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mirna profiling for the early detection and clinical monitoring of diabetic kidney disease

BIOMARKERS IN MEDICINE 2017年第2期11卷 99-102页

作者： DiStefano, Johanna K. Natl Jewish Hlth Ctr Genes Environm & Hlth Dept Biomed Res 1400 Jackson St Denver CO 80206 USA

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Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species

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GENOME BIOLOGY AND EVOLUTION 2017年第10期9卷 2650-2657页

作者： Lima, Matheus Sanita Smith, David Roy Univ Western Ontario Dept Biol London ON Canada

Organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. However, most of the available eukaryotic rna-sequencing (rna-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments. Here, we use publicly available rna-seq data to assess organelle genome transcription in 59 diverse plastid-bearing species. Our rna mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph genomes. In all cases, 85% or more of the organelle genome was recovered from the rna data, including noncoding (intergenic and intronic) regions. These results reinforce the idea that organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. We explore the possibility that transcribed intergenic regions are producing functional noncoding rnas, and that organelle genome noncoding content might provide raw material for generating regulatory rnas.

关键词： mitochondrial transcription noncoding rna organelle gene expression pervasive transcription plastid transcription

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Paternal transmission of early life traumatization through epigenetics: Do fathers play a role?

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MEDICAL HYPOTHESES 2017年 109卷 59-64页

作者： Rowold, Enrique d'Harcourt Schulze, Lara Van der Auwera, Sandra Grabe, Hans Joergen Univ Med Greifswald Dept Psychiat & Psychotherapy Greifswald Germany German Ctr Neurodegenerat Dis DZNE Site Rostock Greifswald Greifswald Germany Univ Med Greifswald Inst Community Med Greifswald Germany

Traumatizing events are known to have consequences for the victim which may lead to the development of several well-known mental disorders. Recent research has shown that traumatic events may affect not only the victims' lives, but also that of their progeny. It is generally accepted that this transmission of trauma occurs through parental behavior;however as has been recently discovered, the effects of trauma may also be inherited due to induced alterations in gene expression. These changes, so called epigenetic modifications, illuminate the interaction between genes and the environment. In contrast to mutations, epigenetic alterations do not change the DNA code, but rather modify the DNA structure, thus being capable of regulating gene expression and in turn making it possible for an individual to genetically respond to environmental changes. There are four possible epigenetic mechanisms: paramutation, DNA methylation, posttranslational modification of histones, and non coding rna. All of these mechanisms can be found both in somatic cells and in germ cells, leading to the putative transmission of alterations upon fertilization. To date, little is known regarding the epigenetic inheritance of trauma in humans. In this review, we elucidate the hypothesis that males may transmit biological correlates of traumatization through the germline to their offspring. This model of epigenetic inheritance has been supported by some evidence from animal studies. Overall, by considering findings on the epigenetic inheritance of traumatizing events in other mammals as well as findings on epigenetic transmission of acquired traits in humans, it should be possible through future research to confirm the transmission of traumatic effects in humans. By doing so, new possibilities of trauma treatment through modulation of epigenetic pathways might arise.

关键词： Posttraumatic stress disorder Epigenetics DNA methylation noncoding rna Histone modifications

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Functional Dissection of the Pol V Largest Subunit CTD in rna-Directed DNA Methylation

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CELL REPORTS 2017年第13期19卷 2796-2808页

作者： Wendte, Jered M. Haag, Jeremy R. Singh, Jasleen McKinlay, Anastasia Pontes, Olga M. Pikaard, Craig S. Indiana Univ Dept Biol 915 East Third St Bloomington IN 47405 USA Indiana Univ Dept Mol & Cellular Biochem 915 East Third St Bloomington IN 47405 USA Indiana Univ Howard Hughes Med Inst 915 East Third St Bloomington IN 47405 USA Washington Univ Div Biol & Biomed Sci St Louis MO 63130 USA Monsanto Co 700 West Chesterfield Pkwy Chesterfield MO 63017 USA

