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Evidence for further non-coding rna genes in the fungal rDNA region

MYCOKEYS 2022年第90期90卷 203-213页

作者： Rosenblad, Magnus Alm Larsson, Ellen Walker, Arttapon Thongklang, Naritsada Wurzbacher, Christian Nilsson, R. Henrik Univ Gothenburg Dept Chem & Mol Biol Lundberg Lab Natl Infrastructure Bioinformat NBIS Gothenburg Sweden Univ Gothenburg Gothenburg Global Biodivers Ctr Dept Biol & Environm Sci Box 461 S-40530 Gothenburg Sweden Mae Fah Luang Univ Ctr Excellence Fungal Res Chiang Rai 57100 Thailand Mae Fah Luang Univ Sch Sci Chiang Rai 57100 Thailand Tech Univ Munich Chair Urban Water Syst Engn Coulombwall 3 D-85748 Garching Germany

non-coding rna (ncrna) genes play important, but incompletely understood, roles in various cellular processes, notably translation and gene regulation. A recent report on the detection of the ncrna Signal Recognition Particle gene in the nuclear ribosomal internal transcribed spacer region of several species of three genera of ectomycorrhizal basidiomycetes prompted a more thorough bioinformatics search for additional ncrna genes in the full fungal ribosomal operon. This study reports on the detection of three ncrna genes hitherto not known from the fungal ribosomal region: nuclear rnase P rna, rnase MRP rna, and a possible snorna U14 in a total of five species ofAuricularia and Inocybe. We verified their presence through resequencing of independent specimens. Two completedAuricularia genomes were found to lack these ncrnas elsewhere than in the ribosomal operon, suggesting that these are functional genes. It seems clear that ncrna genes play a larger role in fungal ribosomal genetics than hitherto thought.

关键词： Basidiomycetes IGS ITS MRP non-coding rna rnase MRP rnase P SRP

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A New rna-Seq Method to Detect the Transcription and non-coding rna in Prostate Cancer

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PATHOLOGY & ONCOLOGY RESEARCH 2014年第1期20卷 43-50页

作者： Zhang, Xiao-Ming Ma, Zhong-Wei Wang, Qiang Wang, Jian-Ning Yang, Ji-Wei Li, Xian-Duo Li, Hao Men, Tong-Yi Shandong Univ Dept Urol Qianfoshan Hosp Jinan 250014 Shandong Peoples R China Hosp Shandong Aluminum Corp Dept Urol Zibo 255069 Peoples R China Chinese Peoples Liberat Army Dept Urol Hosp 309 Beijing 100091 Peoples R China

Prostate cancer is a big killer in many regions especially American men, and this year, the diagnosed rate rises rapidly. We aimed to find the biomarker or any changing in prostate cancer patients. With the development of next generation sequencing, much genomic alteration has been found. Here, basing on the rna-seq result of human prostate cancer tissue, we tried to find the transcription or non-coding rna expressed differentially between normal tissue and prostate cancer tissue. 10 T sample data is the rna-seq data for prostate cancer tissue in this study, we found the differential gene is TFF3-Trefoil factor 3, which was more than seven fold change from prostate cancer tissue to normal tissue, and the most outstanding transcript is C15orf21. Additionally, 9 lncrnas were found according our method. Finally, we found the many important non-coding rna related to prostate cancer, some of them were long non-coding rna (lncrna).

关键词： Prostate cancer rna-seq Transcription non-coding rna lncrna

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The long intergenic non-coding rna CCR492 functions as a let-7 competitive endogenous rna to regulate c-Myc expression

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BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016年第10期1859卷 1322-1332页

作者： Maldotti, Mara Incarnato, Danny Neri, Francesco Krepelova, Anna Rapelli, Stefania Anselmi, Francesca Parlato, Caterina Basile, Giulia Dettori, Daniela Calogero, Raffaele Oliviero, Salvatore Univ Torino Dipartimento Sci Vita & Biol Sistemi Via Accademia Albertina 13 I-10123 Turin Italy Human Genet Fdn HuGeF Via Nizza 52 I-10126 Turin Italy Univ Torino Dipartimento Biotecnol Mol & Sci Salute Via Nizza 52 Turin Italy

