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A Network of noncoding Regulatory rnas Acts in the Mammalian Brain

CELL 2018年第2期174卷 350-+页

作者： Kleaveland, Benjamin Shi, Charlie Y. Stefano, Joanna Bartel, David P. Howard Hughes Med Inst Cambridge MA 02142 USA Whitehead Inst Biomed Res Cambridge MA 02142 USA MIT Dept Biol Cambridge MA 02139 USA Massachusetts Gen Hosp Dept Pathol Boston MA 02114 USA

noncoding rnas (ncrnas) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncrnas-a long ncrna, a circular rna, and two micrornasusing gene editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncrna Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microrna. Cyrano-directed miR-7 degradation is much more effective than previously described examples of target-directed microrna degradation, which come primarily from studies of artificial and viral rnas. By reducing miR-7 levels, Cyrano prevents repression of miR-7-targeted mrnas and enables accumulation of Cdr1as, a circular rna known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as in neurons, in part through enhanced slicing of Cdr1as by a second mirna, miR-671. Thus, several types of ncrnas can collaborate to establish a sophisticated regulatory network.

关键词： TDMD circrna lncrna knockout mammalian gene regulation mirna knockout mirna tailing mirna target-site disruption mirna trimming noncoding rna regulatory network

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A 360° view of circular rnas: From biogenesis to functions

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WILEY INTERDISCIPLINARY REVIEWS-rna 2018年第4期9卷 e1478页

作者： Wilusz, Jeremy E. Univ Penn Dept Biochem & Biophys Perelman Sch Med Philadelphia PA 19104 USA

The first circular rna (circrna) was identified more than 40 years ago, but it was only recently appreciated that circrnas are common outputs of many eukaryotic protein-coding genes. Some circrnas accumulate to higher levels than their associated linear mrnas, especially in the nervous system, and have clear regulatory functions that result in organismal phenotypes. The pre-mrna splicing machinery generates circrnas via backsplicing reactions, which are often facilitated by intronic repeat sequences that base pair to one another and bring the intervening splice sites into close proximity. When spliceosomal components are limiting, circrnas can become the preferred gene output, and backsplicing reactions are further controlled by exon skipping events and the combinatorial action of rna binding proteins. This allows circrnas to be expressed in a tissue- and stage-specific manner. Once generated, circrnas are highly stable transcripts that often accumulate in the cytoplasm. The functions of most circrnas remain unknown, but some can regulate the activities of micrornas or be translated to produce proteins. Circular rnas can further interface with the immune system as well as control gene expression events in the nucleus, including alternative splicing decisions. Circular rnas thus represent a large class of rna molecules that are tightly regulated, and it is becoming increasingly clear that they likely impact many biological processes. This article is categorized under: rna Processing > Splicing Mechanisms rna Structure and Dynamics > Influence of rna Structure in Biological Systems rna Evolution and Genomics > rna and Ribonucleoprotein Evolution rna Evolution and Genomics > Computational Analyses of rna

关键词： alternative splicing backsplicing CDR1as circrna exon skipping immune surveillance Laccase2 microrna noncoding rna pre-mrna splicing R-loop scrambled exons spliceosome translation transposable elements

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Structural Basis for trna Mimicry by a Bacterial Y rna

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STRUCTURE 2018年第12期26卷 1635-+页

作者： Wang, Wei Chen, Xinguo Wolin, Sandra L. Xiong, Yong Yale Univ Dept Mol Biophys & Biochem POB 6666 New Haven CT 06511 USA Yale Sch Med Dept Cell Biol New Haven CT 06536 USA NCI RNA Biol Lab Ctr Canc Res Frederick MD 21702 USA

noncoding Y rnas are present in both animal cells and many bacteria. In all species examined, Y rnas tether the Ro60 protein to an effector protein to perform various cellular functions. Recently, a new Y rna subfamily was identified in bacteria. Bioinformatic analyses of these YrlA (Y rna-like A) rnas predict that the effector-binding domain resembles trna. We present the structure of this domain, the overall folding of which is strikingly similar to canonical trnas. The tertiary interactions that are responsible for stabilizing trna are present in YrlA, making it a close trna mimic. However, YrlA lacks a free CCA end and contains a kink in the stem corresponding to the anticodon stem. Since nucleotides in the D and T stems are conserved among YrlAs, they may be an interaction site for an unknown factor. Our experiments identify YrlA rnas as a new class of trna mimics.

关键词： Y rna YrlA noncoding rna trna-like element

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Repression of Divergent noncoding Transcription by a Sequence-Specific Transcription Factor

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MOLECULAR CELL 2018年第6期72卷 942-+页

作者： Wu, Andrew C. K. Patel, Harshil Chia, Minghao Moretto, Fabien Frith, David Snijders, Ambrosius P. van Werven, Folkert J. Francis Crick Inst Cell Fate & Gene Regulat Lab 1 Midland Rd London NW1 1AT England Francis Crick Inst Bioinformat & Biostat 1 Midland Rd London NW1 1AT England Francis Crick Inst Prot Anal & Prote Platform 1 Midland Rd London NW1 1AT England

Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here, we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1-regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of previously described chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeler. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality toward productive transcription.