Plant multi subunit rna polymerase V(PolV) transcription recruits Argonaute-small interfering rna (sirna) complexes that specify sites of rna-directed DNA methylation (RdDM) for gene silencing. Pol V's largest subunit, NRPE1, evolved from the largest subunit of Pol II but has a distinctive C-terminal domain (CTD). We show that the Pol V CTD is dispensable for catalytic activity in vitro yet essential in vivo. One CTD subdomain (DeCL) is required for Pol V function at virtually all loci. Other CTD subdomains have locus-specific effects. In a yeast two-hybrid screen, the 3' -> 5' exoribonuclease RRP6L1 was identified as an interactor with the DeCL and glutamine-serine (QS)-rich subdomains located downstream of an Argonaute-binding subdomain. Experimental evidence indicates that RRP6L1 trims the 3' ends of Pol V transcripts sliced by Argonaute 4 (AGO4), suggesting a model whereby the CTD enables the spatial and temporal coordination of AGO4 and RRP6L1 rna processing activities.

关键词： Pol V transcription chromatin modification cytosine methylation gene silencing noncoding rna sirna

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Bioinformatic Approach for Prediction of CsrA/RsmA-Regulating Small rnas in Bacteria

Bioinformatic Approach for Prediction of CsrA/RsmA-Regulatin...

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作者： Carl T. Fakhry Kourosh Zarringhalam Rahul V. Kulkarni

CsrA/RsmA is a rna-binding protein that functions as a global regulator controlling important processes such as virulence, secondary metabolism, motility, and biofilm formation in diverse bacterial species. The activity of CsrA/RsmA is regulated by small rnas that contain multiple binding sites for the protein. The expression of these noncoding rnas effectively sequesters the protein and reduces free cellular levels of CsrA/RsmA. While multiple bacterial small rnas that bind to and regulate CsrA/RsmA levels have been discovered, it is anticipated that there are several such small rnas that remain undiscovered. To assist in the discovery of these small rnas, we have developed a bioinformatics approach that combines sequence- and structure-based features to predict small rna regulators of CsrA/RsmA. This approach analyzes structural motifs in the ensemble of low energy secondary structures of known small rna regulators of CsrA/RsmA and trains a binary classifier on these features. The proposed machine learning approach leads to several testable predictions for small rna regulators of CsrA/RsmA, thereby complementing and accelerating experimental efforts aimed at discovery of noncoding rnas in the CsrA/RsmA pathway. less

关键词： Machine Learning Programming Language Sequence Analysis Tools Small rnas noncoding rna Post-transcriptional regulation CsrA RsmA Computational predictions

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Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional noncoding Elements

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GENOME BIOLOGY AND EVOLUTION 2017年第4期9卷 981-992页

作者： Chen, Zhen-Xia Oliver, Brian Zhang, Yong E. Gao, Ge Long, Manyuan Huazhong Agr Univ Coll Life Sci & Technol Wuhan Hubei Peoples R China NIDDK NIH Bethesda MD 20892 USA Peking Univ Coll Life Sci State Key Lab Prot & Plant Gene Res Ctr Bioinformat Beijing Peoples R China Chinese Acad Sci Inst Zool Key Lab Zool Systemat & Evolut Beijing Peoples R China Chinese Acad Sci Inst Zool State Key Lab Integrated Management Pest Insects Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Univ Chicago Dept Ecol & Evolut Chicago IL 60637 USA

