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At least 307 records · Page 17Linked to original sources
PubMed2026

Diving Deeper Into Mechanisms of Acrylamide-Induced Toxicity: RNA Sequencing Reveals Transcriptomic Alteration and Retrotransposon Expression in Drosophila melanogaster.

Given the inevitability of human and animal exposure to acrylamide, there is increasing concern regarding its potential health risks. While a number of molecular mechanisms have been proposed, the complexity of acrylamide toxicological pathways and interactions remains incompletely characterized. In this study, we employed a transcriptomic approach to investigate the transcriptional responses of Drosophila melanogaster following exposure to acrylamide (100 mg/kg). Our analysis identified 634 differentially expressed genes (DEGs), with 362 upregulated and 272 downregulated. Functional analysis revealed these DEGs are enriched in pathways related to reproduction, detoxification, cellular and metabolic processes, signaling, synaptic formation and organization. Notably, acrylamide exposure upregulated the expression of tau and beta-amyloid protein precursor-like genes, both implicated in Alzheimer's disease pathology. An aversive memory test further demonstrated that acrylamide impaired the short-term memory of treated flies. Additionally, acrylamide-induced toxicity altered the expression of nine long terminal repeat retrotransposons, belonging to the gypsy and pao superfamilies. By exploring the potential role of transposable element activity in acrylamide-mediated toxicity, this study provides novel insights into the molecular mechanisms underlying its effects. Collectively, these findings offer a more comprehensive understanding of the mechanisms and pathways associated with the toxic action and detoxification of acrylamide in D. melanogaster.

Animals↗
PubMed2024

Single cell RNA sequencing provides novel cellular transcriptional profiles and underlying pathogenesis of presbycusis.

Age-related hearing loss (ARHL) or presbycusis is associated with irreversible progressive damage in the inner ear, where the sound is transduced into electrical signal; but the detailed mechanism remains unclear. Here, we sought to determine the potential molecular mechanism involved in the pathogeneses of ARHL with bioinformatics methods. A single-cell transcriptome sequencing study was performed on the cochlear samples from young and aged mice. Detection of identified cell type marker allowed us to screen 18 transcriptional clusters, including myeloid cells, epithelial cells, B cells, endothelial cells, fibroblasts, T cells, inner pillar cells, neurons, inner phalangeal cells, and red blood cells. Cell-cell communications were analyzed between young and aged cochlear tissue samples by using the latest integration algorithms Cellchat. A total of 56 differentially expressed genes were screened between the two groups. Functional enrichment analysis showed these genes were mainly involved in immune, oxidative stress, apoptosis, and metabolic processes. The expression levels of crucial genes in cochlear tissues were further verified by immunohistochemistry. Overall, this study provides new theoretical support for the development of clinical therapeutic drugs.

Animals↗
PubMed1984

Evidence against gamma-crystallin DNA or RNA sequences in the chicken.

A cloned cDNA (pM gamma 1 Crl) encoding about two-thirds of a gamma-crystallin polypeptide from the murine lens was used as a hybridization probe to search for the presence of gamma-crystallin-like RNA or DNA sequences in the chicken. The 15-day-old chicken lens did not contain any RNA sequences homologous to the murine gamma-crystallin cDNA, as judged by Northern blot hybridization. An approximate 2.3 Kbp (kilobase pair) Bam HI fragment from the chicken genome hybridized to the murine gamma-crystallin cDNA in Southern blots. Cloning and sequencing of this genomic fragment, however, did not reveal any homology with gamma- or beta-crystallin sequences. A stretch of 22 dG: dC nucleotides was present in the cloned DNA fragment and possibly this hybridized to the cloned gamma-crystallin cDNA via its dG:dC nucleotide tails introduced during the cloning procedure. These data support those of McDevitt and Croft (1977) indicating that the chicken lens lacks gamma-crystallin and provide evidence against gamma-crystallin mRNA or a gamma-crystallin gene or pseudogene in the chicken. The absence of gamma-crystallin mRNA in the embryonic chicken lens cells makes them potentially useful recipients for investigating the expression of cloned gamma-crystallin genes.

Amino Acid Sequence↗
PubMed1981

Complete sequence of an immunoglobulin mRNA using specific priming and the dideoxynucleotide method of RNA sequencing.

The complete sequence of the mouse immunoglobulin kappa light chain MOPC 21 messenger RNA has been determined using a chain termination method and chemically synthesised deoxyoligonucleotides to initiate the synthesis of a DNA molecule complementary to the mRNA template. Five such oligonucleotide primers have been used for the sequence analysis of this messenger RNA. The approach is excellent for comparative studies of mouse k-chain mRNAs because they can be made on impure mRNA preparations. The MOPC 21 light chain mRNA is 943 nucleotides in length excluding the poly(A) region. An unexpected finding was that there are only three bases in the 5' non-coding region and its significance in terms of ribosome binding is discussed; 87 code for the precursor or leader sequence of the protein, 642 for the mature protein and 211 for the 3' non-coding region. The codons for the precursor region allows the previously undetermined amino acid sequence to be predicted. In common with other precursor regions a high proportion of the predicted amino acids are hydrophobic.

