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Results for “RNA sequencing analysis”

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At least 865 records · Page 48Linked to original sources
PubMed2005

SMYD3-NY, a novel SMYD3 mRNA transcript variant, may have a role in human spermatogenesis.

Identification of genes specifically expressed in adult and fetal testis is important to further our understanding of testis development and function. In this study, a novel SMYD3 transcript variant, termed SMYD3-NY (GenBank Accession No. AY186742), was identified by hybridization of adult and fetal human testis cDNA probes with a human cDNA microarray. SMYD3-NY transcript was expressed at 2.3-fold higher levels in adult human testis than in fetal testis, with a low expression level in human spermatozoa. Bioinformatical analysis showed that SMYD3-NY protein has the SET domain that is involved in histone methyltransferase (HTMase) activity. Southern blotting showed that SMYD3-NY is distributed in several tissues, including testis. In summary, SMYD3-NY is a novel transcript variant of the SMYD3 gene, and SMYD3-NY protein may influence transcriptional regulation during spermatogenesis via HTMase activity.

Adult↗
PubMed2005

[Role of AURE sequences in the regulation of mRNA stability].

Post-transcriptional processes influencing mRNA stability are an important control point in gene expression regulation. The best-studied regulatory elements controlling mRNA stability are AU-rich sequences (AURE) found in 3'UTRs of many genes coding cytokines and stress response proteins. The presence of these elements results in short half-life of mRNA, but such mRNA half-life is prolonged upon cell stimulation or exposition to stress factors. Research on AURE-mediated mRNA decay resulted in discovery of AURE-binding proteins and in elucidating signal transduction pathways involved in the process of mRNA stability regulation. Defects in mRNA stability regulation can result in diseases such as lymphomas, neuromas or immunological and inflammatory disorders.

Adenine Nucleotides↗
PubMed2005

Natural antisense as potential regulator of alternative initiation, splicing and termination.

In humans an estimated 35-60% of genes are alternatively spliced. A large number of genes also show alternative initiation or termination. Regulation of these processes is still poorly understood. For alternative splicing it is believed that the relative concentration of certain proteins and the presence of certain regulatory elements are the key factors determining alterations in splicing pattern. However, there is evidence that antisense RNA might be part of the regulatory processes. Antisense RNA molecules could bind to the target pre-mRNA in a sequence-specific fashion, sterically blocking targeted splice sites and redirecting the spliceosome to available and unhindered splice sites. Here we describe an in silico investigation to identify human sense/antisense pairs with alternative initiation or termination in the sense gene and where only one of the isoforms overlaps the antisense transcript. Alternatively spliced genes with antisense transcripts covering the alternatively used splice site are also identified. Our analyses are based on the ASAP splicing annotation database from UCLA, the antisense transcripts data from Yelin et al., 2003, and the H-invitational full-length cDNA database from JBIRC, Japan. These data gives new insight into the complexity of genomic organization and provide candidate loci for experimentalists to study antisense mediated regulation of alternative initiation, splicing and termination. Our result contains 468 clusters with this characteristic genomic organization and can be found at http://aistar.bii.a-star.edu.sg/.

Alternative Splicing↗
PubMed2003

Statistical inference for well-ordered structures in nucleotide sequences.

Distinct, local structures are frequently correlated with functional RNA elements involved in post-transcriptional regulation of gene expression. Discovery of microRNAs (miRNAs) suggests that there are a large class of small non-coding RNAs in eukaryotic genomes. These miRNAs have the potential to form distinct fold-back stem-loop structures. The prediction of those well-ordered folding sequences (WFS) in genomic sequences is very helpful for our understanding of RNA-based gene regulation and the determination of local RNA elements with structure-dependent functions. In this study, we describe a novel method for discovering the local WFS in a nucleotide sequence by Monte Carlo simulation and RNA folding. In the approach the quality of a local WFS is assessed by the energy difference (E(diff)) between the optimal structure folded in the local segment and its corresponding optimal, restrained structure where all the previous base pairings formed in the optimal structure are prohibited. Distinct WFS can be discovered by scanning successive segments along a sequence for evaluating the difference between E(diff) of the natural sequence and those computed from randomly shuffled sequences. Our results indicate that the statistically significant WFS detected in the genomic sequences of Caenorhabditis elegans (C.elegans) F49E12, T07C5, T07D1, T10H9, Y56A3A and Y71G12B are coincident with known fold-back stem-loops found in miRNA precursors. The potential and implications of our method in searching for miRNAs in genomes is discussed.