Inverted duplicates are a type of repetitive DNA motifs consist of two copies of reverse complementary sequences separated by a spacer sequence. They can lead to genome instability and many may have no function, but some functional small rnas are processed from hairpins transcribed from these elements. It is not clear whether the pervasive numbers of such elements in genomes, especially those of mammals, is the result of high generation rates of neutral or slightly deleterious duplication events or positive selection for functionality. To test the functionality of intergenic inverted duplicates without known functions, we used mirror duplicates, a type of repetitive DNA motifs with few reported functions and little potential to form hairpins when transcribed, as a nonfunctional control. We identified large numbers of inverted duplicates within intergenic regions of human and mouse genomes, as well as 19 other vertebrate genomes. Structure characterization of these inverted duplicates revealed higher proportion to form stable hairpins compared with converted mirror duplicates, suggesting that inverted duplicates may produce hairpin rnas. Expression profiling across tissues demonstrated that 7.8% of human and 5.7% of mouse inverted duplicates were expressed even under strict criteria. We found that expressed inverted duplicates were more likely to be structurally stable than both unexpressed inverted duplicates and expressed converted mirror duplicates. By dating inverted duplicates in the vertebrate phylogenetic tree, we observed higher conservation of inverted duplicates than mirror duplicates. These observations support the notion that expressed inverted duplicates may be functional through forming hairpin rnas.

关键词： inverted repeats Homo sapiens Mus musculus noncoding rna mirror repeats hairpin rna

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Novel insights into circular rnas in clinical application of carcinomas

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ONCOTARGETS AND THERAPY 2017年 10卷 2183-2188页

作者： Rong, Dawei Tang, Weiwei Li, Zhouxiao Zhou, Jian Shi, Junfeng Wang, Hanjin Cao, Hongyong Nanjing Med Univ Nanjing Hosp 1 Dept Gen Surg Changle Rd 68 Nanjing 210006 Jiangsu Peoples R China Univ Hosp Munich Dept Plast & Hand Surg Munich Germany Nanjing Med Univ Nanjing Hosp 1 Dept Oncol Surg Nanjing Jiangsu Peoples R China Nanjing Med Univ Nanjing Hosp 1 Dept Oncol Nanjing Jiangsu Peoples R China

Circular rnas (circrnas), formed by nonsequential back-splicing of pre-messenger rna (pre-mrna) transcripts, have been widely concerned in recent years. With advances in high-throughput rna sequencing (rna-seq) technology, previous work has revealed that a large number of circrnas, which are endogenous, abundant and stable in mammalian cells, may be involved in atherosclerotic vascular disease risk, neurological disorders, prion diseases and carcinomas. Remarkably, interaction between circrnas and microrna has already been observed to perform a significant role in a variety of cancers, including gastric cancer and colorectal cancer. Recent work has suggested that circrnas may play critical roles in the initiation and development of cancers and could become potential new biomarkers for cancers. Herein, we review the current understanding of the roles of circrnas in cancers and the potential implications of circrnas in cancer-targeted therapy.

关键词： circular targeted therapy diagnosis microrna noncoding rna

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Host-Pathogen Transcriptomics by Dual rna-Seq

Host-Pathogen Transcriptomics by Dual RNA-Seq

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作者： Alexander J. Westermann Jörg Vogel

Transcriptomics, i.e., the quantification of cellular rna transcripts, is a powerful way to gauge the physiological state of either bacterial or eukaryotic cells under a given condition. However, traditional approaches were unsuitable to measure the abundance of transcripts across kingdoms, which is relevant for biological processes such as bacterial infections of mammalian host cells. This changed with the establishment of “Dual rna-seq,” which profiles gene expression simultaneously in an infecting bacterium and its infected host. Here, we describe a detailed Dual rna-seq protocol optimized for—but not restricted to—the study of human cell culture models infected with the Gram-negative model pathogen Salmonella Typhimurium. Furthermore, we provide experimental data demonstrating the benefits of some of the key steps of this protocol, including transcriptome stabilization (rna fixation), FACS-based enrichment of invaded cells, and double rrna depletion. While our focus is on data generation, we also include a section describing suitable computational methods to analyze the obtained datasets. less

