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The Retrotransposon storm and the dangers of a Collyer's genome

CURRENT OPINION IN GENETICS & DEVELOPMENT 2018年 49卷 95-105页

作者： Dubnau, Josh SUNY Stony Brook Dept Anesthesiol Stony Brook NY 11794 USA SUNY Stony Brook Dept Neurobiol & Behav Stony Brook NY 11794 USA Stony Brook Sch Med Stony Brook NY 11794 USA

Like the famous Collyer's mansion in NY, our genomes have accumulated vast quantities of sequences that have been referred to as 'junk dna,' much of which consists of retrotransposons (RTEs). A recent literature establishes the phenomenology that many RTEs become expressed at progressively higher levels during the course of normal aging. This seems to reflect gradual loss of heterochromatin in old age. In addition, RTEs appear to be precociously expressed in brains of younger animals that are experiencing neurodegenerative decline. Although it is difficult to distinguish cause from consequence, several recent studies support the contention that RTE expression, and even perhaps transposition, causally contribute to both the normal deterioration seen with age and to the precipitous decline in some neurodegenerative disorders. This may reflect a two hit model in which normal age-dependent loss of heterochromatin synergizes with a disruption to posttranscriptional silencing of RTEs caused by genetic and environmental stress.

关键词： RETROTRANSPOSONS HETEROCHROMATIN NEURODEGENERATION non-coding dna TRANSLOCATION (Genetics)

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The role of long noncoding RNAs in cancer: the dark matter matters

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CURRENT OPINION IN GENETICS & DEVELOPMENT 2018年 48卷 8-15页

作者： Hu, Xiaowen Sood, Anil K. Dang, Chi V. Zhang, Lin Univ Penn Ctr Res Reprod & Womens Hlth Philadelphia PA 19104 USA Univ Penn Dept Obstet & Gynecol Philadelphia PA 19104 USA Univ Texas MD Anderson Canc Ctr Ctr RNA Interference & Noncoding RNA Houston TX 77030 USA Univ Texas MD Anderson Canc Ctr Dept Gynecol Oncol & Reprod Med Houston TX 77030 USA Wistar Inst Anat & Biol Philadelphia PA 19104 USA Ludwig Inst Canc Res New York NY 10017 USA

Sequencing technology has facilitated a new era of cancer research, especially in cancer genomics. Using next-generation sequencing, thousands of long noncoding RNAs (lncRNAs) have been identified as abnormally altered in the cancer genome or differentially expressed in tumor tissues. These lncRNAs are associated with imbalanced gene regulation and aberrant biological processes that contribute to malignant transformation. The functions and therapeutic potential of cancer-related lncRNAs have attracted considerable interest in the past few years. Although few lncRNAs have been well-characterized, researchers have recently made impressive progress in understanding lncRNAs and their novel functions, such as regulation of gene expression, metabolism and dna repair. These latest findings reinforce the crucial roles of lncRNAs in cancer initiation and development, as well as their possible clinical applications.

关键词： non-coding dna CANCER risk factors CANCER genetics dna repair GENE expression

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Patterns of variation in cis-regulatory regions: examining evidence of purifying selection

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BMC GENOMICS 2018年第1期19卷 1-14页

作者： Naidoo, Thijessen Sjodin, Per Schlebusch, Carina Jakobsson, Mattias Uppsala Univ Dept Organismal Biol Uppsala Sweden Sci Life Lab Uppsala Sweden

Background: With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements. Results: We disentangle signals of purifying selection acting directly on regulatory elements from the confounding factors of demography and purifying selection linked to e.g. nearby protein coding regions. We confirm the importance of regulatory regions proximal to coding sequence, while also finding differential levels of selection at distal regions. We note differences in purifying selection among transcription factor families. Signals of constraint at some genomic classes were also strongly dependent on their physical location relative to coding sequence. In addition, levels of selection efficacy across genomic classes differed between African and non-African populations. Conclusions: In order to assign a valid signal of selection to a particular class of genomic sequence, we show that it is crucial to isolate the signal by accounting for the effects of demography and linked-purifying selection. Our study highlights the intricate interplay of factors affecting signals of selection on functional elements.

