Journal articles: 'RNA Sequence Analysis'

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Tessier, Laurence, Olivier Côté, and Dorothee Bienzle. "Sequence variant analysis of RNA sequences in severe equine asthma." PeerJ 6 (October 11, 2018): e5759. http://dx.doi.org/10.7717/peerj.5759.

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Background Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant from Tolerant software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping 2 and screening for non-acceptable polymorphism 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson’s Chi-squared test with Yates’ continuity correction, and difference in genotype frequency was calculated using the Fisher’s exact test for count data. Results RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10–20 counts per million) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.

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Eddy, Sean R., and Richard Durbin. "RNA sequence analysis using covariance models." Nucleic Acids Research 22, no. 11 (1994): 2079–88. http://dx.doi.org/10.1093/nar/22.11.2079.

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Zhang, Jianping, Shaolei Teng, Cuncong Zhong, Bo Wang, and Jie Wu. "Current Developments in RNA Sequence Analysis." Bioinformatics and Biology Insights 9s1 (January 2015): BBI.S39980. http://dx.doi.org/10.4137/bbi.s39980.

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Györgyey, János, Danièle Vaubert, José I. Jiménez-Zurdo, Celine Charon, Liliane Troussard, Ádám Kondorosi, and Éva Kondorosi. "Analysis of Medicago truncatula Nodule Expressed Sequence Tags." Molecular Plant-Microbe Interactions® 13, no. 1 (January 2000): 62–71. http://dx.doi.org/10.1094/mpmi.2000.13.1.62.

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Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two hundred fifty-six ESTs exhibited significant similarities to characterized data base entries and 40 of them represented 26 nodulin genes, while 133 had no similarity to sequences with known function. Only 60 out of the 389 cDNA clones corresponded to previously submitted M. truncatula EST sequences. For 117 cDNAs, reverse Northern (RNA) hybridization with root and nodule RNA probes revealed enhanced expression in the nodule, 48 clones are likely to code for novel nodulins, 33 cDNAs are clones of already known nodulin genes, and 36 clones exhibit similarity to other characterized genes. Thus, systematic analysis of the EST sequences and their expression patterns is a powerful way to identify nodule-specific and nodulation-related genes.

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Hanif, Waqar, Hijab Fatima, Muhammad Qasim, Rana Muhammad Atif, and Muhammad Rizwan Javed. "SeqDown: An Efficient Sequence Retrieval Software and Comparative Sequence Retrieval Analysis." Current Trends in OMICS 1, no. 1 (August 2, 2021): 18–29. http://dx.doi.org/10.32350/cto.11.03.

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For any sequence analysis procedure, a single or multiple sequence must be retrieved, stored, organized. One of the most common public databases used for biological sequence retrieval is GenBank which is a comprehensive public database of nucleotide sequences. However, as the length of the sequence to be retrieved increases such as a chromosome, entire genome, scaffold, etc., the elapsed time to download the file gets even elongated due to slower bandwidth to download/retrieve the sequence.[8] In most cases, during sequence analysis, the researcher requires messenger RNA (mRNA), RNA, DNA, protein sequences of the same sequence-of-interest to work with, which consumes a substantial amount of the researcher in finding and retrieving the sequence files. An access to GenBank through JAVA HTTPS protocols is established to request and receive the sequence files associated with the input accessions. SeqDown was shown to be much efficient in terms of retrieval time of the sequences as compared to the other internet browsers and was found to be 15.27% faster than Mozilla Firefox. SeqDown also provides the feature to retrieve coding DNA sequences & protein sequences present in a single chromosome. Sequence retrieval from the most biological databases don’t have proper naming of their files and the user has to deal with the redundantly named sequence files which leads to incorrect and time-consuming analysis and can be solved with SeqDown. SeqDown is available as a free-to-download software at https://bit.ly/3cUwchz

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Matoušek, J. "Viroids: sequence variability and evolution of pathogenic RNA." Plant Protection Science 38, SI 1 - 6th Conf EFPP 2002 (January 1, 2002): 173–76. http://dx.doi.org/10.17221/10348-pps.

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Viroids as the smallest pathogenic circular single-stranded pathogenic RNAs form populations of quasi-species, which has been recently identified by thermodynamic methods like TGGE pre-selection and heteroduplex analysis. It was found that replication under thermal stress led to enormously high level of viroid mutagenesis. Mostly multiple mutants having non-random distribution of base changes were found. A specific “hot spots” were identified in the regions, where a characteristic “pathogenicity domains” are localised in different viroids of the pospiviroidae family. Specific viroid microevolution was observed upon artificial inoculation of non-host plant species. Our results suggest that viroid propagation under physiological stress can be assumed as important factor, which is among others, responsible for an appearance of viroid quasi-species in the nature. Evolution and new viroid patotypes could accumulate due to environmental stress including various pollutants may be a potential danger for cultured plants.

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Klein, Ashwil, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, and David L. Tabb. "Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies." Plants 10, no. 4 (April 14, 2021): 765. http://dx.doi.org/10.3390/plants10040765.

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While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity “genes” varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.

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Evans, Donald, and Thomas Blumenthal. "trans Splicing of PolycistronicCaenorhabditis elegans Pre-mRNAs: Analysis of the SL2 RNA." Molecular and Cellular Biology 20, no. 18 (September 15, 2000): 6659–67. http://dx.doi.org/10.1128/mcb.20.18.6659-6667.2000.

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ABSTRACT Genes in Caenorhabditis elegans operons are transcribed as polycistronic pre-mRNAs in which downstream gene products aretrans spliced to a specialized spliced leader, SL2. SL2 is donated by a 110-nucleotide RNA, SL2 RNA, present in the cell as an Sm-bound snRNP. SL2 RNA can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. Here we report an in vivo mutational analysis of the SL2 RNA. Some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. Interestingly, the spliced leader itself can be dramatically altered, such that the first stem-loop cannot form, with only a relatively small loss intrans-splicing efficiency. However, the primary sequence of stem II is crucial for SL2 trans splicing. Similarly, the conserved primary sequence of the third stem-loop plays a key role intrans splicing. While mutations in stem-loop III allow snRNP formation, a single nucleotide substitution in the loop preventstrans splicing. In contrast, the analogous region of SL1 RNA is not highly conserved, and its mutation does not abrogate function. Thus, stem-loop III appears to confer a specific function to SL2 RNA. Finally, an upstream sequence, previously predicted to be a proximal sequence element, is shown to be required for SL2 RNA expression.

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Toung, J. M., M. Morley, M. Li, and V. G. Cheung. "RNA-sequence analysis of human B-cells." Genome Research 21, no. 6 (May 2, 2011): 991–98. http://dx.doi.org/10.1101/gr.116335.110.