Animals↗
PubMed1998

Apolipoprotein B RNA sequence 3' of the mooring sequence and cellular sources of auxiliary factors determine the location and extent of promiscuous editing.

Apolipoprotein B (apoB) RNA editing involves a cytidine to uridine transition at nucleotide 6666 (C6666) 5' of an essential cis -acting 11 nucleotide motif known as the mooring sequence. APOBEC-1 (apoB editing catalytic sub-unit 1) serves as the site-specific cytidine deaminase in the context of a multiprotein assembly, the editosome. Experimental over-expression of APOBEC-1 resulted in an increased proportion of apoB mRNAs edited at C6666, as well as editing of sites that would otherwise not be recognized (promiscuous editing). In the rat hepatoma McArdle cell line, these sites occurred predominantly 5' of the mooring sequence on either rat or human apoB mRNA expressed from transfected cDNA. In comparison, over-expression of APOBEC-1 in HepG2 (HepG2-APOBEC) human hepatoma cells, induced promiscuous editing primarily 5' of the mooring sequence, but sites 3' of the C6666 were also used more efficiently. The capacity for promiscuous editing was common to rat, rabbit and human sources of APOBEC-1. The data suggested that differences in the distribution of promiscuous editing sites and in the efficiency of their utilization may reflect cell-type-specific differences in auxiliary proteins. Deletion of the mooring sequence abolished editing at the wild type site and markedly reduced, but did not eliminate, promiscuous editing. In contrast, deletion of a pair of tandem UGAU motifs 3' of the mooring sequence in human apoB mRNA selectively reduced promiscuous editing, leaving the efficiency of editing at the wild type site essentially unaffected. ApoB RNA constructs and naturally occurring mRNAs such as NAT-1 (novel APOBEC-1 target-1) that lack this downstream element were not promiscuously edited in McArdle or HepG2 cells. These findings underscore the importance of RNA sequences and the cellular context of auxiliary factors in regulating editing site utilization.

APOBEC-1 Deaminase↗
PubMed1982

5S RNA sequence from the Philosamia silkworm: evidence for variable evolutionary rates in insect 5S RNA.

The primary structure of 5S RNA isolated from the posterior silkgland of Philosamia cynthia ricini was determined using three in vitro labelling techniques. The derived sequence consists of 119 nucleotides and can be folded into the secondary structure model proposed for eukaryotic 5S RNAs. This 5S RNA differs from the Bombyx mori molecule in 9 positions and from the Drosophila melanogaster sequence in 14 positions. The comparison of evolutionary rates in insect 5S RNA with inferred rates in other eukaryotic phyla leads to the conclusion that 5S RNA evolution is not constant in different eukaryotic branches, a condition which must be taken into account in phylogenetic tree constructions.

Animals↗
PubMed1996

Hantavirus S RNA sequence from a fatal case of HPS in New York.

In April, 1995, the second fatal case of hantavirus pulmonary syndrome (HPS) occurred in the northeast in a New York State resident. Using the patient's lung tissue obtained at autopsy, the S genomic RNA segment of a hantavirus, designated H-NY1, was amplified by reverse transcriptase-polymerase chain reaction (RT-PCR), cloned, and sequenced. The S RNA was found to contain 2084 nucleotides, 6 nucleotides longer than reported by Hjelle et al. (1995) for the virus associated with the first northeastern case (RI-1). There were 101 nucleotide differences in the S RNA between the H-NY1 and RI-1, which result in the prediction of a single amino-acid change in the nucleocapsid (N) protein. Rodents were trapped for serologic and virologic studies at the patient's residence and work site. The white-footed mouse (Peromyscus leucopus) was the most frequently captured species and more than 50% of those trapped near the patient's residence showed serologic evidence of hantavirus infection. Using RT-PCR it was possible to amplify hantavirus S RNA sequence from the lung tissues of 8 out of 11 seropositive animals. No difference in nucleotide sequence was found between the HPS patient sequence and the P. leucopus sequence (nucleotides 189 to 599). These data are consistent with those of Hjelle et al. (1995) in suggesting that P. leucopus is the primary rodent vector for the etiologic agent of HPS in the northeastern United States.

Adult↗
PubMed2001

Repression of RNA polymerase I transcription by nucleolin is independent of the RNA sequence that is transcribed.