In mammals the cell-cycle progression through the G1 phase is a tightly regulated process mediated by the transcriptional activation of early genes in response to mitogenic stimuli, whose dysregulation often leads to tumorigenesis. We here report the discovery by rna-seq of cell-cycle regulated (CCR) long intergenic non-coding rna5 (lincrnas), potentially involved in the control of the cell-cycle progression. We identified 10 novel lincrnas expressed in response to serum treatment in mouse embryonic fibroblasts (MEF5) and in BALB/c fibroblasts, comparably to early genes. By loss-of-function experiments we found that lincrna CCR492 is required for G1/S progression, localizes in the cell cytoplasm and contains 4 let-7 microrna recognition elements (MREs). Mechanistically, CCR492 functions as a competing endogenous rna (cerna) to antagonize the function of let-7 micrornas, leading to the de-repression of c-Myc. Moreover, we show that ectopic expression of CCR492 along with a constitutively active H-Ras promotes cell transformation. Thus, we identified a new lincrna expressed as an early gene in mammalian cells to regulate the cell-cycle progression by upregulating c-Myc expression. (C) 2016 Elsevier B.V. All rights reserved.

关键词： non-coding rna c-Myc Let-7 cerna Cell cycle

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Advancing Pan-cancer Gene Expression Survial Analysis by Inclusion of non-coding rna

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rna BIOLOGY 2020年第11期17卷 1666-1673页

作者： Ye, Bo Shi, Jianxin Kang, Huining Oyebamiji, Olufunmilola Hill, Deirdre Yu, Hui Ness, Scott Ye, Fei Ping, Jie He, Jiapeng Edwards, Jeremy Zhao, Ying-Yong Guo, Yan Jiaotong Univ Shanghai Chest Hosp Dept Thorac Surg Shanghai Peoples R China Univ New Mexico Comprehens Canc Ctr Albuquerque NM 87109 USA Vanderbilt Univ Med Ctr Dept Biostat Nashville TN USA Northwest Univ Sch Life Sci Key Lab Resource Biol & Biotechnol Western China Xian Shaanxi Peoples R China

non-coding rnas occupy a significant fraction of the human genome. Their biological significance is backed up by a plethora of emerging evidence. One of the most robust approaches to demonstrate non-coding rna?s biological relevance is through their prognostic value. Using the rich gene expression data from The Cancer Genome Altas (TCGA), we designed Advanced Expression Survival Analysis (AESA), a web tool which provides several novel survival analysis approaches not offered by previous tools. In addition to the common single-gene approach, AESA computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting. AESA offers survival feature selection with post-selection inference and utilizes expanded TCGA clinical data including overall, disease-specific, disease-free, and progression-free survival information. Users can analyse either protein-coding or non-coding regions of the transcriptome. We demonstrated the effectiveness of AESA using several empirical examples. Our analyses showed that non-coding rnas perform as well as messenger rnas in predicting survival of cancer patients. These results reinforce the potential prognostic value of non-coding rnas. AESA is developed as a module in the freely accessible analysis suite MutEx.

关键词： Cancer survival analysis non-coding rna lincrna pseudogene

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Epigenetic regulation of human non-coding rna gene transcription

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BIOCHEMICAL SOCIETY TRANSACTIONS 2022年第2期50卷 723-736页

作者： Morselli, Marco Dieci, Giorgio Univ Parma Dept Chem Life Sci & Environm Sustainabil Parco Area Sci 23-A I-43124 Parma Italy

Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-proteincoding (nc) rnas, including the widespread ncrna-dependent regulation of epigenetic chromatin states and of mrna translation and stability. However, despite its centrality, the epigenetic regulation of ncrna genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncrna gene transcription by the three human nuclear rna polymerases. Emerging common features, like the heterogeneity of chromatin states within ncrna multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.

关键词： chromatin DNA methylation epigenetics non-coding rna rna polymerase

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CCAT1: a pivotal oncogenic long non-coding rna in human cancers

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CELL PROLIFERATION 2016年第3期49卷 255-260页

作者： Xin, Yu Li, Zheng Shen, Jianxiong Chan, Matthew T. V. Wu, William Ka Kei Chinese Acad Med Sci Peking Union Med Coll Hosp Dept Dermatol Beijing 100042 Peoples R China Peking Union Med Coll Beijing 100042 Peoples R China Chinese Acad Med Sci Peking Union Med Coll Hosp Dept Orthoped Surg Beijing 100042 Peoples R China Chinese Univ Hong Kong Dept Anaesthesia & Intens Care Hong Kong 999077 Hong Kong Peoples R China Chinese Univ Hong Kong LKS Inst Hlth Sci State Key Lab Digest Dis Hong Kong 999077 Hong Kong Peoples R China

