scholarly journals Severe Progressive Autism Associated with Two de novo Changes: A 2.6-Mb 2q31.1 Deletion and a Balanced t(14;21)(q21.1;p11.2) Translocation with Long-Range Epigenetic Silencing of LRFN5 Expression

2010 ◽  
Vol 1 (1) ◽  
pp. 46-57 ◽  
Author(s):  
D.R.H. de Bruijn ◽  
A.H.A. van Dijk ◽  
R. Pfundt ◽  
A. Hoischen ◽  
G.F.M. Merkx ◽  
...  
Keyword(s):  
Long Range ◽  
De Novo ◽  
Epigenetic Silencing

De Novo Mutated TUBB2B Associated Pachygyria Diagnosed by Medical Exome Sequencing and Long-Range PCR

2018 ◽  
Vol 38 (1) ◽  
pp. 63-71 ◽  
Author(s):  
Hui Wang ◽  
Shaoyuan Li ◽  
Shengli Li ◽  
Niping Jiang ◽  
Jimin Guo ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Long Range ◽  
De Novo ◽  
Long Range Pcr

scholarly journals Silencing of Mutator Elements in Maize Involves Distinct Populations of Small RNAs and Distinct Patterns of DNA Methylation

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 379-391 ◽  
Author(s):  
Diane Burgess ◽  
Hong Li ◽  
Meixia Zhao ◽  
Sang Yeol Kim ◽  
Damon Lisch
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Small Rnas ◽  
Cytosine Methylation ◽  
De Novo ◽  
Epigenetic Silencing ◽  
Inverted Repeats ◽  
Causal Relationships ◽  
Terminal Inverted Repeats ◽  
Silencing Pathways

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity and silencing. Here, we show that the process of de novo methylation of an active element in maize involves two distinct pathways, one of which is directly implicated in causing epigenetic silencing and one of which is the result of that silencing. Epigenetic changes involve changes in gene expression that can be heritably transmitted to daughter cells in the absence of changes in DNA sequence. Epigenetics has been implicated in phenomena as diverse as development, stress response, and carcinogenesis. A significant challenge facing those interested in investigating epigenetic phenomena is determining causal relationships between DNA methylation, specific classes of small RNAs, and associated changes in gene expression. Because they are the primary targets of epigenetic silencing in plants and, when active, are often targeted for de novo silencing, TEs represent a valuable source of information about these relationships. We use a naturally occurring system in which a single TE can be heritably silenced by a single derivative of that TE. By using this system it is possible to unravel causal relationships between different size classes of small RNAs, patterns of DNA methylation, and heritable silencing. Here, we show that the long terminal inverted repeats within Zea mays MuDR transposons are targeted by distinct classes of small RNAs during epigenetic silencing that are dependent on distinct silencing pathways, only one of which is associated with transcriptional silencing of the transposon. Further, these small RNAs target distinct regions of the terminal inverted repeats, resulting in different patterns of cytosine methylation with different functional consequences with respect to epigenetic silencing and the heritability of that silencing.

scholarly journals Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells

2013 ◽  
Vol 7 (6) ◽  
pp. 1129-1141 ◽  
Author(s):  
Marta Forn ◽  
Mar Muñoz ◽  
Daniele V.F. Tauriello ◽  
Anna Merlos-Suárez ◽  
Verónica Rodilla ◽  
...  
Keyword(s):  
Long Range ◽  
Epigenetic Silencing ◽  
Normal Cells ◽  
Chromatin Domains

scholarly journals Chromatin co-accessibility is highly structured, spans entire chromosomes, and mediates long range regulatory genetic effects

2019 ◽  
Author(s):  
William W. Young Greenwald ◽  
Agnieszka D’Antonio-Chronowska ◽  
Paola Benaglio ◽  
Hiroko Matsui ◽  
Erin N. Smith ◽  
...  
Keyword(s):  
Long Range ◽  
Binding Sites ◽  
De Novo ◽  
Active Regions ◽  
Chromatin Accessibility ◽  
Chromosome Length ◽  
Genetic Effects ◽  
Rna Seq ◽  
Induced Pluripotent ◽  
Length Analysis

AbstractChromatin accessibility identifies active regions of the genome, often at transcription factor (TF) binding sites, enhancers, and promoters, and contains regulatory genetic variation. Functionally related accessible sites have been reported to be co-accessible; however, the prevalence and range of co-accessibility is unknown. We perform ATAC-seq in induced pluripotent stem cells from 134 individuals and integrate it with RNA-seq, WGS, and ChIP-seq, providing the first long-range chromosome-length analysis of co-accessibility. We show that co-accessibility is highly connected, with sites having a median of 24 co-accessible partners up to 250Mb away. We also show that co-accessibility can de novo identify known and novel co-expressed genes, and co-regulatory TFs and chromatin states. We perform a cis and trans-caQTL, a trans-eQTL, and examine allelic effects of co-accessibility, identifying tens of thousands of trans-caQTLs, and showing that trans genetic effects can be propagated through co-accessibility to gene expression for cell-type and disease relevant genes.

