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Related Concept Videos

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Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Determining Epigenetic Targets: A Beginner's Guide to Identifying Genome Functionality Through Database Analysis.

Elizabeth A Hay1, Philip Cowie1, Alasdair MacKenzie2

  • 1Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.

Methods in Molecular Biology (Clifton, N.J.)
|May 31, 2015
PubMed
Summary
This summary is machine-generated.

The cis-regulatory genome, crucial for health, holds vast genetic information and disease variations. New methods utilize databases like ENCODE and UCSC to identify its functional elements and understand epigenetics in health and disease.

Keywords:
BioinformaticsChromatin modificationCis-regulatory genomeDNA methylationEpigeneticsGenome databasesPolymorphic variation

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • The cis-regulatory genome, containing enhancers, silencers, promoters, and insulators, is a major information source essential for human health.
  • It holds significantly more information than the coding genome and is a key reservoir for disease-associated variations.
  • Epigenetic modifications like DNA methylation and chromatin changes significantly impact gene expression and health maintenance.

Purpose of the Study:

  • To describe methods for identifying and characterizing functional elements of the cis-regulatory genome genome-wide.
  • To explore databases for accessing DNA methylation and chromatin modification datasets.
  • To demonstrate superimposing data from NCBI archives onto the UCSC browser for in vivo study insights.

Main Methods:

  • Utilizing genome-wide databases such as ENCODE, UCSC Genome Browser, and NCBI.
  • Exploring UCSC Genome Browser for DNA methylation and chromatin modification datasets.
  • Superimposing NCBI archive data with UCSC browser data for locus-specific in vivo analysis.

Main Results:

  • Established methods for identifying and characterizing cis-regulatory elements at a genome-wide scale.
  • Provided access to comprehensive epigenetic datasets (DNA methylation, chromatin modifications).
  • Enabled integration of diverse datasets for in-depth genomic locus analysis.

Conclusions:

  • The cis-regulatory genome is a critical, largely untapped resource for understanding health and disease.
  • Integrated analysis of genomic and epigenomic data is essential for advancing personalized medicine.
  • Future research directions will leverage these methods to elucidate the role of epigenetics in disease.