关键词： RSC Rap1 directionality divergent noncoding rna promoter repression transcription transcription factor yeast

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Circular rna hsacirc0000745 may serve as a diagnostic marker for gastric cancer

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World Journal of Gastroenterology 2017年第34期23卷 6330-6338页

作者： Mei Huang Yi-Ren He Li-Chuan Liang Qiang Huang Zhi-Qiang Zhu Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery Department of General SurgeryAnhui Provincial Hospital Affiliated to Anhui Medical University Department of General Surgery Anhui Provincial Hospital Affiliated to Anhui Medical University

AIM To determine whether circular rnas(circ rnas) are involved in pathological processes of gastric cancer(GC).METHODS Three circ rnas with differential expression in GC and colorectal cancer were randomly selected for validation by quantitative reverse transcription-polymerase chain reaction(q RT-PCR), using 20 pairs of gastric tissues and normal tissues. Based on the predicted circ rnami rna network, we then focused on hsa_circ_0000745, which was found to be down-regulated in 20 GC tissues compared with normal tissues. The hsa_circ_0000745 levels were further analyzed by q RT-PCR in 60 GC tissues and paired adjacent non-tumor tissues, as well as 60 plasma samples from GC patients and 60 plasma samples from healthy controls. The associations between the levels of hsa_circ_0000745 and the clinicopathological features of GC patients were statistically assessed. A receiver operating characteristic(ROC) curve was used to evaluate the diagnostic value of hsa_circ_0000745 in *** Hsa_circ_0000745 was down-regulated in GC tissues vs non-tumorous tissues(P < 0.001) and in plasma samples from patients with GC vs healthy controls(P < 0.001). The expression level of hsa_circ_0000745 in GC tissues correlated with tumor differentiation, while the expression level in plasma correlated with tumor-nodemetastasis stage. The area under the ROC curve(AUC) of hsa_circ_0000745 in plasma was 0.683, suggesting good diagnostic value. Plasma hsa_circ_0000745 level combined with carcinoembryogenic antigen(CEA) level increased the AUC to *** Hsa_circ_0000745 plays an important role in GC and its expression level in plasma in combination with CEA level is a promising diagnostic marker for this malignancy.

关键词： Circular rna circ_0000745 Gastric cancer Diagnosis noncoding rna

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DLK1-DIO3 imprinted locus deregulation in development, respiratory disease, and cancer

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EXPERT REVIEW OF RESPIRATORY MEDICINE 2017年第9期11卷 749-761页

作者： Enterina, Jhon R. Enfield, Katey S. S. Anderson, Christine Marshall, Erin A. Ng, Kevin W. Lam, Wan L. British Columbia Canc Res Ctr Vancouver BC V5Z 1L3 Canada

Introduction: The imprinted DLK1-DIO3 locus at 14q32.1-32.31 holds biological significance in fetal development, whereby imprinting errors are causal to developmental disorders. Emerging evidence has implicated this locus in other diseases including cancer, highlighting the biological parallels between fetal organ and tumour *** covered: Controlled regulation of gene expression from the imprinted DLK1-DIO3 locus at 14q32.1-32.31 is crucial for proper fetal development. Deregulation of locus gene expression due to imprinting errors has been mechanistically linked to the developmental disorders Kagami-Ogata Syndrome and Temple Syndrome. In adult tissues, deregulation of locus genes has been associated with multiple malignancies although the causal genetic mechanisms remain largely uncharacterised. Here, we summarize the genetic mechanisms underlying the developmental disorders that arise as a result of improper locus imprinting and the resulting developmental phenotypes, emphasizing both the coding and noncoding components of the locus. We further highlight biological parallels common to both fetal development and disease, with a specific focus on lung development, respiratory disease, and lung *** commentary: Many commonalities between respiratory and developmental defects have emerged with respect to the 14q32 locus, emphasizing the importance of studying the effects of imprinting on gene regulation patterns at this locus in both biological settings.

关键词： DLK1-DIO3 locus imprinting uniparental disomy fetal development developmental disorders Temple syndrome Kagami-Ogata syndrome respiratory disease noncoding rna cancer

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DNA-rna interactions are critical for chromosome condensation in Escherichia coli

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2017年第46期114卷 12225-12230页

作者： Qian, Zhong Zhurkin, Victor B. Adhya, Sankar NCI Lab Mol Biol NIH Bethesda MD 20892 USA NCI Lab Cell Biol NIH Bethesda MD 20892 USA

Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding rna, narna4. Here we investigated the molecular mechanism of how narna4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA-DNA contacts (DNA condensation). We demonstrate that narna4 uniquely acts by forming complexes that may not involve long stretches of DNA-rna hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA-rna interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the narna4-mediated DNA condensation process.

