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Long non-coding RNA KCNQ1 opposite strand/antisense transcript 1, a potential biomarker for glaucoma, accelerates glaucoma progression via microRNA-93-5p/Homeobox box 3 axis

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ELECTRONIC JOURNAL OF BIOTECHNOLOGY 2024年 67卷 23-33页

作者： Xie, ZhaoLian Wang, Hui Liu, LinLin Zhang, HaiQing Liu, Jing First Affiliated Hosp Affiliated Hosp 1 Dept Hepatobiliary & Pancreat Surg Ganzhou City 341000 Jiangxi Peoples R China

Background: Glaucoma is marked by retinal neuron death in the ganglion cell layer, leading to irreversible vision loss. Aberrant long non-coding RNA (lncRNA) expression is associated with glaucoma. The study was to explore the latent molecular mechanism of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in N-methyl-D-aspartate (NMDA)-stimulated ***: The data demonstrated that KCNQ1OT1 expression was elevated in glaucoma patients, serving as a diagnostic biomarker of glaucoma. Rats injected with NMDA developed visual loss and retinopathy and expressed high KCNQ1OT1. After treating retinal ganglion cells (RGCs) with NMDA, cell proliferation was suppressed and apoptosis was augmented. Silenced KCNQ1OT1 or HOXB3 or elevated miR-93-5p alleviated NMDA-induced suppression of RGC growth. KCNQ1OT1 mediated miR-93-5p expression by targeting homeobox box 3 (HOXB3). The protection of silenced KCNQ1OT1 in NMDA-treated RGCs was turned around by elevated HOXB3. Conclusions: Overall, KCNQ1OT1 accelerates glaucoma progression via miR-93-5p/HOXB3 *** to cite: Xie ZL, Wang H, Liu LL, et al. Long non-coding RNA KCNQ1 opposite strand/antisense transcript 1, a potential biomarker for glaucoma, accelerates glaucoma progression via microRNA-93-5p/ Homeobox box 3 axis. Electron J Biotechnol 2024;67 . https://***/10.1016/***.2023.10.002.(c) 2023 The Authors. Pontificia Universidad Catolica de Valparaiso. Production and hosting by Elsevier B. V. This is an open access article under the CC BY-NC-ND license (http://***/licenses/by-nc-nd/4.0/).

关键词： antisense transcript Biomarkers Glaucoma Homeobox box 3 Long non-coding RNA MicroRNA-93-5p Neurodegenerative disease Ophthalmic testing Opposite strand Retinal ganglion cells Risk factor

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A Novel ATM antisense transcript ATM-AS Positively Regulates ATM Expression in Normal and Breast Cancer Cells

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Current Medical Science 2022年第4期42卷 681-691页

作者： He CHENG Er-shao ZHANG Xiao SHI Ping-ping CAO Bei-jing PAN Xin-xin SI Yue LIU Nan YANG Ying CHU Xu-chun WANG Xiao HAN Zhi-hong ZHANG Yu-jie SUN Key Laboratory of Human Functional Genomics of Jiangsu Province Nanjing Medical UniversityNanjing 210000China Department of Pathology the First Affiliated Hospital of Nanjing Medical UniversityNanjing 210000China Key Laboratory of Cancer Biomarkers Prevention and TreatmentCollaborative Innovation Center for Personalized Cancer MedicineNanjing Medical UniversityNanjing 210000China Department of Cell Biology Nanjing Medical UniversityNanjing 210000China

Objective:The ataxia telangiectasia mutated(ATM)gene is a master regulator in cellular DNA damage *** dysregulation of ATM expression is frequent in breast cancer,and is known to be involved in the carcinogenesis and prognosis of ***,the underlying mechanism remains *** bioinformatic analysis predicted a potential antisense transcript ATM-antisense(AS)from the opposite strand of the ATM *** purpose of this study was to identify ATM-AS and investigate the possible effect of ATM-AS on the ATM gene ***:Single strand-specific RT-PCR was performed to verify the predicted antisense transcript ATM-AS within the ATM gene ***-PCR and Western blotting were used to detect the expression levels of ATM-AS and ATM in normal and breast cancer cell lines as well as in tissue *** reporter gene assays,biological mass spectrometry,ChIP-qPCR and RIP were used to explore the function of ATM-AS in regulating the ATM *** and host-cell reactivation(HCR)assay were performed to evaluate the biological significance of ATM-AS in ATM-mediated DNA damage *** cancer tissue samples were used for evaluating the correlation of the ATM-AS level with the ATM expression as well as prognosis of the ***:The ATM-AS significantly upregulated the ATM gene activity by recruiting KAT5 histone acetyltransferase to the gene *** reduced ATM-AS level led to the abnormal downregulation of ATM expression,and impaired the ATM-mediated DNA damage repair in normal breast cells in *** ATM-AS level was positively correlated with the ATM expression in the examined breast cancer tissue samples,and the patient ***:The present study demonstrated that ATM-AS,an antisense transcript located within the ATM gene body,is an essential positive regulator of ATM expression,and functions by mediating the binding of KAT5 to the ATM *** findings uncover the novel mechanism und

