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Journal of Plant Physiology Apr 2022Thylakoid formation1 (Thf1), encoded by sll1414 (thf1), is a multifunctional protein conserved in all photosynthetic organisms. thf1 expression is highly induced by high...
Thylakoid formation1 (Thf1), encoded by sll1414 (thf1), is a multifunctional protein conserved in all photosynthetic organisms. thf1 expression is highly induced by high light in Synechocystis during photosynthesis-related stress. In this study, differential RNA sequencing analysis of the Synechocystis sp. PCC 6803 revealed a small antisense RNA (asRNA) gene located on the reverse-complementary strand of the thf1 gene. The full length of this asRNA (designated ThfR) was determined by 5' and 3' RACE analysis. The accumulation of thf1 mRNA was up-regulated synchronously with the ThfR level during survival after high-light stress or nitrogen starvation. Under nitrogen starvation or high-light stress, compared with the wild type, a ThfR overexpression mutant demonstrated relatively more Thf1 protein content, while a ThfR reduced-expression mutant accumulated less Thf1 protein. Furthermore, the overexpression of ThfR enhanced the electron transport rate and the proliferation of cyanobacteria under high-light stress. These results, which we confirmed further using an Escherichia coli sRNA expression platform, suggest that the thf1 gene is positively regulated by ThfR, possibly through protection of the RAUUW element at the RNase E cleavage site. This study represents the first report, to our knowledge, of a cis-transcript antisense RNA that targets thf1 in Synechocystis sp. PCC 6803 and provides evidence that ThfR regulates photosynthesis by positively modulating thf1 under high-light conditions.
Topics: Bacterial Proteins; Light; Photosynthesis; RNA, Antisense; RNA, Messenger; Synechocystis; Thylakoids
PubMed: 35193088
DOI: 10.1016/j.jplph.2022.153642 -
Genes May 2021The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are...
The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of . The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.
Topics: Alternative Splicing; CCCTC-Binding Factor; DNA Methylation; Histone Code; Humans; Jurkat Cells; Leukocyte Common Antigens; Protein Binding; Pseudogenes; RNA, Antisense
PubMed: 34067766
DOI: 10.3390/genes12050759 -
Antisense & Nucleic Acid Drug... Aug 1997Antisense nucleic acids comprise short-chain synthetic oligonucleotides, often oligodeoxyribonucleotides (ODN) of less than approximately 30 nucleotides and... (Review)
Review
Antisense nucleic acids comprise short-chain synthetic oligonucleotides, often oligodeoxyribonucleotides (ODN) of less than approximately 30 nucleotides and substantially longer sequences formed by ribonucleic acids (RNA). Both groups differ with respect to several properties, including their generation, the mode of delivery, and their structure-function relationship. Long-chain antisense RNA transcribed in vitro or endogenously from recombinant genes fold into three-dimensional structures. The pairing reaction with their complementary target strand occurs via largely unknown annealing mechanisms and, depending on the phylogenetic cellular background, in different cellular compartments. The annealing pathway is influenced by a variety of biologic and biochemical parameters that are as yet poorly understood. However, the basal biochemical mechanisms underlying the relationship between RNA structure and efficient annealing could allow one to derive more general rules for the design of in vivo effective antisense RNA in a way that is not dependent on specific cell types. Here, some of the criteria are discussed that are currently thought to have major impact on the design of long-chain antisense RNA.
Topics: Animals; Drug Design; Genome, Viral; HIV-1; Humans; Kinetics; Models, Chemical; Nucleic Acid Conformation; Oligonucleotides, Antisense; RNA, Antisense; RNA, Catalytic; Recombination, Genetic; Transcription, Genetic
PubMed: 9303196
DOI: 10.1089/oli.1.1997.7.439 -
FEBS Letters Jun 2004Eukaryotes regulate gene expression in a number of different ways. On a daily and seasonal timescale, the orchestration of gene expression is to a large extent governed... (Review)
Review
Eukaryotes regulate gene expression in a number of different ways. On a daily and seasonal timescale, the orchestration of gene expression is to a large extent governed by circadian clocks. These endogenous timekeepers enable organisms to prepare for predictable environmental conditions from one day to the next and thus allow adaptation to a given temporal niche. In general, circadian clocks have been shown to employ the classical transcriptional and posttranscriptional control mechanisms to generate rhythmicity. However, the discovery of antisense clock gene transcripts suggests that mechanisms of gene regulation operating through antisense RNA may also be integral to the circadian clockwork. Following a brief history of the impact of genetic and molecular techniques in aiding our understanding of circadian clocks, this review concentrates on the few examples of antisense clock gene transcripts so far investigated and their effect on circadian timing.
