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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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Next-generation technologies and data analytical approaches for epigenomics.

Klaas Mensaert1, Simon Denil, Geert Trooskens

  • 1Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.

Environmental and Molecular Mutagenesis
|December 12, 2013
PubMed
Summary
This summary is machine-generated.

Epigenetics involves heritable traits that alter gene expression without changing DNA sequence. This review covers epigenomics technologies for profiling these traits, crucial for understanding diseases and environmental impacts.

Keywords:
DNA hydroxymethylationDNA methylationbioinformaticsdata analysisepigeneticsepigenomicshistone modificationsnoncoding RNAnucleosome positioningsequencing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Biotechnology

Background:

  • Epigenetics describes heritable gene expression modifications independent of DNA sequence.
  • Epigenetic flexibility aids cellular differentiation and environmental adaptation.
  • Epigenetic alterations are implicated in human diseases like cancer.

Purpose of the Study:

  • To review and compare innovative epigenomics technologies for genome-scale profiling.
  • To highlight methods for assessing DNA methylation, noncoding RNA, histone modifications, and nucleosome positioning.
  • To discuss challenges and solutions in epigenomic data analysis and application to non-model organisms.

Main Methods:

  • Comparison of next-generation sequencing-based epigenomics methods.
  • Inclusion of array- and PCR-based techniques.
  • Discussion of emerging single-molecule sequencing advantages.

Main Results:

  • Several innovative epigenomics technologies have revolutionized the field.
  • Next-generation sequencing methods are widely used, alongside traditional techniques.
  • Data analysis presents a bottleneck, with strategies for preprocessing and statistical analysis outlined.

Conclusions:

  • Accurate and cost-efficient epigenomic profiling is vital for disease research and monitoring environmental exposures.
  • The review provides a comprehensive overview of current epigenomics technologies and analytical considerations.
  • Future directions include leveraging single-molecule sequencing and addressing challenges in non-model species.