Algorithms↗
PubMed1995

Hepatitis C viral quasispecies in hepatitis C virus carriers with normal liver enzymes and patients with type C chronic liver disease.

Hepatitis C virus (HCV) has been reported to conform to a quasispecies nature, which is most evident in hypervariable regions of the putative envelope 2 domain. The aim of this study was to determine the relationship between the nucleotide complexity and diversity of hypervariable region 1 and various stages of the carrier states. The subjects studied were 20 HCV carriers with normal alanine aminotransferase (ALT) levels, 50 patients with chronic hepatitis who showed elevated ALT levels, 22 with cirrhosis, and 24 with hepatocellular carcinoma. The quasispecies complexity was analyzed by means of polymerase chain reaction-mediated single strand conformation polymorphism (PCR-SSCP). The value of nucleotide diversity was calculated by PCR cloning and sequencing. The number of SSCP bands ranged from 1 to 7, with no significant differences in the mean numbers among the stages of HCV infection. There was no correlation between the amounts of serum HCV RNA and the numbers of SSCP bands. No significant difference was found in the values of nucleotide diversity between carriers with normal ALT levels (mean, 6.6 x 10(-2) per site) and patients with chronic hepatitis (7.7 x 10(-2). These findings suggest that the quasispecies complexity of hypervariable region 1 is independent of the stage of chronic HCV infection.

Adolescent↗
PubMed1993

Detection and direct sequence identification of BCR-ABL mRNA in Ph+ chronic myeloid leukemia.

The reverse transcriptase-polymerase chain reaction (RT-PCR) for BCR-ABL mRNA is increasingly used to diagnose and monitor patients with Ph+ chronic myeloid leukemia (CML). We investigated an alternative approach to detect BCR-ABL mRNA in CML in order to overcome some of the potential drawbacks of RT-PCR. Nucleic acid sequence based amplification (NASBA) is a homogeneous, isothermal, in vitro process that provides the direct amplification of RNA. Peripheral blood from seven patients with Ph+ CML and Ph+ EM-2 cells were investigated by NASBA and RT-PCR. A nested set of four primers flanking the BCR-ABL junction was used in two serial NASBA reactions performed for 2 hours. The two methods were fully concordant for detection of transcripts with bcr3-abl2 and bcr2-abl2 junctions. Ethidium bromide fluorescence with NASBA indicated in repeated experiments that similar quantities of total RNA from patient material contained different amounts of BCR-ABL mRNA. The data suggest that direct amplification of RNA is suitable for identifying and monitoring patients with Ph+ CML and may provide a means to quantify BCR-ABL mRNA levels.

Base Sequence↗
PubMed1995

Genomic characterization of type 2 polioviruses isolated from vaccine-associated cases in Brazil.

Twenty strains of P2/Sabin-related polioviruses isolated in Brazil were analyzed; ten from persistent paralytic poliomyelitis cases, three from suspected polio cases with transient paralysis, and seven from healthy contacts. The serotypes of the viral isolates were identified by the neutralization test with hyperimmune equine sera. The relationship of the isolates to the P2/Sabin strain was demonstrated by molecular hybridization and polymerase chain reaction (PCR). Partial sequencing demonstrated mutations at nucleotide 481 in the 5' noncoding region and at amino acid 143 of the capsid protein VP1 in most of these isolates from vaccine-associated cases in Brazil. These data support previous studies on the importance of mutations at these attenuated determinants in the establishment of the disease. However, the existence of isolates without mutations at these positions suggests that they are not essential. The results also strengthen the possibility of the participation of a mutation at nucleotide 398 in the establishment of the disease, and suggest that a mutation at nucleotide 491 or 500 may also be involved in this process. The isolates from healthy contacts presented the same mutations as the isolates from vaccine-associated cases with which they were in contact. This strengthens the observation that, although mutations in the genome of the P2/Sabin strain are important for the establishment of the disease, host factors are also involved.

