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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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Detection of non-coding rna in bacteria and archaea using the DETR'PROK Galaxy pipeline

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METHODS 2013年第1期63卷 60-65页

作者： Toffano-Nioche, Claire Luo, Yufei Kuchly, Claire Wallon, Claire Steinbach, Delphine Zytnicki, Matthias Jacq, Annick Gautheret, Daniel Univ Paris 11 CNRS UMR 8621 Inst Genet & Microbiol F-91405 Orsay France INRA URGI F-78026 Versailles France

rna-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. non-coding elements include untranslated regions (UTRs) of mrnas, independent small rna genes (srnas) and transcripts produced from the antisense strand of genes (asrna). Here we present a computational pipeline (DETR'PROK: detection of ncrnas in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, srnas and asrnas. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli. (C) 2013 The Authors. Published by Elsevier Inc. All rights reserved.

关键词： non-coding rna Bacteria Archaea Small rna Antisense rna Untranslated regions

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Small non-coding rna profiling and the role of pirna pathway genes in the protection of chicken primordial germ cells

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BMC GENOMICS 2014年第1期15卷 1-15页

作者： Rengaraj, Deivendran Lee, Sang In Park, Tae Sub Lee, Hong Jo Kim, Young Min Sohn, Yoon Ah Jung, Myunghee Noh, Seung-Jae Jung, Hojin Han, Jae Yong Seoul Natl Univ Dept Agr Biotechnol Coll Agr & Life Sci Seoul 151921 South Korea Seoul Natl Univ Res Inst Agr & Life Sci Coll Agr & Life Sci Seoul 151921 South Korea Chung Ang Univ Dept Anim Sci & Technol Anseong 456756 South Korea Seoul Natl Univ Grad Sch Int Agr Technol Pyeongchang Gun 232916 Gangwon Do South Korea Seoul Natl Univ Inst Green Bio Sci & Technol Pyeongchang Gun 232916 Gangwon Do South Korea Insilicogen Inc Codes Div Suwon 441813 South Korea

Background: Genes, rnas, and proteins play important roles during germline development. However, the functions of non-coding rnas (ncrnas) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncrnas, including micro rnas (mirnas), small-interfering rnas (sirnas), and PIWI-interacting rnas (pirnas). These ncrnas are functionally important in the genome, however, the identification and annotation of ncrnas in a genome is challenging. The aim of this study was to identify different types of small ncrnas particularly pirnas, and the role of pirna pathway genes in the protection of chicken primordial germ cells (PGCs). Results: At first, we performed next-generation sequencing to identify ncrnas in chicken PGCs, and we performed ab initio predictive analysis to identify putative pirnas in PGCs. Then, we examined the expression of three repetitive sequence-linked pirnas and 14 genic-transcript-linked pirnas along with their linked genes using real-time PCR. All pirnas and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known pirna pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using sirnas. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative pirna-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs. Conclusions: Our results increase the understanding of PGC-expressed pirnas and the role of pirna pathway genes in the protection of germ cells.

关键词： Aves non-coding rna pirna Primordial Germ Cells

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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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Role of the Long non-coding rna Growth Arrest-Specific 5 in Glucocorticoid Response in Children with Inflammatory Bowel Disease

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BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY 2018年第1期122卷 87-93页

作者： Lucafo, Marianna Di Silvestre, Alessia Romano, Maurizio Avian, Alice Antonelli, Roberta Martelossi, Stefano Naviglio, Samuele Tommasini, Alberto Stocco, Gabriele Ventura, Alessandro Decorti, Giuliana De Iudicibus, Sara Univ Trieste Dept Med Surg & Hlth Sci Trieste Italy Univ Trieste PhD Sch Sci Reprod & Dev Trieste Italy Univ Trieste Dept Life Sci Trieste Italy Scuola Int Super Studi Avanzati Dept Neurosci Trieste Italy IRCCS Burlo Garofolo Inst Maternal & Child Hlth Trieste Italy