关键词： antisense transcript ataxia telangiectasia mutated ataxia telangiectasia mutatedantisense breast cancer KAT5

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Regulation of human Mcl-1 by a divergently-expressed antisense transcript

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GENE 2020年 762卷 145016-145016页

作者： Rad, S. M. Ali Hosseini Tan, Grace Min Yi Poudel, Aarati He, Kevin McLellan, Alexander D. Univ Otago Dept Microbiol & Immunol Dunedin 9010 Otago New Zealand

Mcl-1 is a member of the Bcl-2 anti-apoptotic protein family with important roles in the development, lifespan and metabolism of lymphocytes, as well as oncogenesis. Mcl-1 displays the shortest half-life of all Bcl-2 family members, with miRNA interference and proteasomal degradation being major pathways for Mcl-1 downregulation. In this study, we have identified a previously undescribed control mechanism active at the RNA level. A divergently transcribed lncRNA LOC107985203 (named here mcl1-AS1) negatively modulated Mcl-1 expression resulting in downregulation of Mcl-1 at both mRNA and protein level in a time-dependent manner. Using reporter assays, we confirmed that the mcl1-AS1 lncRNA promoter was located within Mcl-1 coding region. We next placed mcl1-AS1 under tetracycline-inducible control and demonstrated decreased viability in HEK293 cells upon doxycycline induction. Inhibition of mcl1-AS1 with shRNA reversed drug sensitivity. Bioinformatics surveys predicted direct mcl1-AS1 lncRNA binding to Mcl-1 transcripts, suggesting its mechanism in Mcl-1 expression is at the transcriptional level, consistent with a common role for anti-sense transcripts. The identification of a bi-directional promoter and lncRNA controlling Mcl-1 expression will have implications for controlling Mcl-1 activity in cancer cells, or for the purpose of enhancing the lifespan and quality of anti-cancer T lymphocytes.

关键词： Long non-coding RNA LOC107985203 Mcl-1 antisense transcript

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Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2016年第48期113卷 E7846-E7855页

作者： Fedak, Halina Palusinska, Malgorzata Krzyczmonik, Katarzyna Brzezniak, Lien Yatusevich, Ruslan Pietras, Zbigniew Kaczanowski, Szymon Swiezewski, Szymon Inst Biochem & Biophys Dept Prot Biosynth PL-02106 Warsaw Poland Inst Biochem & Biophys Dept Bioinformat PL-02106 Warsaw Poland

Seed dormancy is one of the most crucial process transitions in a plant's life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1). DOG1 is the major quantitative trait locus for seed dormancy in Arabidopsis and has been shown to control dormancy in many other plant species. This is reflected by the evolutionary conservation of the functional short alternatively polyadenylated form of the DOG1 mRNA. Notably, the 3' region of DOG1, including the last exon that is not included in this transcript isoform, shows a high level of conservation at the DNA level, but the encoded polypeptide is poorly conserved. Here, we demonstrate that this region of DOG1 contains a promoter for the transcription of a noncoding antisense RNA, asDOG1, that is 5' capped, polyadenylated, and relatively stable. This promoter is autonomous and asDOG1 has an expression profile that is different from known DOG1 transcripts. Using several approaches we show that asDOG1 strongly suppresses DOG1 expression during seed maturation in cis, but is unable to do so in trans. Therefore, the negative regulation of seed dormancy by asDOG1 in cis results in allele-specific suppression of DOG1 expression and promotes germination. Given the evolutionary conservation of the asDOG1 promoter, we propose that this cis-constrained noncoding RNA-mediated mechanism limiting the duration of seed dormancy functions across the Brassicaceae.