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Cook, Jonathan P., and Malcolm A. McCrae. "Sequence analysis of the guanylyltransferase (VP3) of group A rotaviruses." Journal of General Virology 85, no. 4 (April 1, 2004): 929–32. http://dx.doi.org/10.1099/vir.0.19629-0.

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The RNA segment encoding the guanylyltransferase (VP3) from 12 group A rotavirus isolates has been sequenced following RT-PCR and molecular cloning of the full-length amplicons produced. Alignment of the derived amino acid sequences including those of the four VP3 sequences available from GenBank revealed two levels of sequence divergence. Virus isolates from humans showed greater than 94 % sequence identity, whereas those isolated from different mammalian species showed as low as 79 % sequence identity. The exceptions were avian virus isolates, which diverged ∼45 % from those of mammalian origin, and the human virus isolates DS1 and 69M, which showed much closer (over 90 %) identity to viruses of bovine origin, suggesting that these human isolates may have undergone recent reassortment events with a bovine virus. Analysis of the sequences for a putative enzymic active site has revealed that the KXTAMDXEXP and KXXGNNH motifs around amino acids 385 and 545, respectively, are conserved across both group A and C rotaviruses.

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Izmailova, Elena, and Anna Aldovini. "Functional Analysis of the Murine Sarcoma Virus RNA Packaging Sequence." Journal of Virology 76, no. 9 (May 1, 2002): 4643–48. http://dx.doi.org/10.1128/jvi.76.9.4643-4648.2002.

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ABSTRACT We investigated the features of the Moloney murine sarcoma virus leader sequence necessary for RNA packaging function by using a deletion analysis approach. We found that sequences that extend beyond those characterized genetically in previous reports are important for optimal packaging efficiency. A fragment covering a minimum of four potential stem-loop structures is required for the shortest packaging element compatible with gene transfer. Our results reveal the extent to which each of the segments of the packaging sequence contribute to packaging efficiency.

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Schnattinger, T., U. Schoning, A. Marchfelder, and H. A. Kestler. "RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments." Bioinformatics 29, no. 23 (September 16, 2013): 3102–4. http://dx.doi.org/10.1093/bioinformatics/btt536.

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Black, D. L., and A. L. Pinto. "U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6." Molecular and Cellular Biology 9, no. 8 (August 1989): 3350–59. http://dx.doi.org/10.1128/mcb.9.8.3350-3359.1989.

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To understand how the U5 small nuclear ribonucleoprotein (snRNP) interacts with other spliceosome components, its structure and binding to the U4/U6 snRNP were analyzed. The interaction of the U5 snRNP with the U4/U6 snRNP was studied by separating the snRNPs in HeLa cell nuclear extracts on glycerol gradients. A complex running at 25S and containing U4, U5, and U6 but not U1 or U2 snRNAs was identified. In contrast to results with native gel electrophoresis to separate snRNPs, this U4/U5/U6 snRNP complex requires ATP to assemble from the individual snRNPs. The structure of the U5 RNA within the U5 snRNP and the U4/5/6 snRNP complexes was then compared. Oligonucleotide-targeted RNase H digestion identified one RNA sequence in the U5 snRNP capable of base pairing to other nucleic acid sequences. Chemical modification experiments identified this sequence as well as two other U5 RNA sequences as accessible to modification within the U5 RNP. One of these regions is a large loop in the U5 RNA secondary structure whose sequence is conserved from Saccharomyces cerevisiae to humans. Interestingly, no differences in modification of free U5 snRNP as compared to U5 in the U4/U5/U6 snRNP complex were observed, suggesting that recognition of specific RNA sequences in the U5 snRNP is not required for U4/U5/U6 snRNP assembly.

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Black, D. L., and A. L. Pinto. "U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6." Molecular and Cellular Biology 9, no. 8 (August 1989): 3350–59. http://dx.doi.org/10.1128/mcb.9.8.3350.

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To understand how the U5 small nuclear ribonucleoprotein (snRNP) interacts with other spliceosome components, its structure and binding to the U4/U6 snRNP were analyzed. The interaction of the U5 snRNP with the U4/U6 snRNP was studied by separating the snRNPs in HeLa cell nuclear extracts on glycerol gradients. A complex running at 25S and containing U4, U5, and U6 but not U1 or U2 snRNAs was identified. In contrast to results with native gel electrophoresis to separate snRNPs, this U4/U5/U6 snRNP complex requires ATP to assemble from the individual snRNPs. The structure of the U5 RNA within the U5 snRNP and the U4/5/6 snRNP complexes was then compared. Oligonucleotide-targeted RNase H digestion identified one RNA sequence in the U5 snRNP capable of base pairing to other nucleic acid sequences. Chemical modification experiments identified this sequence as well as two other U5 RNA sequences as accessible to modification within the U5 RNP. One of these regions is a large loop in the U5 RNA secondary structure whose sequence is conserved from Saccharomyces cerevisiae to humans. Interestingly, no differences in modification of free U5 snRNP as compared to U5 in the U4/U5/U6 snRNP complex were observed, suggesting that recognition of specific RNA sequences in the U5 snRNP is not required for U4/U5/U6 snRNP assembly.

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Kumari, Uma, Monu Malik, and Devendra Kumar. "Computational Analysis of SARS-CoV-2 Genome Representing Intraspecific Variability." International Journal for Research in Applied Science and Engineering Technology 11, no. 5 (May 31, 2023): 347–52. http://dx.doi.org/10.22214/ijraset.2023.51486.

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Abstract: The US National Institutes of Health, it is the successor to SARS-CoV-1, which was the virus that causedSARS outbreak in 2002-2004. SARS-CoV-2 is a virus of the species severe acute respiratory syndrome–related coronavirus (SARSCoV-2) Genomic analysis of 566SARS CoV2 virus populations to identify mutations as substitutions, deletions, insertions,and single nucleotide polymorphisms(SNPs).Clustal,ClustalOmega and MAFFT in order to align the Indian 566 SARS-CoV-2 sequences. SARS-CoV-2 is an enveloped virus consisting of a positive sense, single-stranded RNA genome of approximately 30 kb. There will be 3 possible reading frames in each direction of the RNA. So total 6 possible reading frame or (6 horizontal bars) would be there for every RNA sequence. +1, +2, +3 and -1, -2 and -3 ( in the reverse strand) are the 6 possible reading frames. The graphical abstract of the human coronavirus NL 63 genome of BLAST is represented by a red bar, which shows the most similar sequences. Bit score is anotherbiostatistical indicator used in addition to the e-value in a blast output and where comparing the sequence similarities search i.e. pairwise multiple sequence alignment shows a way of arranging protein or DNA sequence to identify region or similarity in clustal omega

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Aarons, Simon, Abdelhamid Abbas, Claire Adams, Anne Fenton, and Fergal O'Gara. "A Regulatory RNA (PrrB RNA) Modulates Expression of Secondary Metabolite Genes in Pseudomonas fluorescensF113." Journal of Bacteriology 182, no. 14 (July 15, 2000): 3913–19. http://dx.doi.org/10.1128/jb.182.14.3913-3919.2000.