关键词： Regulatory regions Purifying selection Selection efficacy non-coding dna Functional elements Population genetics

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Reading Between the Genes: Computational Models to Discover Function from noncoding dna 23rd

Reading Between the Genes: Computational Models to Discover ...

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23rd Pacific Symposium on Biocomputing (PSB)

作者： Lussier, Yves A. Berghout, Joanne Vitali, Francesca Ramos, Kenneth S. Kann, Maricel Moore, Jason H. Univ Arizona UA Canc Ctr Ctr Biomed Informat & Biostat BIO5 InstCtr Appl Genet & Genom Med 1657 E Helen St Tucson AZ 85719 USA Univ Arizona Dept Med 1657 E Helen St Tucson AZ 85719 USA Univ Maryland Baltimore Cty Dept Biol Sci 1000 Hilltop Circle Baltimore MD 21250 USA Univ Penn Dept Biostat Epidemiol & Informat 3700 Hamilton Walk Philadelphia PA 19104 USA

ISBN: (纸本)9789813235533;9789813235526

noncoding dna - once called "junk" has revealed itself to be full of function. Technology development has allowed researchers to gather genome-scale data pointing towards complex regulatory regions, expression and function of noncoding RNA genes, and conserved elements. Variation in these regions has been tied to variation in biological function and human disease. This PSB session tackles the problem of handling, analyzing and interpreting the data relating to variation in and interactions between noncoding regions through computational biology. We feature an invited speaker to how variation in transcription factor coding sequences impacts on sequence preference, along with submitted papers that span graph based methods, integrative analyses, machine learning, and dimension reduction to explore questions of basic biology, cancer, diabetes, and clinical relevance.

关键词： non-coding dna intergenic LncRNA microRNA sncRNA miRNA piRNA LINEs LINE1 repetitive elements

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FATHMM-XF: accurate prediction of pathogenic point mutations via extended features

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BIOINFORMATICS 2018年第3期34卷 511-513页

作者： Rogers, Mark F. Shihab, Hashem A. Mort, Matthew Cooper, David N. Gaunt, Tom R. Campbell, Colin Univ Bristol Intelligent Syst Lab Bristol BS8 1UB Avon England Univ Bristol MRC Integrat Epidemiol Unit IEU Bristol BS8 2BN Avon England Cardiff Univ Inst Med Genet Cardiff CF14 4XN Wales

aSummary: We present FATHMM-XF, a method for predicting pathogenic point mutations in the human genome. Drawing on an extensive feature set, FATHMM-XF outperforms competitors on benchmark tests, particularly in non-coding regions where the majority of pathogenic mutations are likely to be found. Availability and implementation: The FATHMM-XF web server is available at http://***/fathmm-xf/, and as tracks on the Genome Tolerance Browser: http://***. Predictions are provided for human genome version GRCh37/hg19. The data used for this project can be downloaded from: http://***/fathmm-xf/ Contact: mark. rogers@*** or ***@*** Supplementary information: Supplementary data are available at Bioinformatics online.

关键词： HUMAN genome MUTATION (Biology) PATHOGENIC microorganisms MICROBIAL genetics non-coding dna

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Biological Function of MicroRNA193a-3p in Health and Disease

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INTERNATIONAL JOURNAL OF GENOMICS 2017年第1期2017卷 1-13页

作者： Grossi, Ilaria Salvi, Alessandro Abeni, Edoardo Marchina, Eleonora De Petro, Giuseppina Univ Brescia Dept Mol & Translat Med Div Biol & Genet Brescia Italy