Topics: Animals; Circadian Rhythm; Drosophila; Gene Expression Regulation; Models, Biological; Models, Genetic; Neurospora; Oligonucleotides, Antisense; RNA; RNA Processing, Post-Transcriptional; RNA, Antisense; RNA, Messenger; Time Factors
PubMed: 15165892
DOI: 10.1016/j.febslet.2004.04.073 -
Molekuliarnaia Genetika, Mikrobiologiia... Aug 1990The data on the effects of antisense RNA in plants is reviewed. Results of expression of the genes for selective markers, antisense reporter genes, functioning and viral... (Review)
Review
The data on the effects of antisense RNA in plants is reviewed. Results of expression of the genes for selective markers, antisense reporter genes, functioning and viral genes are analyzed. The molecular mechanisms for inhibiting effects of antisense RNA and the potential use of the phenomenon in the plants biotechnology are discussed. The formation of long duplexes between the antisense RNA and messenger RNA are supposed to be irrelevant to suppression of gene expression in plants by the antisense RNA.
Topics: Genetic Engineering; Plants; RNA, Antisense
PubMed: 2233788
DOI: No ID Found -
Human Molecular Genetics Sep 2014Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements... (Review)
Review
Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising from what was previously thought to be 'junk DNA'. Roughly defined as non-coding regulatory RNA transcribed from the opposite strand of a coding gene locus, NATs are proving to be a heterogeneous group with high potential for therapeutic application. Here, we attempt to summarize the rapidly growing knowledge about this important non-coding RNA subclass.
Topics: Gene Expression; Gene Targeting; Genome; Humans; RNA, Antisense; RNA, Untranslated; Transcription, Genetic
PubMed: 24838284
DOI: 10.1093/hmg/ddu207 -
Trends in Genetics : TIG Jul 1991One of the two major classes of regulatory strategies that control plasmid copy number involves recognition via base pairing between two plasmid-encoded complementary... (Review)
Review
One of the two major classes of regulatory strategies that control plasmid copy number involves recognition via base pairing between two plasmid-encoded complementary RNAs. The detailed analysis of this control circuitry has revealed some features of regulatory mechanisms based on RNA-RNA interaction that distinguish them from those based on protein-nucleic acid interaction. These features provide a framework with which to understand other regulatory mechanisms based on RNA-RNA interaction, and will aid in the design of efficient artificial antisense RNA systems.
Topics: Bacterial Proteins; Bacteriocin Plasmids; DNA Replication; DNA, Bacterial; Gene Amplification; RNA, Antisense; RNA-Binding Proteins
PubMed: 1887504
DOI: 10.1016/0168-9525(91)90370-6 -
Biochimie Dec 2020Ephrin type-A receptor 2 (EPHA2) is a receptor tyrosine kinase (RTK), whose over-expression has been observed in a variety of cancers, including breast cancer. EPHA2...