关键词： seed dormancy DOG1 gene cis-acting ncRNA antisense transcript

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Long noncoding RNA FGFR3-AS1 promotes osteosarcoma growth through regulating its natural antisense transcript FGFR3

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MOLECULAR BIOLOGY REPORTS 2016年第5期43卷 427-436页

作者： Sun, Jiabing Wang, Xuming Fu, Chunjiang Wang, Xiaoyu Zou, Jilong Hua, Hanbing Bi, Zhenggang Harbin Med Univ Dept Orthoped Affiliated Hosp 1 23 Youzheng St Harbin 150001 Heilongjiang Peoples R China

Long noncoding RNAs (lncRNAs), a new class of RNAs with no protein-coding potential, have been reported to have crucial roles in the regulation of a variety of tumors. However, the functions and molecular mechanisms of lncRNAs to osteosarcoma are still largely unknown. The purpose of this study is to examine the expression, functions and molecular mechanisms of a new lncRNA FGFR3 antisense transcript 1 (FGFR3-AS1) in osteosarcoma. The expression of FGFR3-AS1 was examined by real-time quantitative PCR. The regulation of FGFR3 by FGFR3-AS1 was examined by RNase protection assay, real-time quantitative PCR, western blotting, and luciferase reporter assay. The effects of FGFR3-AS1 on osteosarcoma cell proliferation and cell cycle were determined by Cell Counting Kit-8, Ethynyl deoxyuridine incorporation assay and flow cytometry. FGFR3-AS1 was upregulated in osteosarcoma. Increased FGFR3-AS1 expression correlates with large tumor size, advanced Enneking stage, metastasis and poor survival. Through antisense pairing with FGFR3 3'UTR, FGFR3-AS1 increases FGFR3 mRNA stability and upregulates FGFR3 expression. The expression of FGFR3-AS1 and FGFR3 is positively correlated in osteosarcoma tissues. Knockdown of FGFR3-AS1 inhibits the proliferation and cell cycle progression of osteosarcoma cells in vitro. Moreover, knockdown of FGFR3-AS1 inhibits xenograft tumor growth of osteosarcoma cells in vivo. These data demonstrate the mechanisms of how antisense noncoding RNA regulate the expression of sense genes, and show the pivotal functions of FGFR3-AS1 in osteosarcoma.

关键词： Osteosarcoma Long noncoding RNA antisense transcript Proliferation

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H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast

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BMC GENOMICS 2015年第1期16卷 1-11页

作者： Gu, Muxin Naiyachit, Yanin Wood, Thomas J. Millar, Catherine B. Univ Manchester Fac Life Sci Manchester M13 9PT Lancs England

Background: The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. Results: We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in budding yeast, where it co-localises with histone marks associated with active promoters. By comparing H2A.Z binding to global gene expression in budding yeast strains engineered so that normally unstable transcripts are abundant, we show that H2A.Z is required for normal levels of antisense transcripts as well as sense ones. High levels of H2A.Z at antisense promoters are associated with decreased antisense transcript levels when H2A.Z is deleted, indicating that H2A.Z has an activating effect on antisense transcripts. Decreases in antisense transcripts affected by H2A.Z are accompanied by increased levels of paired sense transcripts. Conclusions: The effect of H2A.Z on protein coding gene expression is a reflection of its importance for normal levels of both sense and antisense transcripts.

关键词： antisense transcript Chromatin H2A.Z Histone variant Htz1

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RAG-seq:NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells

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Genomics, Proteomics & Bioinformatics 2024年第5期22卷 73-84页

作者： Ping Xu Zhiheng Yuan Xiaohua Lu Peng Zhou Ding Qiu Zhenghao Qiao Zhongcheng Zhou Li Guan Yongkang Jia Xuan He Ling Sun Youzhong Wan Ming Wang Yang Yu China-Japan Union Hospital of Jilin University Jilin UniversityChangchun 130033China School of Life Sciences Jilin UniversityChangchun 130012China Guangzhou Women and Children's Medical Center Guangzhou Medical UniversityGuangzhou 510623China Institute of Biophysics Chinese Academy of SciencesBeijing 100101China Center for Reproductive Medicine Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhou 510623China

Single-cell RNA sequencing(scRNA-seq)has transformed our understanding of cellular diversity with unprecedented ***,many current methods are limited in capturing full-length transcripts and discerning strand ***,we present RAG-seq,an innovative strand-specific total RNA sequencing technique that combines not-so-random(NSR)primers with Tn5 transposase-mediated ***-seq overcomes previous limitations by delivering comprehensive transcript coverage and maintaining strand orientation,which are essential for accurate quantification of overlapping genes and detection of antisense *** optimized reverse transcription with oligo-dT primers,rRNA depletion via Depletion of Abundant Sequences by Hybridization(DASH),and linear amplification,RAG-seq enhances sensitivity and reproducibility,especially for low-input samples and single *** to mouse oocytes and early embryos highlights RAG-seq's superior performance in identifying stage-specific antisense transcripts,shedding light on their regulatory roles during early *** advancement represents a significant leap in transcriptome analysis within complex biological contexts.