MicroRNAs (miRNAs) are a class of small noncoding RNAs that act mainly as negative regulators of gene expression. Several studies demonstrated that miRNAs take part in numerous biological processes, such as proliferation, apoptosis, and migration. The dysregulation of miRNAs has been frequently observed in different types of disease, including cancer. Here, we provide a comprehensive review on the human miR-193a-3p by considering its role in both physiological and pathological contexts. Different mechanisms involved in regulating miR-193a-3p expression have been reported, including epigenetic modifications and transcription factors. In physiological contexts, miR-193a-3p seemed able to limit proliferation and cell cycle progression in normal cells. Remarkably, several publications demonstrated that miR-193a-3p acted as a tumor suppressor miRNA in cancer by targeting different genes involved in proliferation, apoptosis, migration, invasion, and metastasis. Furthermore, the downregulation of miR-193a-3p has been observed in many primary tumors and altered levels of circulating miR-193a-3p have been identified in serum or plasma of cancer patients and subjects affected by Parkinson's disease or by schizophrenia. In a clinical perspective, further studies are needed to explore the antitumor effects of the miR-193a-3p mimics delivery and the relevance of this miRNA detection as a possible diagnostic and prognostic biomarker.

关键词： MICRORNA non-coding dna non-coding RNA GENE expression NUCLEOTIDES

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Phylogenetic utility of the trnH-psbA IGR and stem-loop diversity of the 3' UTR in Cactaceae (Caryophyllales)

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PLANT SYSTEMATICS AND EVOLUTION 2017年第3期303卷 299-315页

作者： Hernandez-Ledesma, Patricia Barcenas, Rolando T. Univ Autonoma Queretaro Fac Ciencias Nat Lab Genet Mol & Ecol Evolut Campus Aeropuerto Queretaro 76140 Queretaro Mexico

The ultrastructure of the psbA-trnH intergenic region (hereafter IGR) of the Cactaceae was characterised based on 642 sequences identifying a conserved region and a mutational hot spot with different evolutionary rates. The first section of the IGR includes a highly conserved 3' UTR of the psbA containing a TATA-box and a stem-loop. The second section of the IGR is a highly variable intergenic spacer (hereafter IGS) with a mutational hot spot. The phylogenetic utility of this IGR was tested by applying four different partitioned schemes to the same data set and searching for trees under different evolutionary models. The IGR showed 90 different stem-loop conformations with the highest diversity found in the Cactoideae with 78 architectures, the Opuntioideae with nine and the Pereskioideae with seven different architectures. The shortest stem-loop was recovered for Rhipsalis paradoxa with 47 nt, while the longest stem-loop was found in five species of Echinocereus. The organisation of the IGR in the Cactaceae follows the overall general organisation analysed for other angiosperms, and it seems that within the family, there is a general tendency to the reduction in length of the IGR in Maihuenia + Opuntioideae + Cacteae compared with Pereskia. The over-partition of the data set reduces resolution and support, while the un-partitioned analysis, disregarding primary homology assessment, shows good support and resolution but builds a phylogeny on ambiguous grounds. The best proposal scheme for this IGR is a partitioned analysis including three different regions that shows high support and resolution and considers primary homology assessment as a fundamental step in phylogeny reconstruction.

关键词： Cactineae Hairpin architecture non-coding dna Phylogenetic reconstruction RNA secondary structure TATA-box

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Characterization of non-coding Regions in B Mating Loci of Agrocybe salicacola Groups: Target Sites for B Mating Type Identification

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CURRENT MICROBIOLOGY 2017年第6期74卷 772-778页

作者： Chen, Weimin Chai, Hongmei Yang, Weixian Zhang, Xiaolei Chen, Yuhui Zhao, YongChang Yunnan Acad Agr Sci Biotechnol & Germplasm Resources Inst Kunming 650223 Yunnan Peoples R China Yunnan Prov Key Lab Agr Biotechnol Kunming 650223 Yunnan Peoples R China Minist Agr Key Lab Southwestern Crop Gene Resources & Germpl Kunming 650223 Yunnan Peoples R China Southwest Forestry Univ Coll Life Sci Kunming 650224 Yunnan Peoples R China