Glucocorticoids (GCs) are widely employed in inflammatory, autoimmune and neoplastic diseases, and, despite the introduction of novel therapies, remain the first-line treatment for inducing remission in inflammatory bowel disease (IBD). Given the high incidence of suboptimal response, associated with a significant number of side-effects, that are particularly severe in paediatric patients, the identification of subjects that are most likely to respond poorly to GCs is extremely important. Recent evidence suggests that the long non-coding rna (lncrna) GAS5 could be a potential marker of GC resistance. To address this issue, we evaluated the association between the lncrna GAS5 and the efficacy of steroids, in terms of inhibition of proliferation, in two cell lines derived from colon and ovarian cancers, to confirm the sensitivity and specificity of these lncrnas. These cells showed a different sensitivity to GCs and revealed differential expression of GAS5 after treatment. GAS5 was up-regulated in GC-resistant cells and accumulated more in the cytoplasm compared to the nucleus in response to the drug. The functions of GAS5 were assessed by silencing, and we found that GAS5 knock-down reduced the proliferation during GC treatment. Furthermore, for the first time, we measured GAS5 levels in 19 paediatric IBD patients at diagnosis and after the first cycle of GCs, and we demonstrated an up-regulation of the lncrna in patients with unfavourable steroid response. Our preliminary results indicate that GAS5 could be considered a novel pharmacogenomic marker useful for the personalization of GC therapy.

关键词： INFLAMMATORY bowel diseases GLUCOCORTICOIDS PEDIATRICS non-coding rna INTESTINAL diseases STEROIDS

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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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Cancer-linked satellite 2 DNA hypomethylation does not regulate Sat2 non-coding rna expression and is initiated by heat shock pathway activation

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EPIGENETICS 2012年第8期7卷 903-913页

作者： Tilman, Gaelle Arnoult, Nausica Lenglez, Sandrine Van Beneden, Amandine Loriot, Axelle De Smet, Charles Decottignies, Anabelle Catholic Univ Louvain Fac Pharm & Biomed Sci de Duve Inst Genet & Epigenet Alterat Genomes Res Grp Brussels Belgium

Epigenetic dysfunctions, including DNA methylation alterations, play major roles in cancer initiation and progression. Although it is well established that gene promoter demethylation activates transcription, it remains unclear whether hypomethylation of repetitive heterochromatin similarly affects expression of non-coding rna from these loci. Understanding how repetitive non-coding rnas are transcriptionally regulated is important given that their established upregulation by the heat shock (HS) pathway suggests important functions in cellular response to stress, possibly by promoting heterochromatin reconstruction. We found that, although pericentromeric satellite 2 (Sat2) DNA hypomethylation is detected in a majority of cancer cell lines of various origins, DNA methylation loss does not constitutively hyperactivate Sat2 expression, and also does not facilitate Sat2 transcriptional induction upon heat shock. In melanoma tumor samples, our analysis revealed that the HS response, frequently upregulated in tumors, is probably the main determinant of Sat2 rna expression in vivo. Next, we tested whether HS pathway hyperactivation may drive Sat2 demethylation. Strikingly, we found that both hyperthermia and hyperactivated RasV12 oncogene, another potent inducer of the HS pathway, reduced Sat2 methylation levels by up to 27% in human fibroblasts recovering from stress. Demethylation occurred locally on Sat2 repeats, resulting in a demethylation signature that was also detected in cancer cell lines with moderate genome-wide hypomethylation. We therefore propose that upregulation of Sat2 transcription in response to HS pathway hyperactivation during tumorigenesis may promote localized demethylation of the locus. This, in turn, may contribute to tumorigenesis, as demethylation of Sat2 was previously reported to favor chromosomal rearrangements.

关键词： DNA hypomethylation pericentromeric satellite DNA non-coding rna heat shock response Ras oncogene

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Dynamic developmental regulation of the large non-coding rna associated with the mouse 7C imprinted chromosomal region

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DEVELOPMENTAL BIOLOGY 2005年第2期286卷 587-600页

作者： Le Meur, E Watrin, F Landers, M Sturny, R Lalande, M Muscatelli, F NMDA IBDM F-13288 Marseille France Univ Connecticut Ctr Hlth Dept Genet & Dev Biol Farmington CT 06030 USA

The mouse ortholog of the Prader-Willi/Angelman syndrome imprinted domain contains several paternal-specific transcripts and the maternally expressed gene encoding ubiquitin protein ligase E3A (Ube3a). A Large paternal non-coding rna, encompassing Snurf-Snrpn exons and the Ube3a Antisense Transcript (Ube3a-ATS), has been recently characterized and named here LNCAT Potential roles of LNCAT in imprinting, gene regulation, and disease are likely but have not been investigated. In order to establish the function(s) of LNCAT, we first determined its in vivo spatio-temporal expression pattern at the cellular level during development and in different adult brain tissues. We show here that LNCAT is developmentally regulated, with transcript variants being specifically expressed through neuronal differentiation in postmitotic neurons. We demonstrate that the LNCAT and Snurf-Snrpn transcripts are independent although they share common exons. We show an absence of expression of LNCAT through gametogenesis and in early embryo excluding a role of LNCAT in the imprint establishment. We also report a range of observations that challenges the widely accepted model of imprinted gene silencing of Ube3a. Although these last data do not completely exclude that the LNCAT variants including "Ube3a-ATS" exons could repress the paternal allele of Ube3a, they do allow us to propose an alternative and consistent model. (C) 2005 Elsevier Inc. All rights reserved.