Long non-coding rnas (lncrnas) compose a group of non-protein-coding rnas - more than 200 nucleotides in length. Recent studies have shown that lncrnas play important roles in different cellular processes, including proliferation, differentiation, migration and invasion. Deregulation of lncrnas has been widely reported in human tumours, in which they are able to function as either oncogenes (on the one hand) or tumour suppressor genes (on the other). Deregulation of CCAT1 (colon cancer-associated transcript-1), an oncogenic lncrna, has been documented in different types of malignancy, such as gastric cancer, colorectal cancer and hepatocellular carcinoma. In this regard, enforced expression of CCAT1 exerts potent tumorigenic effects by promoting cell proliferation, invasion and migration. Recent evidence has also shown that CCAT1 may serve as a prognostic cancer biomarker. In this review, we provide an overview of current evidence relating to the role and biological function of CCAT1 in tumour development.

关键词： COLON cancer non-coding rna CANCER cell migration GENETIC transcription CANCER cells -- Proliferation CANCER invasiveness

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CCLS96.1, a member of a multicopy gene family, may encode a non-coding rna preferentially transcribed in reproductive organs of Silene latifolia

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DNA RESEARCH 2003年第5期10卷 213-220页

作者： Sugiyama, R Kazama, Y Miyazawa, Y Matsunaga, S Kawano, S Univ Tokyo Dept Integrated Biosci Grad Sch Frontier Sci Kashiwa Chiba 2778562 Japan Univ Tokyo Dept Biol Sci Grad Sch Sci Bunkyo Ku Tokyo 1130033 Japan RIKEN Plant Funct Lab Inst Physiol & Chem Res Wako Saitama 3510198 Japan

Dioecy in the model dioecious plant Silene latifolia is determined genetically by its heteromorphic sex chromosomes. A bacterial artificial chromosome (BAC) clone, #19B12, was isolated by screening a BAC library from S. latifolia using polymerase chain reaction (PCR) with a set of sequence tagged site (STS) primers, ScD05, which are specific to the Y chromosome. A portion of #19B12 was subcloned to construct plasmid #25-1, with an insert of 7.8 kb. This 7.8-kb fragment encodes ScD05 homolog and an anther-specific gene, CCLS96.1. Northern blot analysis of CCLS96.1 indicated a faint band of 1.8 kb in male and female flower buds. 5' and 3' rapid amplification of cDNA ends (RACE) indicated that transcripts of CCLS96.1 are very varied in size. Moreover, semi-quantitative reverse transcription-PCR (RT-PCR) showed that CCLS96.1 was also expressed in both male and female leaves. RACE produced at least ten species of transcripts, with 79-97% similarity among them. However, no significant ORFs could be predicted from their nucleotide sequences, since each has numerous stop codons throughout all three reading frames. Genomic Southern hybridization showed that the S. latifolia genome contains numerous CCLS96.1 homologs. These results suggest that the transcripts of CCLS96.1 play some role as multiple non-coding rnas in S. latifolia.

关键词： CCLS96.1 dioecious plant multicopy gene family non-coding rna Silene latifolia

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Aberrant allele-switch imprinting of a novel IGF1R intragenic antisense non-coding rna in breast cancers

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EUROPEAN JOUrnaL OF CANCER 2015年第2期51卷 260-270页

作者： Kang, Lihua Sun, Jingnan Wen, Xue Cui, Jiuwei Wang, Guanjun Hoffman, Andrew R. Hu, Ji-Fan Li, Wei Jilin Univ Affiliated Hosp 1 Stem Cell & Canc Ctr Changchun 130061 Jilin Peoples R China Stanford Univ Sch Med Stanford CA 94305 USA

