding a polypeptide of 262 amino acids with a predicted Mr of 28.8K. In vitro transcription and translation of the clone produced a protein which comigrated with TSWV-I N and was immunoprecipitated by TSWV-I antibodies. Hybridization analysis of lithium chloride-precipitated RNA from healthy and TSWV-I-infected tissue detected a virus-specific 1.2 kb subgenomic RNA. The TSWV-I S RNA terminal consensus sequence (8 nucleotides) was identical to that of TSWV; the remaining TSWV-I untranslated region showed only 51% identity with that of TSWV. Comparison of the TSWV-I and TSWV N proteins showed 67% identity at the amino acid level. The degree of similarity in the terminal sequence, untranslated region and N ORF is similar to that expected between distinct serogroups within certain genera of the Bunyaviridae.
Amino Acid Sequence↗
Nucleotide sequence of tomato ringspot virus RNA-2.
The sequence of tomato ringspot virus (TomRSV) RNA-2 has been determined. It is 7273 nucleotides in length excluding the 3' poly(A) tail and contains a single long open reading frame (ORF) of 5646 nucleotides in the positive sense beginning at position 78 and terminating at position 5723. A second in-frame AUG at position 441 is in a more favourable context for initiation of translation and may act as a site for initiation of translation. The TomRSV RNA-2 3' noncoding region is 1550 nucleotides in length. The coat protein is located in the C-terminal region of the large polypeptide and shows significant but limited amino acid sequence similarity to the putative coat proteins of the nepoviruses tomato black ring (TBRV), Hungarian grapevine chrome mosaic (GCMV) and grapevine fanleaf (GFLV). Comparisons of the coding and non-coding regions of TomRSV RNA-2 and the RNA components of TBRV, GCMV, GFLV and the comovirus cowpea mosaic virus revealed significant similarity for over 300 amino acids between the coding region immediately to the N-terminal side of the putative coat proteins of TomRSV and GFLV; very little similarity could be detected among the non-coding regions of TomRSV and any of these viruses.
Amino Acid Sequence↗
Nucleotide sequence of tomato aspermy virus RNA 2.
RNA 2 of the V strain of tomato aspermy virus (TAV) consists of 3074 nucleotides and contains one open reading frame of 2487 nucleotides. Thus, it resembles RNA 2 of cucumber mosaic virus (CMV) strains Q and Fny (62% identical to both), brome mosaic virus (42% identical) and cowpea chlorotic mottle virus (40% identical). In comparisons between amino acid sequences, three different regions of similarity could be distinguished. These were the central part (amino acids 224 to 757 for V-TAV), which was most similar among the four viruses, and the N and C ends; sequences conserved among RNA polymerase species were found in the C half of the central part. Hydrophobicity patterns, and distributions of acidic and basic amino acids in the proteins encoded by V-TAV RNA 2, Q-CMV RNA 2 and Fny-CMV RNA 2 were very similar except at the extreme ends of the molecules. Structures that have been reported to act as regulatory signals for minus- and plus-strand synthesis were found in the 5' and 3' non-coding regions of the RNA.
Amino Acid Sequence↗