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Related Concept Videos

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
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
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Genomic methods in profiling DNA accessibility and factor localization.

David C Klein1, Sarah J Hainer2

  • 1Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.

Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology
|November 29, 2019
PubMed
Summary
This summary is machine-generated.

New sequencing technologies reveal DNA accessibility and protein binding sites on chromatin. These methods help identify gene regulatory regions and understand gene expression control.

Keywords:
ATACCUT&RUNChIPChromatinDNaseMNasegenomicsnucleosome occupancytranscription factors

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Next-generation sequencing advances enable genome-wide DNA accessibility and protein localization studies.
  • Chromatin accessibility and histone occupancy correlate with gene expression regulation.
  • Identifying regulatory elements like enhancers and promoters is crucial for understanding gene control.

Purpose of the Study:

  • To review techniques for assessing DNA accessibility and nucleosome positioning.
  • To discuss methods for detecting and characterizing chromatin-bound proteins.
  • To compare the advantages, disadvantages, and development of these genomic techniques.

Main Methods:

  • DNA accessibility and nucleosome positioning: DNase-seq, FAIRE-seq, MNase-seq, ATAC-seq.
  • Chromatin-bound protein detection: ChIP-seq, DamID, CUT&RUN.
  • Review of protocols, optimization, resolution, specificity, and ease of use.

Main Results:

  • Various techniques offer different resolutions, specificities, and ease of use for genomic analysis.
  • Complementary methods provide comprehensive insights into chromatin architecture.
  • These approaches are essential for mapping regulatory elements and protein-DNA interactions.

Conclusions:

  • Techniques for analyzing DNA accessibility and protein binding are vital for understanding gene regulation.
  • Comparative analysis aids researchers in selecting appropriate methods for their studies.
  • These genomic tools offer an unparalleled view of chromatin structure and function.