Base Sequence↗
PubMed2024

Protocol to decode the role of transcriptionally active microbes in SARS-CoV-2-positive patients using an RNA-seq-based approach.

The elucidation of the role of microorganisms in human infections has been hindered by difficulties using conventional culture-based techniques. Here, we present a protocol for the investigation of transcriptionally active microbes (TAMs) using an RNA sequencing (RNA-seq)-based approach. We describe the steps for RNA isolation, viral genome sequencing, RNA-seq library preparation, and metatranscriptomic and transcriptomic analysis. This protocol permits a comprehensive evaluation of TAMs' contributions to the differential severity of infectious diseases, with a particular focus on diseases such as COVID-19. For complete details on the use and execution of this protocol, please refer to Devi et al.1.

Humans↗
PubMed2002

Functional exploration of the C. elegans genome using DNA microarrays.

Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans. Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types. Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function. Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C. elegans development.

Animals↗
PubMed1994

Applications of statistical criteria in protein sequence analysis: case study of yeast RNA polymerase II subunits.

We have recently proposed statistical techniques to identify unusual protein sequence features. Extensive mapping of these features to particular groups of proteins may afford new ways of protein classification. Here we present a case study of such analysis by discussing special features of the amino acid sequences of yeast RNA polymerase II, the first eukaryotic RNA polymerase for which all subunits have been sequenced. Specific new suggestions derived from this analysis include: (i) based on unusual charge configurations in some of the sequences, electrostatic forces may play a significant role in subunit interactions; (ii) RPB4, on account of similar charge distribution, may well be grouped together with RNA polymerase II transcription initiation factors.

Amino Acid Sequence↗
PubMed1996

A phylogenetic study of Rubrobacter radiotolerans by sequence analysis of the 16S ribosomal RNA gene.

Partial sequence of the 16S ribosomal RNA gene of an extremely high radiotolerant bacterium, Rubrobacter radiotolerans (reclassified from Arthrobacter radiotolerans by chemical characteristics) was determined by PCR-amplification from a small amount of heat-lysed biomass, followed by direct sequencing of the PCR product. The sequence was aligned with seven species of Arthrobacter and also with representatives of various other bacterial groups. R. radiotolerans was confirmed to be out of the Arthrobacter group justifying the reclassification. Moreover, it has an individual position among the selected representatives being closer to the eubacterial groups.

Arthrobacter↗
PubMed1996

Molecular analysis of a novel schizosaccharomyces pombe gene containing two RNP consensus-sequence RNA-binding domains.

Proteins containing RNP consensus-sequence RNA-binding domains (CS-RBDs) play diverse roles in many aspects of RNA metabolism. Using a PCR strategy, we cloned portions of six new Schizosaccharomyces pombe genes encoding RBD proteins, including a putative homolog of the mammalian splicing factor SAP49. The genomic locus corresponding to a second PCR product, designated rnp24a, was cloned and characterized in detail. Sequence analysis revealed that the Rnp24 protein is highly charged and contains a second RBD with an unusually long Loop-3 sequence. Strains containing a disrupted copy of the rnp24 gene display neither loss of viability nor any discernible growth defects under a variety of conditions, suggesting that the function of Rnp24p overlaps with that of another fission yeast protein. Although database searches did not identify proteins that share extensive amino-acid identity with Rnp24p, phylogenetic analysis suggests that its closest relatives are metazoan hnRNP proteins. The lack of an observable phenotype in S. pombe cells lacking Rnp24p is consistent with this classification, since hnRNP proteins in higher cells include several distinct subfamilies with similar sequences and RNA-binding specificities.

Amino Acid Sequence↗