scholarly journals First World War on Europe and the War Literature in Periods of Great Difficulty

2017 ◽  
Vol 7 (1) ◽  
pp. 11
Author(s):  
Ricardo Santos David
Keyword(s):  
Nineteenth Century ◽  
Long Range ◽  
De Novo ◽  
War Literature ◽  
Great Difficulty ◽  
First World War ◽  
World War ◽  
Western Front ◽  
Four Horsemen ◽  
First World

Nowadays, one hundred years after the greatest sea and trench battles, a question is posed: how could this Great European War change not only the continental configurations, but also the concepts of war and war literature? Until the nineteenth century, many saw war as some heroic act through which men could prove their bravery in an open fight, facing the enemy directly. By means of new weapon technology, death comes invisibly: gas, submarines, long-range artilleries, mines, airplanes, tanks, and machine guns. War strategies are altered and the feeling of a worthy fight in order to defend one’s homeland is ended. In this article, the great disillusion with war will be exemplified in the following romances: Erich Maria Remarque’s All Quiet in the Western Front (1929); concerning land warfare, Vicente Blasco Ibáñez’s The Four Horsemen of the Apocalypse (1916), as well as Reinhard Göring’s Expressionist drama Seeschlacht (1917).Primeira Guerra Mundial sobre a Europa e a Literatura de Guerra em Períodos de Grandes DificuldadesHoje, cem anos depois das maiores batalhas navais e de trincheiras, cabe a pergunta: como esta Grande Guerra Europeia mudou não somente as configurações do continente, mas também os conceitos de guerra e de literatura de guerra? Até o século XIX, a guerra era vista por muitos como um ato heroico, pelo qual os homens podiam comprovar a sua valentia numa luta aberta, encarando diretamente o inimigo. Com a nova tecnologia de armas, a morte vem de forma invisível: gás, submarinos, artilharias de longo alcance, minas, aviões, tanques e metralhadoras. Muda-se a estratégia bélica e finda o sentimento de uma luta nobre para defender a pátria. Neste artigo, a grande desilusão com a guerra será exemplificada através dos romances Nada de novo no front (1929) de Erich Maria Remarque, Os quatro cavaleiros do Apocalipse (1916) de Vicente Blasco Ibáñez, abarcando a guerra terrestre, assim como o drama expressionista Batalha naval (1917) de Reinhard Göring.

scholarly journals SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

2019 ◽  
Author(s):  
Lidong Guo ◽  
Mengyang Xu ◽  
Wenchao Wang ◽  
Shengqiang Gu ◽  
Xia Zhao ◽  
...  
Keyword(s):  
Quality Improvement ◽  
Next Generation Sequencing ◽  
Long Range ◽  
De Novo ◽  
Next Generation ◽  
Negative Effects ◽  
Complementary Information ◽  
Screening Algorithm ◽  
Long Reads ◽  
Generation Sequencing

AbstractSynthetic long reads (SLR) with long-range co-barcoding information have been recently developed and widely applied in genomics researches. We proposed a scaffolding model of the co-barcoding information and developed a scaffolding tool with adopting a top-to-bottom scheme to make full use of the complementary information in SLR datasets and a screening algorithm to reduce negative effects from misassembled contigs in an input assembly. In comparison with other available SLR scaffolding tools, our tool obtained the best quality improvement for different input assemblies, especially for those assembled by the next-generation sequencing reads, where the improvement of contiguity is about several hundred-folds.

scholarly journals Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

2019 ◽  
Author(s):  
Zhoutao Chen ◽  
Long Pham ◽  
Tsai-Chin Wu ◽  
Guoya Mo ◽  
Yu Xia ◽  
...  
Keyword(s):  
Long Range ◽  
De Novo ◽  
Low Cost ◽  
Cost Effective ◽  
De Novo Genome Assembly ◽  
Short Read ◽  
Single Tube ◽  
Haplotype Phasing ◽  
A Genome ◽  
Long Read

AbstractLong-range sequencing information is required for haplotype phasing, de novo assembly and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirement. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-Seq™) technology, which enables a low-cost, high-accuracy and high-throughput short-read next generation sequencer to routinely generate over 100 Kb long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcode linked reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate mega-base-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.

scholarly journals Identification of Long-Range Epigenetic Silencing on Chromosome 15q25 and Its Clinical Implication in Gastric Cancer

2015 ◽  
Vol 185 (3) ◽  
pp. 666-678 ◽  
Author(s):  
Jee-Youn Kang ◽  
Sang-Hyun Song ◽  
Jiyeon Yun ◽  
Mi-Seong Jeon ◽  
Yongjun Cha ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Long Range ◽  
Clinical Implication ◽  
Epigenetic Silencing
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