关键词： non-coding rna imprinting Prader-Willi Angelman Ube3a Snrpn

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Emerging Roles of non-coding rna Transcription

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TRENDS IN BIOCHEMICAL SCIENCES 2018年第9期43卷 654-667页

作者： Kaikkonen, Minna U. Adelman, Karen Univ Eastern Finland AI Virtanen Inst Mol Sci POB 1627 Kuopio 70211 Finland Harvard Med Sch Dept Biol Chem & Mol Pharmacol Boston MA 02115 USA

Metazoan genomes are broadly transcribed by rna polymerase II (rnaPII), but surprisingly few of these rnas encode proteins. Accordingly, there is great interest in understanding the origins and potential roles of the vast array of non-coding rnas (ncrnas) that are produced. We present here emerging evidence that the act of transcription and the presence of nascent rna at a locus is often central to function, rather than specific ncrna sequences or structures. We highlight examples wherein transcription elongation through a regulatory region modulates chromatin structure and/or transcription factor occupancy, and describe how nascent rna contributes to the local epigenetic landscape through sequence-independent interactions with chromatin regulators. Finally, we discuss current strategies for probing the potential functions of ncrna transcription.

关键词： non-coding rna lncrna enhancer gene regulation chromatin structure transcriptional interference

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Identification of novel non-coding rna-based negative feedback regulating the expression of the oncogenic transcription factor GLI1

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MOLECULAR ONCOLOGY 2014年第5期8卷 912-926页

作者： Villegas, Victoria E. Rahman, Mohammed Ferdous-Ur Fernandez-Barrena, Maite G. Diao, Yumei Liapi, Eleni Sonkoly, Eniko Stahle, Mona Pivarcsi, Andor Annaratone, Laura Sapino, Anna Ramirez Clavijo, Sandra Burglin, Thomas R. Shimokawa, Takashi Ramachandran, Saraswathi Kapranov, Philipp Fernandez-Zapico, Martin E. Zaphiropoulos, Peter G. Karolinska Inst Dept Biosci & Nutr Huddinge Sweden Univ Rosario Fac Nat Sci & Math Bogota Colombia Univ Rosario Doctoral Program Biomed Sci Bogota Colombia Mayo Clin Schulze Ctr Novel Therapeut Rochester MN USA Karolinska Inst Dept Med Unit Dermatol & Venereol Solna Sweden Univ Turin Dept Med Sci Turin Italy St Laurent Inst Cambridge MA USA

non-coding rnas are a complex class of nucleic acids, with growing evidence supporting regulatory roles in gene expression. Here we identify a non-coding rna located head-to-head with the gene encoding the Glioma-associated oncogene 1 (GLI1), a transcriptional effector of multiple cancer-associated signaling pathways. The expression of this three-exon GLI1 antisense (GLI1AS) rna in cancer cells was concordant with GLI1 levels. sirnas knockdown of GLI1AS up-regulated GLI1 and increased cellular proliferation and tumor growth in a xenograft model system. Conversely, GLI1AS overexpression decreased the levels of GLI1, its target genes PTCH1 and PTCH2, and cellular proliferation. Additionally, we demonstrate that GLI1 knockdown reduced GLI1AS, while GLI1 overexpression increased GLI1AS, supporting the role of GLI1AS as a target gene of the GLI1 transcription factor. Activation of TGF beta and Hedgehog signaling, two known regulators of GLI1 expression, conferred a concordant up-regulation of GLI1 and GLI1AS in cancer cells. Finally, analysis of the mechanism underlying the interplay between GLI1 and GLI1AS indicates that the non-coding rna elicits a local alteration of chromatin structure by increasing the silencing mark H3K27me3 and decreasing the recruitment of rna polymerase II to this locus. Taken together, the data demonstrate the existence of a novel non-coding rna-based negative feedback loop controlling GLI1 levels, thus expanding the repertoire of mechanisms regulating the expression of this oncogenic transcription factor. (C) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

关键词： non-coding rna Gene expression Transcription Chromatin GLI1 Cancer

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