关键词： antisense transcript Full-length Mouse early embryonic development Single-cell RNA sequencing Strand-specific

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Timing without coding: How do long non-coding RNAs regulate circadian rhythms

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SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY 2022年 126卷 79-86页

作者： Mosig, Rebecca A. Kojima, Shihoko Virginia Tech Fralin Life Sci Inst Dept Biol Sci 1015 Life Sci Circle Blacksburg VA 24061 USA

Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and demonstrated that lncRNAs regulate core clock genes and the core clock machinery in mammals. In this review, we provide an overview of our current understanding of how lncRNAs regulate the circadian clock without coding a protein. We also offer additional insights into the challenges in understanding the functions of lncRNAs and other unresolved questions in the field. We do not cover other regulatory ncRNAs even though they also play important roles;readers are highly encouraged to refer to other excellent reviews on this topic.

关键词： Long non-coding RNA antisense transcript Circadian rhythms Molecular clock

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Exogenous and endogenous dsRNAs perceived by plant Dicer-like 4 protein in the RNAi-depleted cellular context

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CELLULAR & MOLECULAR BIOLOGY LETTERS 2023年第1期28卷 64-64页

作者： Leonetti, Paola Consiglio, Arianna Arendt, Dennis Golbik, Ralph Peter Rubino, Luisa Gursinsky, Torsten Behrens, Sven-Erik Pantaleo, Vitantonio CNR Inst Sustainable Plant Protect Dept Biol Agr & Food Sci Bari Unit Bari Italy CNR Inst Biomed Technol Dept Biomed Sci Bari Unit Bari Italy Martin Luther Univ Halle Wittenberg Inst Biochem & Biotechnol Sect Microbial Biotechnol Halle An Der Saale Germany

Background: In plants, RNase III Dicer-like proteins (DCLs) act as sensors of dsRNAs and process them into short 21- to 24-nucleotide (nt) (s)RNAs. Plant DCL4 is involved in the biogenesis of either functional endogenous or exogenous (i.e. viral) short interfering (si)RNAs, thus playing crucial antiviral roles. Methods: In this study we expressed plant DCL4 in Saccharomyces cerevisiae, an RNAi-depleted organism, in which we could highlight the role of dicing as neither Argonautes nor RNA-dependent RNA polymerase is present. We have therefore tested the DCL4 functionality in processing exogenous dsRNA-like substrates, such as a replicase-assisted viral replicon defective-interfering RNA and RNA hairpin substrates, or endogenous antisense transcripts. Results: DCL4 was shown to be functional in processing dsRNA-like molecules in vitro and in vivo into 21- and 22-nt sRNAs. Conversely, DCL4 did not efficiently process a replicase-assisted viral replicon in vivo, providing evidence that viral RNAs are not accessible to DCL4 in membranes associated in active replication. Worthy of note, in yeast cells expressing DCL4, 21- and 22-nt sRNAs are associated with endogenous loci. Conclusions: We provide new keys to interpret what was studied so far on antiviral DCL4 in the host system. The results all together confirm the role of sense/antisense RNA-based regulation of gene expression, expanding the sense/antisense atlas of S. cerevisiae. The results described herein show that S. cerevisiae can provide insights into the functionality of plant dicers and extend the S. cerevisiae tool to new biotechnological applications.

关键词： RNAi Yeast Plant viruses DCL4 dsRNAs antisense transcript Short RNAs

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Differential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcripts

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ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023年第4期113卷 e22026-e22026页

作者： Aydemir, Habes Bilal Aydemir, Merve Nur Korkmaz, Ertan Mahir Tokat Gaziosmanpasa Univ Fac Sci & Letters Dept Mol Biol & Genet Tokat Turkiye Sivas Cumhuriyet Univ Fac Sci Dept Mol Biol & Genet Sivas Turkiye

The transcription of the mitogenome shows a unique pattern that is both similar to and different from the nuclear and bacterial patterns. Mitochondrial transcription generates five polycistronic units from three promoters in Drosophila melanogaster, and different expression levels of genes were observed in both different and, interestingly, the same polycistronic units in D. melanogaster. This study was conducted to test this phenomenon in the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae). RNA isolation and DNase digestion were performed using only one whole individual, and real-time polymerase chain reaction analyses were performed with complementary DNAs of 11 gene regions using gene-specific primers. It was found that the expression level of each gene exhibited differences from each other, and some genes (e.g., cox genes, and rrnS) were interestingly expressed at significant levels in the corresponding antisense chain. Additionally, the mitogenome of S. parreyssi was found to have the capacity to encode 169 additional peptides from 13 known protein-coding genes, most of which were encoded in antisense transcript units. One of the unique findings was a potential open reading frame sequence that was potentially encoded in the antisense rrnL gene and included a conserved cox3 domain.

关键词： antisense transcript differential gene expression Hymenoptera lncRNAs mitochondrial gene expression Syrista parreyssi

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