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ABSTRACT The GacS-GacA two-component signal transduction system, which is highly conserved in gram-negative bacteria, is required for the production of exoenzymes and secondary metabolites inPseudomonas spp. Screening of a Pseudomonas fluorescens F113 gene bank led to the isolation of a previously undefined locus which could restore secondary metabolite production to both gacS and gacA mutants of F113. Sequence analysis of this locus demonstrated that it did not contain any obviousPseudomonas protein-coding open reading frames or homologues within available databases. Northern analysis indicated that the locus encodes an RNA (PrrB RNA) which is able to phenotypically complement gacS and gacA mutants and is itself regulated by the GacS-GacA two-component signal transduction system. Primer extension analysis of the 132-base transcript identified the transcription start site located downstream of a ς70promoter sequence from positions −10 to −35. Inactivation of theprrB gene in F113 resulted in a significant reduction of 2,4-diacetylphloroglucinol (Phl) and hydrogen cyanide (HCN) production, while increased metabolite production was observed whenprrB was overexpressed. The prrB gene sequence contains a number of imperfect repeats of the consensus sequence 5′-AGGA-3′, and sequence analysis predicted a complex secondary structure featuring multiple putative stem-loops with the consensus sequences predominantly positioned at the single-stranded regions at the ends of the stem-loops. This structure is similar to the CsrB and RsmB regulatory RNAs in Escherichia coli and Erwinia carotovora, respectively. Results suggest that a regulatory RNA molecule is involved in GacA-GacS-mediated regulation of Phl and HCN production in P. fluorescens F113.

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Martignetti, J. A., and J. Brosius. "BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript." Molecular and Cellular Biology 15, no. 3 (March 1995): 1642–50. http://dx.doi.org/10.1128/mcb.15.3.1642.

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Rodent BC1 RNA represents the first example of a neural cell-specific RNA polymerase III (Pol III) transcription product. By developing a rat brain in vitro system capable of supporting Pol III-directed transcription, we showed that the rat BC1 RNA intragenic promoter elements, comprising an A box element and a variant B box element, as well as its upstream region, containing octamer-binding consensus sequences and functional TATA and proximal sequence element sites, are necessary for transcription. The BC1 B box, lacking the invariant A residue found in the consensus B boxes of tRNAs, represents a functionally related and possibly distinct promoter element. The transcriptional activity of the BC1 B box element is greatly increased, in both a BC1 RNA and a chimeric tRNA(Leu) gene construct, when the BC1 5' flanking region is present and is appropriately spaced. Moreover, a tRNA consensus B-box sequence can efficiently replace the BC1 B box only if the BC1 upstream region is removed. These interactions, identified only in a homologous in vitro system, between upstream Pol II and intragenic Pol III promoters suggest a mechanism by which the tissue-specific BC1 RNA gene and possibly other Pol III-transcribed genes can be regulated.

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Xu, Jian, Barbara C. McCabe, and Gerald B. Koudelka. "Function-Based Selection and Characterization of Base-Pair Polymorphisms in a Promoter of Escherichia coli RNA Polymerase-ς70." Journal of Bacteriology 183, no. 9 (May 1, 2001): 2866–73. http://dx.doi.org/10.1128/jb.183.9.2866-2873.2001.

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ABSTRACT We performed two sets of in vitro selections to dissect the role of the −10 base sequence in determining the rate and efficiency with which Escherichia coli RNA polymerase-ς70forms stable complexes with a promoter. We identified sequences that (i) rapidly form heparin-resistant complexes with RNA polymerase or (ii) form heparin-resistant complexes at very low RNA polymerase concentrations. The sequences selected under the two conditions differ from each other and from the consensus −10 sequence. The selected promoters have the expected enhanced binding and kinetic properties and are functionally better than the consensus promoter sequence in directing RNA synthesis in vitro. Detailed analysis of the selected promoter functions shows that each step in this multistep pathway may have different sequence requirements, meaning that the sequence of a strong promoter does not contain the optimal sequence for each step but instead is a compromise sequence that allows all steps to proceed with minimal constraint.

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Bennett, J. L., and D. A. Clayton. "Efficient site-specific cleavage by RNase MRP requires interaction with two evolutionarily conserved mitochondrial RNA sequences." Molecular and Cellular Biology 10, no. 5 (May 1990): 2191–201. http://dx.doi.org/10.1128/mcb.10.5.2191-2201.1990.

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RNase MRP is a site-specific endonuclease that processes primer mitochondrial RNA from the leading-strand origin of mitochondrial DNA replication. Using deletional analysis and saturation mutagenesis, we have determined the substrate requirements for cleavage by mouse mitochondrial RNase MRP. Two regions of sequence homology among vertebrate mitochondrial RNA primers, conserved sequence blocks II and III, were found to be critical for both efficient and accurate cleavage; a third region of sequence homology, conserved sequence block I, was dispensable. Analysis of insertion and deletion mutations within conserved sequence block II demonstrated that the specificity of RNase MRP accommodates the natural sequence heterogeneity of conserved sequence block II in vivo. Heterologous assays with human RNase MRP and mutated mouse mitochondrial RNA substrates indicated that sequences essential for substrate recognition are conserved between mammalian species.

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Bennett, J. L., and D. A. Clayton. "Efficient site-specific cleavage by RNase MRP requires interaction with two evolutionarily conserved mitochondrial RNA sequences." Molecular and Cellular Biology 10, no. 5 (May 1990): 2191–201. http://dx.doi.org/10.1128/mcb.10.5.2191.

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RNase MRP is a site-specific endonuclease that processes primer mitochondrial RNA from the leading-strand origin of mitochondrial DNA replication. Using deletional analysis and saturation mutagenesis, we have determined the substrate requirements for cleavage by mouse mitochondrial RNase MRP. Two regions of sequence homology among vertebrate mitochondrial RNA primers, conserved sequence blocks II and III, were found to be critical for both efficient and accurate cleavage; a third region of sequence homology, conserved sequence block I, was dispensable. Analysis of insertion and deletion mutations within conserved sequence block II demonstrated that the specificity of RNase MRP accommodates the natural sequence heterogeneity of conserved sequence block II in vivo. Heterologous assays with human RNase MRP and mutated mouse mitochondrial RNA substrates indicated that sequences essential for substrate recognition are conserved between mammalian species.