Agrocybe salicacola is a delicious and cultivable mushroom. It is important to understand this species' inherent characteristics, especially to elucidate the constitution and segregation of mating genes. In this study, two compatible B mating loci in strain YAASM0711 of A. salicacola were cloned from the monokaryons, and sequence and phylogeny analyses showed two conserved genes encoding pheromone receptors maybe lost mating activity, which determined by comparing with those of other mushrooms. In the conserved regions of mating loci, partial insertion/deletion fragments made non-coding regions posses polymorphisms, and monokaryotic strains of different mating types were distinguished from each other according to the amplification profile of variable regions, which suggested mating loci were integrally assigned to offspring strains during mitosis in A. salicacola. As our known, it is the first to develop molecular markers for B mating-type identification using variable non-coding fragments of mating loci in basidiomycetes.

关键词： EDIBLE mushrooms non-coding dna HETEROTHALLISM in fungi PHEROMONE receptors PLANT phylogeny MITOSIS in plants MITOSIS in fungi

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Mining the Unknown: Assigning Function to noncoding Single Nucleotide Polymorphisms

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TRENDS IN GENETICS 2017年第1期33卷 34-45页

作者： Nishizaki, Sierra S. Boyle, Alan P. Univ Michigan Dept Human Genet Ann Arbor MI 48109 USA Univ Michigan Dept Computat Med & Bioinformat Ann Arbor MI 48109 USA

One of the formative goals of genetics research is to understand how genetic variation leads to phenotypic differences and human disease. Genome-wide association studies (GWASs) bring us closer to this goal by linking variation with disease faster than ever before. Despite this, GWASs alone are unable to pinpoint disease-causing single nucleotide polymorphisms (SNPs). noncoding SNPs, which represent the majority of GWAS SNPs, present a particular challenge. To address this challenge, an array of computational tools designed to prioritize and predict the function of noncoding GWAS SNPs have been developed. However, fewer than 40% of GWAS publications from 2015 utilized these tools. We discuss several leading methods for annotating noncoding variants and how they can be integrated into research pipelines in hopes that they will be broadly applied in future GWAS analyses.

关键词： NUCLEOTIDES GENETIC polymorphisms non-coding dna COMPUTATIONAL biology HUMAN genetics variation

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Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

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SYSTEMATIC BIOLOGY 2017年第5期66卷 857-879页

作者： Reddy, Sushma Kimball, Rebecca T. Pandey, Akanksha Hosner, Peter A. Braun, Michael J. Hackett, Shannon J. Han, Kin-Lan Harshman, John Huddleston, Christopher J. Kingston, Sarah Marks, Ben D. Miglia, Kathleen J. Moore, William S. Sheldon, Frederick H. Witt, Christopher C. Yuri, Tamaki Braun, Edward L. Loyola Univ Chicago Dept Biol 1032 W Sheridan Rd Chicago IL 60660 USA Univ Florida Dept Biol Gainesville FL 32607 USA Univ Florida Florida Museum Nat Hist Gainesville FL 32607 USA Univ Maryland Behav Ecol Evolut & Program College Pk MD 20742 USA Field Museum Nat Hist Chicago IL 60605 USA 74869 Pepperwood Way San Jose CA 95124 USA Smithsonian Inst Collect Program Natl Museum Nat Hist 4210 Silver Hill Rd Suitland MD 20746 USA Dept Biol & Coastal Studies Ctr Bowdoin Coll Coll Stn Brunswick ME 04011 USA Wayne State Univ Dept Biol Sci 5047 Gullen Mall Detroit MI 48202 USA Louisiana State Univ Museum Nat Sci & Dept Biol Sci 119 Foster Hall Baton Rouge LA 70803 USA

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [similar to 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade;and 2) collecting fewer characters (similar to 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich datamatrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of whic

关键词： Birds coding exons GTR model model fit Neoaves non-coding dna phylogenomics taxon sampling

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