The insulin-like growth factor type I receptor (IGF1R) is frequently dysregulated in breast cancers, yet the molecular mechanisms are unknown. A novel intragenic long non-coding rna (lncrna) IRAIN within the IGF1R locus has been recently identified in haematopoietic malignancies using rna-guided chromatin conformation capture (R3C). In breast cancer tissues, we found that IRAIN lncrna was transcribed from an intronic promoter in an antisense direction as compared to the IGF1R coding mrna. Unlike the IGF1R coding rna, this non-coding rna was imprinted, with monoallelic expression from the paternal allele. In breast cancer tissues that were informative for single nucleotide polymorphism (SNP) rs8034564, there was an imbalanced expression of the two parental alleles, where the 'G' genotype was favorably imprinted over the 'A' genotype. In breast cancer patients, IRAIN was aberrantly imprinted in both tumours and peripheral blood leucocytes, exhibiting a pattern of allele-switch: the allele expressed in normal tissues was inactivated and the normally imprinted allele was expressed. Epigenetic analysis revealed that there was extensive DNA demethylation of CpG islands in the gene promoter. These data identify IRAIN lncrna as a novel imprinted gene that is aberrantly regulated in breast cancer. (C) 2014 Elsevier Ltd. All rights reserved.

关键词： Genomic imprinting IRAIN non-coding rna Breast cancer IGF1R Allelic expression Gene regulation DNA methylation

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Suggestive evidence for chromosomal localization of non-coding rna from imprinted LIT1

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JOUrnaL OF HUMAN GENETICS 2007年第11期52卷 926-933页

作者： Murakami, Kazuhiro Oshimura, Mitsuo Kugoh, Hiroyuki Tottori Univ Grad Sch Med Sci Dept Biomed Sci Yonago Tottori 6838503 Japan

The non-coding rna LIT1/KCNQ1OT1, itself the product of an imprinted gene, is involved in cis-limited silencing within an imprinted cluster on human chromosome 11p15.5. Although the locus serves as an imprinting center, the mechanism of transcriptional regulation is not clear. To help understand the function of the LIT1 non-coding rna, we used fluorescence in situ hybridization (FISH) to examine the sub-cellular localization of LIT1 rna molecules. LIT1 rna signals were observed in most of the interphase human lymphoblast and fibroblast cells. The rna also appeared to accumulate on neighboring regions of chromatin containing the SLC22A18/IMPT1 and CDKN1C/p57KIP2 genes, as shown by high-resolution fiber rna FISH and modified rna TRAP (tagging and recovery of associated proteins) methods. These results suggest that LIT1 rna stably localizes to a specific chromatin region and plays an important role in the transcriptional silencing of the imprinting domain.

关键词： Chromosome immunoprecipitation Fluorescence in situ hybridization Genomic imprinting KCNQ1OT1 LIT1 non-coding rna rna TRAP

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The Long non-coding rna Cyrano Is Dispensable for Pluripotency of Murine and Human Pluripotent Stem Cells

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STEM CELL REPORTS 2020年第1期15卷 13-21页

作者： Hunkler, Hannah J. Hoepfner, Jeannine Huang, Cheng-Kai Chatterjee, Shambhabi Jara-Avaca, Monica Gruh, Ina Bolesani, Emiliano Zweigerdt, Robert Thum, Thomas Baer, Christian Hannover Med Sch Inst Mol & Translat Therapeut Strategies IMTTS Hannover Germany Hannover Med Sch REBIRTH Ctr Translat Regenerat Med Hannover Germany Hannover Med Sch Dept Cardiac Thorac Transplantat & Vasc Surg Leibniz Res Labs Biotechnol & Artificial Organs L Hannover Germany

Pluripotency is tightly regulated and is crucial for stem cells and their implementation for regenerative medicine. non-coding rnas, espe-cially long non -coding rnas (lncrnas) emerged as orchestrators of versatile (patho)-physiological processes on the transcriptional and post-transcriptional level. Cyrano , a well-conserved lncrna, is highly expressed in stem cells suggesting an important role in pluripo-tency, which we aimed to investigate in loss-off-function (LOF) experiments. Cyrano was described previously to be essential for the main- tenance of mouse embryonic stem cell (ESC) pluripotency. In contrast, using different genetic models, we here found Cyrano to be dispensable in murine and human iPSCs and in human ESCs. rna sequencing revealed only a moderate influence of Cyrano on the global transcriptome. In line, Cyrano-depleted iPSCs retained the potential to differentiate into the three germ layers. In conclusion, different methods were applied for LOF studies to rule out potential off-target effects. These approaches revealed that Cyrano does not impact pluripotency.

关键词： CRISPR/Cas Cyrano OIP5-AS1 iPSCs lncrna non-coding rna pluripotency stem cells

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