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Yokoi, Kakeru, Takeshi Wakamiya, and Hidemasa Bono. "Meta-Analysis of the Public RNA-SEQ Data of the Western Honeybee Apis Mellifera to Construct Reference Transcriptome Data." Insects 13, no. 10 (October 14, 2022): 931. http://dx.doi.org/10.3390/insects13100931.

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The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. Approximately 50–60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune-response-related RNA-Seq and reference transcriptome data. Three to twenty candidate transcripts including autophagy-related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera.

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Brock, J. E., R. C. Dietrich, and R. A. Padgett. "Mutational analysis of the U12-dependent branch site consensus sequence." RNA 14, no. 11 (September 16, 2008): 2430–39. http://dx.doi.org/10.1261/rna.1189008.

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Xu, Zhongneng, and Shuichi Asakawa. "Physiological RNA dynamics in RNA-Seq analysis." Briefings in Bioinformatics 20, no. 5 (June 29, 2018): 1725–33. http://dx.doi.org/10.1093/bib/bby045.

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Abstract Physiological RNA dynamics cause problems in transcriptome analysis. Physiological RNA accumulation affects the analysis of RNA quantification, and physiological RNA degradation affects the analysis of the RNA sequence length, feature site and quantification. In the present article, we review the effects of physiological degradation and accumulation of RNA on analysing RNA sequencing data. Physiological RNA accumulation and degradation probably led to such phenomena as incorrect estimations of transcription quantification, differential expressions, co-expressions, RNA decay rates, alternative splicing, boundaries of transcription, novel genes, new single-nucleotide polymorphisms, small RNAs and gene fusion. Thus, the transcriptomic data obtained up to date warrant further scrutiny. New and improved techniques and bioinformatics software are needed to produce accurate data in transcriptome research.

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Valiunas, Deividas, Rasa Jomantiene, and Robert Edward Davis. "Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny." International Journal of Systematic and Evolutionary Microbiology 63, Pt_10 (October 1, 2013): 3904–14. http://dx.doi.org/10.1099/ijs.0.051912-0.

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Phytoplasmas are classified into 16Sr groups and subgroups and ‘Candidatus Phytoplasma ’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘Ca. Phytoplasma ’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene (rpoB) exists as a single copy in the phytoplasma genome, we explored the use of rpoB for phytoplasma classification and phylogenetic analysis. We sequenced a clover phyllody (CPh) phytoplasma genetic locus containing ribosomal protein genes, a complete rpoB gene and a partial rpoC gene encoding the β′-subunit of DpRp. Primers and reaction conditions were designed for PCR-mediated amplification of rpoB gene fragments from diverse phytoplasmas. The rpoB gene sequences from phytoplasmas classified in groups 16SrI, 16SrII, 16SrIII, 16SrX and 16SrXII were subjected to sequence similarity and phylogenetic analyses. The rpoB gene sequences were more variable than 16S rRNA gene sequences, more clearly distinguishing among phytoplasma lineages. Phylogenetic trees based on 16S rRNA and rpoB gene sequences had similar topologies, and branch lengths in the rpoB tree facilitated distinctions among closely related phytoplasmas. Virtual RFLP analysis of rpoB gene sequences also improved distinctions among closely related lineages. The results indicate that the rpoB gene provides a useful additional marker for phytoplasma classification that should facilitate studies of disease aetiology and epidemiology.

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Wilkinson, David A., Léa Joffrin, Camille Lebarbenchon, and Patrick Mavingui. "Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses." Journal of General Virology 101, no. 12 (December 1, 2020): 1261–69. http://dx.doi.org/10.1099/jgv.0.001494.

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The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.

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Vieth, Simon, Andrew E. Torda, Marcel Asper, Herbert Schmitz, and Stephan Günther. "Sequence analysis of L RNA of Lassa virus." Virology 318, no. 1 (January 2004): 153–68. http://dx.doi.org/10.1016/j.virol.2003.09.009.

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Rubino, L., M. Russo, and G. P. Martelli. "Sequence analysis of pothos latent virus genomic RNA." Journal of General Virology 76, no. 11 (November 1, 1995): 2835–39. http://dx.doi.org/10.1099/0022-1317-76-11-2835.

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Lane, William J., and Seth A. Darst. "Molecular Evolution of Multisubunit RNA Polymerases: Sequence Analysis." Journal of Molecular Biology 395, no. 4 (January 2010): 671–85. http://dx.doi.org/10.1016/j.jmb.2009.10.062.

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Walia, Jeewan Jyot, Nida M. Salem, and Bryce W. Falk. "Partial Sequence and Survey Analysis Identify a Multipartite, Negative-Sense RNA Virus Associated with Fig Mosaic." Plant Disease 93, no. 1 (January 2009): 4–10. http://dx.doi.org/10.1094/pdis-93-1-0004.

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RNA and nucleotide sequence-based analyses were used to identify viruses in fig mosaic (FM)-affected fig (Ficus carica) trees. Nucleotide sequence analyses of 267 cloned cDNAs identified sequences corresponding to four viruses representing four distinct taxa from fig trees in California. Virus sequences corresponding to members of the family Closteroviridae were most common (55 sequences). We also found two sequences for an Umbravirus, one sequence corresponding to a Luteovirus-associated RNA, and two sequences that showed homology to European mountain ash ringspot-associated virus (EMARAV). Reverse transcription–polymerase chain reaction (RT-PCR) and northern hybridization analyses were used to confirm the presence of specific virus RNAs in fig trees. A survey of 184 fig trees from a germplasm collection, a commercial orchard, backyards, and feral fig trees showed that one virus was most common (detected in 96% of tested samples), while none of the other virus sequences were detected in more than 36% of the fig trees. Based on its association with FM-affected trees, nucleotide sequence-based phylogenetic association, and previous reported properties, we suggest the name of this virus as Fig mosaic-associated virus (FMaV).

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Roca-Martínez, Joel, Hrishikesh Dhondge, Michael Sattler, and Wim F. Vranken. "Deciphering the RRM-RNA recognition code: A computational analysis." PLOS Computational Biology 19, no. 1 (January 23, 2023): e1010859. http://dx.doi.org/10.1371/journal.pcbi.1010859.