关键词： chromosome structure DNA-rna interaction noncoding rna Escherichia coli HU protein

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Discovery of novel stroke-responsive lncrnas in the mouse cortex using genome-wide rna-seq

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NEUROBIOLOGY OF DISEASE 2017年 108卷 204-212页

作者： Bhattarai, Sunil Pontarelli, Fabrizio Prendergast, Emily Dharap, Ashutosh JFK Med Ctr Lab Stroke Res & Noncoding RNA Biol Neurosci Inst 65 James St Edison NJ 08820 USA Middlesex Cty Coll Dept Nat Sci Edison NJ 08837 USA

Long noncoding rnas (lncrnas) play major roles in regulating gene expression in mammals, but are poorly understood in ischemic stroke. Using a mouse model of transient focal ischemia, we applied rna-seq to evaluate for the first time the unbiased, genome-wide expression of lncrnas as a function of reperfusion time in the cerebral cortex. Focal ischemia was induced in adult male C57BL/6 mice followed by reperfusion for 6, 12 or 24 h. Total rna from ipsilateral cortices was used for Illumina sequencing and reads were mapped to the mouse reference genome (GRCm38). Annotated and novel transcript isoforms were identified and differential expression between the groups was estimated. We observed that the baseline expression of lncrnas in the healthy cortex was low, but many were highly altered after stroke. Very few of these altered lncrnas were previously annotated. A total of 259 lncrna isoforms at 6 h, 378 isoforms at 12 h, and 217 isoforms at 24 h of reperfusion were differentially expressed versus sham controls. Of these, 213, 322 and 171 isoforms at 6, 12 and 24 h of reperfusion, respectively, were novel lncrnas. Reperfusion time-point-specific analyses revealed that the Incrnas reached peak expression levels at 6 h of reperfusion. Positional analysis of ischemia-responsive lncrnas with respect to ischemia-responsive protein-coding genes identified potential gene-regulatory relationships. Overall, this work shows that transient focal ischemia induces widespread changes in the expression of lncrnas in the mouse cortex with distinct reperfusion time-point-dependent expression characteristics that may underlie progression of the ischemic pathophysiology. The detection of hundreds of novel ischemia-responsive lncrnas marks the discovery of new disease-related genomic regions in the adult cortex and may help identify novel opportunities for therapeutic targeting.

关键词： Ischemic stroke Cerebral cortex noncoding rna lncrna rna-seq

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A method for extracting and characterizing rna from urine: For downstream PCR and rnaseq analysis

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ANALYTICAL BIOCHEMISTRY 2017年 536卷 8-15页

作者： Zhou, Kun Spillman, Monique A. Behbakht, Kian Komatsu, Julia M. Abrahante, Juan E. Hicks, Douglas Schotl, Brent Odean, Evan Jones, Kenneth L. Graner, Michael W. Bemis, Lynne T. Univ Minnesota Med Sch Duluth 1035 Univ Dr Duluth MN 55812 USA Baylor Univ Med Ctr Texas A&M Univ Sch Med Dallas TX USA Univ Colorado Anschutz Med Campus Aurora CO 80045 USA Univ Minnesota Inst Informat Minneapolis MN USA

Readily accessible samples such as urine or blood are seemingly ideal for differentiating and stratifying patients;however, it has proven a daunting task to identify reliable biomarkers in such samples. Non-coding rna holds great promise as a source of biomarkers distinguishing physiologic wellbeing or illness. Current methods to isolate and characterize rna molecules in urine are limited. In this proof of concept study, we present a method to extract and identify small noncoding rnas in urine. Initially, quantitative reverse transcription PCR was applied to confirm the presence of micrornas in total rna extracted from urine. Once the presence of micro rna in urine was confirmed, we developed a method to scale up rna extraction to provide adequate amounts of rna for next generation sequence analysis. The method described in this study is applicable to detecting a broad range of small noncoding rnas in urine;thus, they have wide applicability for health and disease analyses. (C) 2017 Elsevier Inc. All rights reserved.

关键词： noncoding rna Extracellular rna in urine Ovarian cancer Small rna next generation sequencing trna fragments

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Circular rnas: Unexpected outputs of many protein-coding genes

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rna BIOLOGY 2017年第8期14卷 1007-1017页

作者： Wilusz, Jeremy E. Univ Penn Perelman Sch Med Dept Biochem & Biophys Philadelphia PA 19104 USA

Pre-mrnas from thousands of eukaryotic genes can be non-canonically spliced to generate circular rnas, some of which accumulate to higher levels than their associated linear mrna. Recent work has revealed widespread mechanisms that dictate whether the spliceosome generates a linear or circular rna. For most genes, circular rna biogenesis via backsplicing is far less efficient than canonical splicing, but circular rnas can accumulate due to their long half-lives. Backsplicing is often initiated when complementary sequences from different introns base pair and bring the intervening splice sites close together. This process is further regulated by the combinatorial action of rna binding proteins, which allow circular rnas to be expressed in unique patterns. Some genes do not require complementary sequences to generate rna circles and instead take advantage of exon skipping events. It is still unclear what most mature circular rnas do, but future investigations into their functions will be facilitated by recently described methods to modulate circular rna levels.

关键词： Alternative splicing backsplicing biogenesis circularization circrna cirna exon skipping noncoding rna pre-mrna splicing rna stability

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