Population Epigenetics

Mobile genetic elements are discrete DNA elements that can move around and copy themselves in a genome. As a ubiquitous component of the genome, mobile elements contribute to both genetic and epigenetic variation. Therefore, it is important to determine the genome-wide distribution of mobile elements. Here we present a targeted high-throughput sequencing protocol called Mobile Element Scanning (ME-Scan) for genome-wide mobile element detection. We will describe oligonucleotides design, sequencing library construction, and computational analysis for the ME-Scan protocol.

[1]  C. Bock.  Analysing and interpreting DNA methylation data , 2012, Nature Reviews Genetics.

[2]  Reiner Schulz,et al.  Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers , 2012, GigaScience.

[3]  J. V. Moran,et al.  Dynamic interactions between transposable elements and their hosts , 2011, Nature Reviews Genetics.

[4]  G. Kristiansen,et al.  Development of a diagnostic microarray assay to assess the risk of recurrence of prostate cancer based on PITX2 DNA methylation. , 2010, The Journal of molecular diagnostics : JMD.

[5]  T. Bestor,et al.  Eukaryotic cytosine methyltransferases. , 2005, Annual review of biochemistry.

[6]  G. Kristiansen,et al.  Improved PCR Performance Using Template DNA from Formalin-Fixed and Paraffin-Embedded Tissues by Overcoming PCR Inhibition , 2013, PloS one.

[7]  E. Birney,et al.  An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). , 2008, Genome research.

[8]  L. E. McDonald,et al.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[9]  L. Bereczki,et al.  Optimization of PCR amplification for B-and T-cell clonality analysis on formalin-fixed and paraffin-embedded samples , 2008, Pathology & Oncology Research.

[10]  G. Kristiansen,et al.  DNA Methylation Analysis of Free-Circulating DNA in Body Fluids. , 2018, Methods in molecular biology.

[11]  Huanming Yang,et al.  The DNA Methylome of Human Peripheral Blood Mononuclear Cells , 2010, PLoS biology.

[12]  Shankar Balasubramanian,et al.  Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine , 2013, Nature Protocols.

[13]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[14]  J. Kuykendall,et al.  Efficiency of DNA-histone crosslinking induced by saturated and unsaturated aldehydes in vitro. , 1992, Mutation research.

[15]  Stephan Beck,et al.  Taking the measure of the methylome , 2010, Nature Biotechnology.

[16]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[17]  R. Stewart,et al.  Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells , 2011, Nature.

[18]  Peter L Molloy,et al.  DNA methylation: Bisulphite modification and analysis , 2006, Nature Protocols.

[19]  Christian Pilarsky,et al.  Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. , 2009, Clinical chemistry.

[20]  J. Rogers,et al.  DNA methylation profiling of human chromosomes 6, 20 and 22 , 2006, Nature Genetics.

[21]  M. Batzer,et al.  The impact of retrotransposons on human genome evolution , 2009, Nature Reviews Genetics.

[22]  Joakim Lundeberg,et al.  Generations of sequencing technologies. , 2009, Genomics.

[23]  Stephan Beck,et al.  Methylome analysis using MeDIP-seq with low DNA concentrations , 2012, Nature Protocols.

[24]  D. Dietrich,et al.  SHOX2 DNA Methylation Is a Biomarker for the Diagnosis of Lung Cancer in Plasma , 2011, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[25]  G. Kristiansen,et al.  Diagnostic and Prognostic Value of SHOX2 and SEPT9 DNA Methylation and Cytology in Benign, Paramalignant and Malignant Pleural Effusions , 2013, PloS one.

[26]  M. Lacey,et al.  DNA methylation and differentiation: silencing, upregulation and modulation of gene expression. , 2013, Epigenomics.

[27]  M. Batzer,et al.  Repetitive Elements May Comprise Over Two-Thirds of the Human Genome , 2011, PLoS genetics.

[28]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[29]  N. Blow.  Tissue preparation: Tissue issues , 2007, Nature.

[30]  Thomas Rösch,et al.  Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer , 2013, Gut.

[31]  G. Reifenberger,et al.  MGMT promoter methylation in malignant gliomas: ready for personalized medicine? , 2010, Nature Reviews Neurology.