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RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eukaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recognition code has remained elusive. An increasing number of experimental structures of RRM-RNA complexes has become available in recent years. Here, we perform an in-depth computational analysis to derive an RNA recognition code for canonical RRMs. We present and validate a computational scoring method to estimate the binding between an RRM and a single stranded RNA, based on structural data from a carefully curated multiple sequence alignment, which can predict RRM binding RNA sequence motifs based on the RRM protein sequence. Given the importance and prevalence of RRMs in humans and other species, this tool could help design RNA binding motifs with uses in medical or synthetic biology applications, leading towards the de novo design of RRMs with specific RNA recognition.

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Risager, Peter Christian, Ulrik Fahnøe, Maria Gullberg, Thomas Bruun Rasmussen, and Graham J. Belsham. "Analysis of classical swine fever virus RNA replication determinants using replicons." Journal of General Virology 94, no. 8 (August 1, 2013): 1739–48. http://dx.doi.org/10.1099/vir.0.052688-0.

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Self-replicating RNAs (replicons), with or without reporter gene sequences, derived from the genome of the Paderborn strain of classical swine fever virus (CSFV) have been produced. The full-length viral cDNA, propagated within a bacterial artificial chromosome, was modified by targeted recombination within Escherichia coli. RNA transcripts were produced in vitro and introduced into cells by electroporation. The translation and replication of the replicon RNAs could be followed by the accumulation of luciferase (from Renilla reniformis or Gaussia princeps) protein expression (where appropriate), as well as by detection of CSFV NS3 protein production within the cells. Inclusion of the viral E2 coding region within the replicon was advantageous for replication efficiency. Production of chimeric RNAs, substituting the NS2 and NS3 coding regions (as a unit) from the Paderborn strain with the equivalent sequences from the highly virulent Koslov strain or the vaccine strain Riems, blocked replication. However, replacing the Paderborn NS5B coding sequence with the RNA polymerase coding sequence from the Koslov strain greatly enhanced expression of the reporter protein from the replicon. In contrast, replacement with the Riems NS5B sequence significantly impaired replication efficiency. Thus, these replicons provide a system for determining specific regions of the CSFV genome required for genome replication without the constraints of maintaining infectivity.

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Kim, Bum-Joon, Seung-Hyun Lee, Mi-Ae Lyu, Seo-Jeong Kim, Gill-Han Bai, Sang-Jae Kim, Gue-Tae Chae, Eui-Chong Kim, Chang-Yong Cha, and Yoon-Hoh Kook. "Identification of Mycobacterial Species by Comparative Sequence Analysis of the RNA Polymerase Gene (rpoB)." Journal of Clinical Microbiology 37, no. 6 (1999): 1714–20. http://dx.doi.org/10.1128/jcm.37.6.1714-1720.1999.

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For the differentiation and identification of mycobacterial species, the rpoB gene, encoding the β subunit of RNA polymerase, was investigated. rpoB DNAs (342 bp) were amplified from 44 reference strains of mycobacteria and clinical isolates (107 strains) by PCR. The nucleotide sequences were directly determined (306 bp) and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Comparative sequence analysis of rpoB DNAs provided the basis for species differentiation within the genusMycobacterium. Slowly and rapidly growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. Pathogenic Mycobacterium kansasii was easily differentiated from nonpathogenic M. gastri; this differentiation cannot be achieved by using 16S rRNA gene (rDNA) sequences. By being grouped into species-specific clusters with low-level sequence divergence among strains of the same species, all of the clinical isolates could be easily identified. These results suggest that comparative sequence analysis of amplified rpoB DNAs can be used efficiently to identify clinical isolates of mycobacteria in parallel with traditional culture methods and as a supplement to 16S rDNA gene analysis. Furthermore, in the case of M. tuberculosis, rifampin resistance can be simultaneously determined.

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Wang, Xiaochun, Jiamin Zhang, Jie Lu, Fuming Yi, Chuanfeng Liu, and Yuanyang Hu. "Sequence analysis and genomic organization of a new insect picorna-like virus, Ectropis obliqua picorna-like virus, isolated from Ectropis obliqua." Journal of General Virology 85, no. 5 (May 1, 2004): 1145–51. http://dx.doi.org/10.1099/vir.0.19638-0.

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The complete nucleotide sequence of a new insect picorna-like virus, Ectropis obliqua picorna-like virus (EoPV), which causes a fatal infection of Ectropis obliqua larvae, has been determined. The genomic RNA of EoPV is 9394 nt in length and contains a single, large open reading frame (nt 391–9351) encoding a polyprotein of 2987 aa. Sequence comparisons with other viral polyproteins revealed that the consensus sequences for picornavirus RNA helicase, protease and RNA-dependent RNA polymerase proteins are found on the genome in order in the 5′→3′ direction. All structural genes were located at the 5′ terminus. In terms of sequence similarity, identity and genome organization, EoPV resembles mammalian picornaviruses and three other insect picorna-like viruses: Infectious flacherie virus of silkworm, Sacbrood virus of honeybee and Perina nuda picorna-like virus (PnPV). Phylogenetic analysis showed that EoPV is most closely related to PnPV and suggests that these four insect picorna-like viruses might constitute a new group of insect-infectious RNA viruses.

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Meng, E., Baozhen Tang, Francisco Sanchez-Garcia, Ting Qiao, Lang Fu, Yu Wang, You-Ming Hou, Jiang-Lin Wu, and Zhi-Ming Chen. "The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1)." Viruses 11, no. 3 (March 13, 2019): 257. http://dx.doi.org/10.3390/v11030257.

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The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins, hypothetical proteins, matrix proteins, glycoproteins, and RNA-dependent RNA polymerases. Sequence analysis indicated that the RNA-dependent RNA polymerase of TbRV-1 shares a 65% nucleotide and 67% amino acid sequence identity with Hubei dimarhabdovirus 2, suggesting that TbRV-1 is a member of the dimarhabdovirus supergroup. This corresponded to the result of the phylogenetic analysis. The affiliation of TbRV-1 with members of the family Rhabdoviridae was further validated by similar transcription termination motifs (GGAACUUUUUUU) to the Drosophila sigmavirus. The prevalence of TbRV-1 in all tissues suggested that the virus was constitutive of, and not specific to, any wasp tissue. To our knowledge, this is the first report on the complete genome sequence of a dimarhabdovirus in parasitoids.

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Li, Hongliang, and Bin Liu. "BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo." PLOS Computational Biology 19, no. 6 (June 20, 2023): e1011214. http://dx.doi.org/10.1371/journal.pcbi.1011214.