关键词： Transcriptomics rna-seq Cell Separation And Isolation Illumina Sequencing Cell Lysis rna Extraction Library Preparation Cell And Tissue Culture Light Microscopy Microbial Culture Spectroscopy Quantitative Reverse Transcription PCR FACS Fluorescence Microscopy Real-time PCR Statistical Calculation Capillary Electrophoresis (CE) rna-Seq Analysis Electrophoresis TruSeq Salmonella Salmonella enterica subsp. enterica serovar Typhimurium Saccharomyces cerevisiae HeLa S3 Fixation rrna depletion Infection noncoding rna Host-pathogen interaction

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Meeting Report of the Fifth International Cancer Epigenetics Conference in Beijing, China, October 2016

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EPIGENOMICS 2017年第7期9卷 937-941页

作者： Gao, Dan Herman, James G. Cui, Hengmi Jen, Jin Fuks, Francois Brock, Malcolm V. Ushijima, Toshikazu Croce, Carlo Akiyama, Yoshimitsu Guo, Mingzhou Chinese Peoples Liberat Army Gen Hosp Dept Gastroenterol & Hepatol Beijing 100853 Peoples R China Nankai Univ Sch Med Tianjin 300071 Peoples R China Univ Pittsburgh Dept Med Sch Med Pittsburgh PA 15232 USA Yangzhou Univ Inst Epigenet & Epigen Yangzhou 225000 Jiangsu Peoples R China Mayo Clin Dept Lab Med & Pathol Rochester MN 55905 USA ULB ULB Canc Res Ctr U CRC Fac Med Lab Canc Epigenet B-1070 Brussels Belgium Johns Hopkins Univ Ctr Oncol Baltimore MD 21231 USA Natl Canc Ctr Div Epigen Res Inst Tokyo 1040045 Japan Ohio State Univ Ctr Comprehens Canc Coll Med Dept Canc Biol & Genet Columbus OH 43210 USA Tokyo Med & Dent Univ Grad Sch Med & Dent Sci Dept Mol Oncol Tokyo 1138519 Japan

This meeting reported many new findings in the field of cancer epigenetics, including basic science, translational and clinical studies. In this report, we summarize some of the main advancements and prospects in canc... 详细信息

关键词： 5hmc DNA methylation histone modification imprinting noncoding rna rna methylation

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High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC)

High-Resolution, High-Throughput Analysis of Hfq-Binding Sit...

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作者： Brandon Sy Julia Wong Sander Granneman David Tollervey David Gally Jai J. Tree

Small regulatory nonprotein-coding rnas (srnas) have emerged as ubiquitous and abundant regulators of gene expression in a diverse cross section of bacteria. They play key roles in most aspects of bacterial physiology, including central metabolism, nutrient acquisition, virulence, biofilm formation, and outer membrane composition. rna sequencing technologies have accelerated the identification of bacterial regulatory rnas and are now being employed to understand their functions. Many regulatory rnas require protein partners for activity, or modulate the activity of interacting proteins. Understanding how and where proteins interact with the transcriptome is essential to elucidate the functions of the many srnas. Here, we describe the implementation in bacteria of a UV-crosslinking technique termed CRAC that allows stringent, transcriptome-wide recovery of bacterial rna–protein interaction sites in vivo and at base-pair resolution. We have used CRAC to map protein–rna interaction sites for the rna chaperone Hfq and ribonuclease rnase E in pathogenic E. coli, and toxins from toxin–antitoxin systems in Mycobacterium smegmatis, demonstrating the broad applicability of this technique. less

关键词： Cross-linking rna-seq Microbial Culture Snap Freeze Cell Lysis Nickel Affinity Chromatography Western Blot PCR CLIP-Seq Enhanced Cross-linking Immunoprecipitation High-throughput Sequencing Assay Library Preparation Statistical Calculation Bowtie Genome Annotation Genome Visualization Peak Calling Agarose Gel Electrophoresis Autoradiography Data analysis DNA Ligation bedtools Escherichia coli Escherichia coli O157 rna-binding protein Small rna RBP noncoding rna Protein–rna interaction Anti-FLAG

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