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Related Concept Videos

Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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LTR Retrotransposons03:08

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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
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DNA-only Transposons02:57

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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Retroviruses02:33

Retroviruses

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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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Epigenetic Regulation01:37

Epigenetic Regulation

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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.
X-chromosome...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements.

Lorenzo de la Rica1, Jatinder S Stanley1, Miguel R Branco2

  • 1Blizard Institute, School of Medicine and Dentistry, QMUL, E1 2AT, London, UK.

Methods in Molecular Biology (Clifton, N.J.)
|February 20, 2016
PubMed
Summary
This summary is machine-generated.

This study details three methods to measure DNA methylation and hydroxymethylation, crucial epigenetic modifications. These techniques enable precise analysis of retrotransposon activity and epigenetic regulation in mammals.

Keywords:
BisulfiteDNA hydroxymethylationDNA methylationHigh-throughput sequencingMethylation-sensitive restriction enzymeOxidative bisulfitePyrosequencingQuantitative PCR

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Genomics

Background:

  • DNA methylation is a critical epigenetic regulator of mammalian retrotransposable elements.
  • Oxidation to DNA hydroxymethylation is associated with retrotransposon demethylation and reactivation.

Purpose of the Study:

  • To provide detailed protocols for three methods measuring DNA methylation and hydroxymethylation at specific genomic loci.
  • To enable accurate surveying of retrotransposable element epigenetics.

Main Methods:

  • GlucMS-qPCR for measuring DNA methylation and hydroxymethylation.
  • Pyrosequencing and high-throughput sequencing of bisulfite- and oxidative bisulfite-modified DNA.
  • Single-base resolution analysis of epigenetic modifications.

Main Results:

  • All three methods provide absolute measurements of DNA methylation and hydroxymethylation levels.
  • The study discusses method-specific differences in throughput and target coverage.
  • These techniques are foundational for epigenetics research on retrotransposable elements.

Conclusions:

  • The described protocols offer robust tools for quantifying DNA methylation and hydroxymethylation.
  • Accurate measurement of these epigenetic marks is essential for understanding retrotransposon dynamics.
  • The methods facilitate detailed epigenomic analyses of retrotransposable elements.