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As the key for biological sequence structure and function prediction, disease diagnosis and treatment, biological sequence similarity analysis has attracted more and more attentions. However, the exiting computational methods failed to accurately analyse the biological sequence similarities because of the various data types (DNA, RNA, protein, disease, etc) and their low sequence similarities (remote homology). Therefore, new concepts and techniques are desired to solve this challenging problem. Biological sequences (DNA, RNA and protein sequences) can be considered as the sentences of “the book of life”, and their similarities can be considered as the biological language semantics (BLS). In this study, we are seeking the semantics analysis techniques derived from the natural language processing (NLP) to comprehensively and accurately analyse the biological sequence similarities. 27 semantics analysis methods derived from NLP were introduced to analyse biological sequence similarities, bringing new concepts and techniques to biological sequence similarity analysis. Experimental results show that these semantics analysis methods are able to facilitate the development of protein remote homology detection, circRNA-disease associations identification and protein function annotation, achieving better performance than the other state-of-the-art predictors in the related fields. Based on these semantics analysis methods, a platform called BioSeq-Diabolo has been constructed, which is named after a popular traditional sport in China. The users only need to input the embeddings of the biological sequence data. BioSeq-Diabolo will intelligently identify the task, and then accurately analyse the biological sequence similarities based on biological language semantics. BioSeq-Diabolo will integrate different biological sequence similarities in a supervised manner by using Learning to Rank (LTR), and the performance of the constructed methods will be evaluated and analysed so as to recommend the best methods for the users. The web server and stand-alone package of BioSeq-Diabolo can be accessed at http://bliulab.net/BioSeq-Diabolo/server/.

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Iwata, Yasuhide, Kazuo Takahashi, Xie Peng, Koji Fukuda, Koei Ohno, Tsuguhiro Ogawa, Kenji Gonda, Norio Mori, Shin-ichi Niwa, and Shiro Shigeta. "Detection and Sequence Analysis of Borna Disease Virus p24 RNA from Peripheral Blood Mononuclear Cells of Patients with Mood Disorders or Schizophrenia and of Blood Donors." Journal of Virology 72, no. 12 (December 1, 1998): 10044–49. http://dx.doi.org/10.1128/jvi.72.12.10044-10049.1998.

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ABSTRACT Borna disease virus (BDV) p24 RNA was detected in the peripheral blood mononuclear cells (PBMCs) of psychiatric patients and blood donors by nested reverse transcriptase PCR (RT-PCR). The prevalences of BDV p24 RNA in patients with mood disorders (4%) and schizophrenia (4%) were not significantly different from that in blood donors (2%). This finding was inconsistent with previous reports that showed either a high prevalence or absence of BDV p24 RNA in patients with psychiatric disorders. The differences in BDV p24 RNA prevalence in these studies may be due to differences in the criteria for positivity, the number of PBMCs used for RNA extraction, or the amount of RNA tested for nested RT-PCR or to laboratory contamination. Sequence analysis of BDV p24 RNA from the PBMCs of patients and blood donors showed a high nucleotide sequence conservation but definite nucleotide mutations compared with horse BDV p24 RNA sequences. In comparison with human BDV p24 RNA sequences previously reported from Japan and Germany, there were several positions with silent nucleotide mutations among these clones.

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Panagiotis, Chatzinikolaou, Makris Christos, Dimitrios Vlachakis, and Sophia Kossida. "A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data." International Journal of Systems Biology and Biomedical Technologies 2, no. 4 (October 2013): 86–98. http://dx.doi.org/10.4018/ijsbbt.2013100106.

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In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

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Clarke, Andrew M., Krysta L. Engel, Keith E. Giles, Chad M. Petit, and David A. Schneider. "NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I." Proceedings of the National Academy of Sciences 115, no. 50 (November 27, 2018): E11633—E11641. http://dx.doi.org/10.1073/pnas.1809421115.

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DNA sequence motifs that affect RNA polymerase transcription elongation are well studied in prokaryotic organisms and contribute directly to regulation of gene expression. Despite significant work on the regulation of eukaryotic transcription, the effect of DNA template sequence on RNA polymerase I (Pol I) transcription elongation remains unknown. In this study, we examined the effects of DNA sequence motifs on Pol I transcription elongation kinetics in vitro and in vivo. Specifically, we characterized how the spy rho-independent terminator motif from Escherichia coli directly affects Saccharomyces cerevisiae Pol I activity, demonstrating evolutionary conservation of sequence-specific effects on transcription. The insight gained from this analysis led to the identification of a homologous sequence in the ribosomal DNA of S. cerevisiae. We then used native elongating transcript sequencing (NETSeq) to determine whether Pol I encounters pause-inducing sequences in vivo. We found hundreds of positions within the ribosomal DNA (rDNA) that reproducibly induce pausing in vivo. We also observed significantly lower Pol I occupancy at G residues in the rDNA, independent of other sequence context, indicating differential nucleotide incorporation rates for Pol I in vivo. These data demonstrate that DNA template sequence elements directly influence Pol I transcription elongation. Furthermore, we have developed the necessary experimental and analytical methods to investigate these perturbations in living cells going forward.

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Niubò, Jordi, Wuyi Li, Keith Henry, and Alejo Erice. "Recovery and Analysis of Human Immunodeficiency Virus Type 1 (HIV) RNA Sequences from Plasma Samples with Low HIV RNA Levels." Journal of Clinical Microbiology 38, no. 1 (January 2000): 309–12. http://dx.doi.org/10.1128/jcm.38.1.309-312.2000.

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ABSTRACT Amplification of human immunodeficiency virus type 1 (HIV) reverse transcriptase (RT) and protease (PT) sequences from plasma is difficult when HIV RNA levels are low, and it usually cannot be accomplished in samples with <1,000 HIV RNA copies/ml. Because the RNA extraction step is critical for the success of subsequent amplifications and sequence analyses, two RNA extraction methods were compared to study plasma samples with low HIV RNA levels. Forty-four plasma samples containing <500 HIV RNA copies/ml in a branched-DNA (bDNA) assay (Quantiplex HIV RNA assay version 2.0 [Chiron Corp., Emeryville, Calif.]) were studied. RNA was extracted by using two commercial kits (QIAamp Viral RNA kit [Qiagen, Hilden, Germany] and NucliSens kit [Organon Teknika, Boxtel, The Netherlands]). Fragments (1,144 bp) encompassing HIV PT and RT sequences were amplified by nested PCRs. Amplified products were sequenced by using a commercial kit (Applied Biosystems). HIV RNA was recovered from a total of 21 plasma samples, including 20 samples after extraction by the NucliSens method, and 8 samples after extraction by the QIAamp method ( P < 0.05). Mean HIV RNA levels in these samples, measured by an ultrasensitive bDNA assay (Quantiplex HIV RNA assay version 3.0; Chiron Corp., Emeryville, Calif.), were 848 copies/ml (median, 666; range, 154 to 2,606 copies/ml). Analysis of RT and PT sequences in five samples demonstrated an average of 3.8 and 2.4 resistance mutations in these regions, respectively. The NucliSens RNA extraction kit is a valuable method for obtaining HIV RNA for genotypic studies from plasma fractions of individuals with low HIV RNA levels.