Ephrin type-A receptor 2 (EPHA2) is a receptor tyrosine kinase (RTK), whose over-expression has been observed in a variety of cancers, including breast cancer. EPHA2 expression may be causally related to tumorigenesis; therefore, it is important to understand how EPHA2 gene (EPHA2) expression is regulated. Here, we report that EPHA2 antisense RNA (EPHA2-AS), a natural antisense transcript, is an important modulator of EPHA2 mRNA levels. EPHA2-AS is a ∼1.8 kb long non-coding RNA (lncRNA) with a poly(A) tail that encodes two splice variants, EPHA2-AS1/2. They are constitutively expressed in a concordant manner with EPHA2 mRNA in human breast adenocarcinoma cell lines and in patient samples, with the highest levels detected in the triple-negative breast cancer (TNBC) subtype. The silencing of EPHA2-AS1/2 by a sense oligonucleotide or over-expression of an antisense oligoribonucleotide, which were both designed from the EPHA2 mRNA region (nt 2955-2974) targeted by AS1/2, showed that EPHA2-AS1/2 modulated EPHA2 mRNA levels by interacting with the specific AS1/2-complementary region in the mRNA. The EPHA2-AS1/2 did not prevent microRNAs from acting on the relevant microRNA response elements shared by EPHA2-AS1/2 and EPHA2 mRNA. Our studies demonstrate a crucial role played by EPHA2-AS1/2 in modulating EPHA2 mRNA levels, and hence production of EPHA2 protein, a key oncogenic RTK that contributes to the tumorigenesis of TNBC cells.
Topics: Cell Line, Tumor; Ephrin-A2; Female; Gene Expression Regulation, Neoplastic; Gene Silencing; Humans; MicroRNAs; RNA, Antisense; RNA, Long Noncoding; RNA, Messenger; Receptor, EphA2; Response Elements; Triple Negative Breast Neoplasms
PubMed: 33022313
DOI: 10.1016/j.biochi.2020.10.002 -
Clinica Chimica Acta; International... Apr 2020More and more evidence indicates that long non-coding RNAs (lncRNAs), as a kind of non-coding endogenous single-stranded RNA, play an essential role as oncogenes or... (Review)
Review
More and more evidence indicates that long non-coding RNAs (lncRNAs), as a kind of non-coding endogenous single-stranded RNA, play an essential role as oncogenes or tumour suppressors in the occurrence and development of human cancers. The tumour protein P73 antisense RNA 1 (TP73-AS1) was initially found to be down-regulated in oligodendroglioma and may act as a non-protein-encoding RNA. Since its discovery, TP73-AS1 has been identified as a carcinogenic regulator of many malignancies. At the same time, the high expression of TP73-AS1 is related to the clinicopathological features of patients with cancer. It also regulates cell proliferation, anti-apoptosis, invasion and metastasis through a variety of potential mechanisms, suggesting that it may be a promising biomarker and therapeutic target for cancer. In this review, we summarize the biological functions, mechanisms, and potential clinical implications of TP73-AS1 dysregulation in tumourigenesis and progression.
Topics: Apoptosis; Carcinogenesis; Cell Proliferation; Disease Progression; Humans; Neoplasm Invasiveness; Neoplasms; RNA, Antisense; RNA, Long Noncoding; Tumor Protein p73
PubMed: 31978409
DOI: 10.1016/j.cca.2019.12.025 -
RNA (New York, N.Y.) Apr 2005The recent identification of antisense RNA in the transcriptomes of many eukaryotes has generated enormous interest. The presence of antisense RNA in Plasmodium...
The recent identification of antisense RNA in the transcriptomes of many eukaryotes has generated enormous interest. The presence of antisense RNA in Plasmodium falciparum, the causative agent of severe malaria, remains controversial. Elucidation of the mechanism of antisense RNA in P. falciparum synthesis is critical in order to demonstrate the origin and function of these transcripts. Therefore, a systematic analysis of antisense and sense RNA synthesis was performed using direct labeling experiments. Nuclear run on experiments with single-stranded DNA probes demonstrated that antisense RNA is synthesized in the nucleus at several genomic loci. Antisense RNA synthesis is sensitive to the potent RNA polymerase II inhibitor alpha-amanitin. Antisense and sense transcription was also detected in nuclei isolated from synchronized parasites, suggesting concurrent synthesis. In summary, our experiments directly demonstrate that antisense RNA synthesis is a common transcriptional phenomenon in P. falciparum, and is catalyzed by RNA polymerase II.
Topics: Animals; Blotting, Southern; DNA, Single-Stranded; Plasmodium falciparum; RNA Polymerase II; RNA, Antisense; RNA, Protozoan; Transcription, Genetic
PubMed: 15703443
DOI: 10.1261/rna.7940705