Nucleolin is one of the most abundant non-ribosomal proteins of the nucleolus. Several studies in vitro have shown that nucleolin is involved in several steps of ribosome biogenesis, including the regulation of rDNA transcription, rRNA processing, and ribosome assembly. However, the different steps of ribosome biogenesis are highly coordinated, and therefore it is not clear to what extent nucleolin is involved in each of these steps. It has been proposed that the interaction of nucleolin with the rDNA sequence and with nascent pre-rRNA leads to the blocking of RNA polymerase I (RNA pol I) transcription. To test this model and to get molecular insights into the role of nucleolin in RNA pol I transcription, we studied the function of nucleolin in Xenopus oocytes. We show that injection of a 2-4-fold excess of Xenopus or hamster nucleolin in stage VI Xenopus oocytes reduces the accumulation of 40 S pre-rRNA 3-fold, whereas transcription by RNA polymerase II and III is not affected. Direct analysis of rDNA transcription units by electron microscopy reveals that the number of polymerase complexes/rDNA unit is drastically reduced in the presence of increased amounts of nucleolin and corresponds to the level of reduction of 40 S pre-rRNA. Transcription from DNA templates containing various combinations of RNA polymerase I or II promoters in fusion with rDNA or CAT sequences was analyzed in the presence of elevated amounts of nucleolin. It was shown that nucleolin leads to transcription repression from a minimal polymerase I promoter, independently of the nature of the RNA sequence that is transcribed. Therefore, we propose that nucleolin affects RNA pol I transcription by acting directly on the transcription machinery or on the rDNA promoter sequences and not, as previously thought, through interaction with the nascent pre-rRNA.

Animals↗
PubMed1985

Subdivision of the acute non-lymphoblastic leukaemias by measurement of the relative abundance of a specific RNA sequence.

A recombinant plasmid library representing the more abundant polyadenylated RNA of a relapsed acute myelomonocytic leukaemic (FAB class M4) has been constructed. One recombinant, designated pAM6, contains a DNA sequence complementary to an RNA of about 1100 nucleotides in length. The relative concentrations of pAM6 RNA in the RNAs from cloned human haematopoietic cell lines and from fractionated leukaemic leukocytes and normal bone marrow cells, measured by an RNA dot hybridization method, indicated that pAM6 RNA occurs in myeloid cells, probably those of the monocyte lineage at the earlier stages in differentiation. Similar assays showed that pAM6 RNA could not be detected in the peripheral blood leukocytes of normal individuals, or of ALL and CLL patients, but that the relative abundance of pAM6 RNA varied widely in leukocytes from CGL chronic phase, CGL acute phase, and ANLL. No correlation between pAM6 RNA occurrence and FAB classification of ANLL could be made; thus it would appear that the relative abundance of pAM6 RNA in ANLL leukocytes can be used to subdivide the ANLLs in a novel manner. It is suggested that this criterion, in conjunction with existing diagnostic markers, may provide a subclassification of the ANLLs that could be of some prognostic and therapeutic value.

Acute Disease↗
PubMed1990

Efficient site-specific cleavage by RNase MRP requires interaction with two evolutionarily conserved mitochondrial RNA sequences.

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.

Animals↗
PubMed2004

RNA sequences in the Moloney murine leukemia virus genome bound by the Gag precursor protein in the yeast three-hybrid system.

Encapsidation of the Moloney murine leukemia virus (MMLV) genome is mediated through a specific interaction between the major viral structural protein, Gag, and an RNA packaging signal, Psi. Many studies have investigated this process in vivo, although the specific examination of the Gag-RNA interaction in this context is difficult due to the variety of other viral functions involved in virion assembly in vivo. The Saccharomyces cerevisiae three-hybrid assay was used to directly examine the interaction between MMLV Gag and Psi. In this system, MMLV RNA regions exhibiting high-affinity Gag binding were mapped. All Gag-binding regions were located 3' to the viral splice donor sequence of the viral RNA transcript. No single short RNA sequence within Psi supported strong Gag interaction. Instead, an RNA comprised of nearly the entire Psi region was necessary to demonstrate an appreciable Gag interaction in the yeast three-hybrid system. These finding support the notion that two stem-loops (C and D) are not sufficient to form a core MMLV encapsidation signal.

Amino Acid Sequence↗
PubMedDate not supplied

RNA-sequence-mediated gene regulation in HIV-1.

The quantity and quality of human immunodeficiency virus type 1 (HIV-1) gene expression is controlled in large part by the action of two small nuclear viral regulatory proteins termed Tat and Rev. Tat is unique among transcriptional trans-activators in that it acts via a structured RNA target sequence, termed TAR, to induce high levels of transcription from the HIV-1 long terminal repeat promoter element. The activity of the viral Rev protein is also unprecedented in that this protein functions to induce the nuclear export of a specific class of viral RNA species that are otherwise sequestered in the nucleus by the action of cellular factors. Like Tat, Rev also interacts with a highly specific cis-acting target sequence termed, in this case, the Rev Response Element. In this review, I provide an outline of our current understanding of the roles and mechanisms of action of these two novel RNA-sequence-dependent regulatory proteins.

Base Sequence↗
PubMed1982

The 3' terminal RNA sequences of bunyaviruses and nairoviruses (Bunyaviridae): evidence of end sequence generic differences within the virus family.

The 3' terminal nucleotide sequences of the three virus RNA species of viruses representing eight serogroups of bunyaviruses (genus Bunyavirus, Bunyaviridae) and six serogroups of nairoviruses (genus Nairovirus, Bunyaviridae) have been characterized. Members of the Bunyavirus genus have conserved 3' end sequences (generally, 3' UCAUCACAUGA...) that differ from the conserved 3' end sequences of members of the Nairovirus genus (generally, 3' AGAGUUUCU...).

Base Sequence↗