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40

Zhu, Y. "Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA." RNA 12, no. 5 (March 15, 2006): 699–706. http://dx.doi.org/10.1261/rna.2284906.

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P. Tourova, Tatjana, Andrey B. Poltoraus, Irina A. Lebedeva, Iraida A. Tsaplina, Tatjana I. Bogdanova, and Gregory I. Karavaiko. "16S Ribosomal RNA (rDNA) Sequence Analysis and Phylogenetic Position of Sulfobacillus thermosulfidooxidans." Systematic and Applied Microbiology 17, no. 4 (February 1995): 509–12. http://dx.doi.org/10.1016/s0723-2020(11)80069-x.

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Moriya, Shigeharu. "Simple mapping-based quantification of a mock microbial community using total RNA-seq data." PLOS ONE 16, no. 7 (July 16, 2021): e0254556. http://dx.doi.org/10.1371/journal.pone.0254556.

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Most microbes in the natural environment are difficult to cultivate. Thus, culture-independent analysis for microbial community structure is important for the understanding of its ecological functions. An immense ribosomal RNA sequence collection is available from phylogenetic research on organisms in all domains. These sequences are available for use in genetic research. However, the amplicon-seq process using PCR requires the construction of a sequence library. Construction can introduce bias into quantitative analyses, and each domain of species needs its own primer set. Total RNA sequencing has the advantage of analyzing an entire microbial community, including bacteria, archea, and eukaryote, at once. Such analysis yields large amounts of ribosomal RNA sequences that can be used for analysis without PCR bias. Evaluation using total RNA-seq for quantitative analysis of microbial communities and comparison with amplicon-seq is still rare. In the present study, we developed a mapping-based total RNA-seq analysis to obtain quantitative information on microbial community structure and compared our results with ordinary amplicon-seq methods. We read total RNA sequences from a commercially available mock community (ATCC MSA-2003) and divided reads into small subunit ribosomal RNA (ssrRNA) origin reads and others, such as mRNA origin reads. We then mapped ssrRNA origin reads on annotated assembled contigs and obtained quantitative results under several analysis strategies. Removal of low complexity sequences, sorting ssrRNA with paired-in mode, and performing homology-based taxonomical assignments (BLAST+ or vsearch) showed superior outcomes to other strategies. Results with this approach showed a median relative abundance among ten mock community members of ~10%; ordinary amplicon-seq showed a much lower percentage. Thus, total RNA-seq can be a powerful tool for analyzing microbial community structure and is not limited to analyzing gene expression profiling of microbiomes.

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Schaal, Thomas D., and Tom Maniatis. "Selection and Characterization of Pre-mRNA Splicing Enhancers: Identification of Novel SR Protein-Specific Enhancer Sequences." Molecular and Cellular Biology 19, no. 3 (March 1, 1999): 1705–19. http://dx.doi.org/10.1128/mcb.19.3.1705.

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ABSTRACT Splicing enhancers are RNA sequences required for accurate splice site recognition and the control of alternative splicing. In this study, we used an in vitro selection procedure to identify and characterize novel RNA sequences capable of functioning as pre-mRNA splicing enhancers. Randomized 18-nucleotide RNA sequences were inserted downstream from a Drosophila doublesex pre-mRNA enhancer-dependent splicing substrate. Functional splicing enhancers were then selected by multiple rounds of in vitro splicing in nuclear extracts, reverse transcription, and selective PCR amplification of the spliced products. Characterization of the selected splicing enhancers revealed a highly heterogeneous population of sequences, but we identified six classes of recurring degenerate sequence motifs five to seven nucleotides in length including novel splicing enhancer sequence motifs. Analysis of selected splicing enhancer elements and other enhancers in S100 complementation assays led to the identification of individual enhancers capable of being activated by specific serine/arginine (SR)-rich splicing factors (SC35, 9G8, and SF2/ASF). In addition, a potent splicing enhancer sequence isolated in the selection specifically binds a 20-kDa SR protein. This enhancer sequence has a high level of sequence homology with a recently identified RNA-protein adduct that can be immunoprecipitated with an SRp20-specific antibody. We conclude that distinct classes of selected enhancers are activated by specific SR proteins, but there is considerable sequence degeneracy within each class. The results presented here, in conjunction with previous studies, reveal a remarkably broad spectrum of RNA sequences capable of binding specific SR proteins and/or functioning as SR-specific splicing enhancers.

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Ogert, Robert A., and Karen L. Beemon. "Mutational Analysis of the Rous Sarcoma Virus DR Posttranscriptional Control Element." Journal of Virology 72, no. 4 (April 1, 1998): 3407–11. http://dx.doi.org/10.1128/jvi.72.4.3407-3411.1998.

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ABSTRACT The direct repeat (DR) sequences flanking the src gene in Rous sarcoma virus are essential posttranscriptional control elements; at least one copy of this sequence is necessary for cytoplasmic accumulation of unspliced viral RNA. These sequences promote Rev-independent human immunodeficiency virus type 1 expression, suggesting they act as constitutive transport elements (CTEs). To determine which regions of this sequence are critical for CTE function, mutations in the downstream DR were generated and tested in a viral deletion construct lacking src and the upstream DR. Two single-point mutations and three different clustered mutations caused substantial reductions in reverse transcriptase activity, Gag protein levels, and unspliced viral RNA in the cytoplasm. Three conserved regions of the CTE, including nucleotides 8844 to 8847, 8862 to 8864, and 8868 to 8870, were most sensitive to inactivation by mutagenesis.

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Sun, Cheng-He, Yang-Liang Gu, Da-Wei Liu, Hong-Wei Du, and Chang-Hu Lu. "Sequencing and Analysis of the Complete Mitochondrial Genome of Lentipes ikeae." Animals 14, no. 6 (March 19, 2024): 943. http://dx.doi.org/10.3390/ani14060943.

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We sequenced and analyzed the complete mitochondrial genome of Lentipes ikeae and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of L. ikeae was determined using the Illumina HiSeq X Ten sequencing platform, and the gene structural characteristics and base composition were analyzed. Based on the mitochondrial genome sequences of 28 Sicydiinae species published in GenBank and mitochondrial protein-coding genes (PCGs), Acanthogobius flavimanus (Gobionellinae) was selected as an outgroup to construct phylogenetic trees of Sicydiinae using the maximum likelihood and Bayesian inference methods. The mitochondrial genome of L. ikeae (GenBank number: OP764680) has a total length of 16,498 bp and encodes 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop (control) region. Gene rearrangement is not observed. The mitochondrial genome of L. ikeae exhibits an AT preference, with AT skew > 0 and GC skew < 0 across the entire genome. The phylogenetic relationships of Sicydiinae based on 13 mitochondrial PCG sequences are Sicydium + (Stiphodon + (Sicyopus + Lentipes)) + Sicyopterus, indicating that Sicydium, Sicyopterus, Lentipes, and Stiphodon are all monophyletic groups.

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46

Lee, Yun-Shien, Yau-Heiu Hsu, and Na-Sheng Lin. "Generation of Subgenomic RNA Directed by a Satellite RNA Associated with Bamboo Mosaic Potexvirus: Analyses of Potexvirus Subgenomic RNA Promoter." Journal of Virology 74, no. 22 (November 15, 2000): 10341–48. http://dx.doi.org/10.1128/jvi.74.22.10341-10348.2000.

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ABSTRACT Satellite RNA of bamboo mosaic potexvirus (satBaMV), a single-stranded positive-sense RNA encoding a nonstructural protein of 20 kDa (P20), depends on bamboo mosaic potexvirus (BaMV) for replication and encapsidation. A full-length cDNA clone of satBaMV was used to examine the sequences required for the synthesis of potexvirus subgenomic RNAs (sgRNAs). Subgenomic promoter-like sequences (SGPs), 107 nucleotides (nt) upstream from the capsid protein (CP) gene of BaMV-V, were inserted upstream of the start codon of the P20 gene of satBaMV. Insertion of SGPs gave rise to the synthesis of sgRNA of satBaMV in protoplasts ofNicotiana benthamiana and leaves of Chenopodium quinoa when coinoculated with BaMV-V genomic RNA. Moreover, both the satBaMV cassette and its sgRNA were encapsidated. From analysis of the SGPs by deletion mutation, we concluded that an SGP contains one core promoterlike sequence (nt −30 through +16), two upstream enhancers (nt −59 through −31 and −91 through −60), and one downstream enhancer (nt +17 through +52), when the transcription initiation site is taken as +1. Site-directed mutagenesis and compensatory mutation to disrupt and restore potential base pairing in the core promoter-like sequence suggest that the stem-loop structure is important for the function of SGP in vivo. Likewise, the insertion of a putative SGP of the BaMV open reading frame 2 gene or a heterologous SGP of potato virus X resulted in generation of an sgRNA. The satBaMV cassette should be a useful tool to gain insight into sequences required for the synthesis of potexvirus sgRNAs.

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47

Zhang, Yuting, Jingwen Song, Min Zhang, and Zhongyuan Deng. "Analysis Polyadenylation Signal Usage in Sus scrofa." Animals 12, no. 2 (January 13, 2022): 194. http://dx.doi.org/10.3390/ani12020194.

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RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3′ ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation.

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Nicholson-Shaw, Tim, and Jens Lykke-Andersen. "Tailer: a pipeline for sequencing-based analysis of nonpolyadenylated RNA 3′ end processing." RNA 28, no. 5 (February 18, 2022): 645–56. http://dx.doi.org/10.1261/rna.079071.121.

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Post-transcriptional trimming and tailing of RNA 3′ ends play key roles in the processing and quality control of noncoding RNAs (ncRNAs). However, bioinformatic tools to examine changes in the RNA 3′ “tailome” are sparse and not standardized. Here we present Tailer, a bioinformatic pipeline in two parts that allows for robust quantification and analysis of tail information from next-generation sequencing experiments that preserve RNA 3′ end information. The first part of Tailer, Tailer-processing, uses genome annotation or reference FASTA gene sequences to quantify RNA 3′ ends from SAM-formatted alignment files or FASTQ sequence read files produced from sequencing experiments. The second part, Tailer-analysis, uses the output of Tailer-processing to identify statistically significant RNA targets of trimming and tailing and create graphs for data exploration. We apply Tailer to RNA 3′ end sequencing experiments from three published studies and find that it accurately and reproducibly recapitulates key findings. Thus, Tailer should be a useful and easily accessible tool to globally investigate tailing dynamics of nonpolyadenylated RNAs and conditions that perturb them.

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Turcich, Michael P., Amana Bokhari-Riza, Douglas A. Hamilton, and Joseph P. Mascarenhas. "Sequence and expression of a microspore cDNA clone with homology to a ribosomal protein." Acta Societatis Botanicorum Poloniae 65, no. 1-2 (2014): 61–63. http://dx.doi.org/10.5586/asbp.1996.011.

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A cDNA library was made to RNA from corn anthers containing developing pollen at the uninucleate microspore stage. A randomly selected clone from this library which contained an insert (531 bp) was isolated and sequenced. An open reading frame of 330 bp was located. Computer alignments of the putative amino acid sequence with sequences from GenBank and the SwissProt protein databases indicated homology to L12, an acidic ribosomal protein. RNA blot analysis showed highest levels of this mRNA in mature pollen. The significance of this observation in light of the known biochemistry of ribosome synthesis in developing pollen is discussed.

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Arkhipova, I. R. "Promoter elements in Drosophila melanogaster revealed by sequence analysis." Genetics 139, no. 3 (March 1, 1995): 1359–69. http://dx.doi.org/10.1093/genetics/139.3.1359.

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Abstract A Drosophila Promoter Database containing 252 independent Drosophila melanogaster promoter entries has been compiled. The database and its subsets have been searched for overrepresented sequences. The analysis reveals that the proximal promoter region displays the most dramatic nucleotide sequence irregularities and exhibits a tripartite structure, consisting of TATA at -25/-30 bp, initiator (Inr) at +/- 5 bp and a novel class of downstream elements at +20/+30 bp from the RNA start site. These latter elements are also strand-specific. However, they differ from TATA and Inr in several aspects: (1) they are represented not by a single, but by multiple sequences, (2) they are shorter, (3) their position is less strictly fixed with respect to the RNA start site, (4) they emerge as a characteristic feature of Drosophila promoters and (5) some of them are strongly overrepresented in the TATA-less, but not TATA-containing, subset. About one-half of known Drosophila promoters can be classified as TATA-less. The overall sequence organization of the promoter region is characterized by an extended region with an increase in GC-content and a decrease in A, which contains a number of binding sites for Drosophila transcription factors.

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Journal articles on the topic 'RNA Sequence Analysis'

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