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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...

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Related Experiment Video

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Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

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Published on: March 9, 2022

High nucleosome occupancy is encoded at human regulatory sequences.

Desiree Tillo1, Noam Kaplan, Irene K Moore

  • 1Department of Molecular Genetics, University of Toronto, Toronto, Canada.

Plos One
|February 18, 2010
PubMed
Summary

Human regulatory DNA sequences, including promoters and transcription factor binding sites (TFBSs), exhibit high intrinsic nucleosome occupancy, unlike in yeast. This suggests a mechanism for restricting access to regulatory information in the human genome.

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Active eukaryotic regulatory sites typically feature open chromatin.
  • Yeast promoters and transcription factor binding sites (TFBSs) generally display low intrinsic nucleosome occupancy.

Purpose of the Study:

  • To investigate and contrast intrinsic nucleosome occupancy at human regulatory DNA elements compared to yeast.
  • To explore the genomic features correlating with nucleosome occupancy at human regulatory sites.

Main Methods:

  • Analysis of DNA sequences for intrinsic nucleosome preference.
  • Comparison of intrinsic nucleosome occupancy with experimentally measured in vivo nucleosome occupancy.
  • Correlation analysis between G+C content, poly-A sequence depletion, and nucleosome occupancy.

Main Results:

  • Human promoters, enhancers, and TFBSs generally encode high intrinsic nucleosome occupancy.
  • Experimentally measured nucleosome occupancy in vivo often aligns with high intrinsic occupancy at these human elements.
  • High G+C content positively correlates with intrinsic nucleosome occupancy and is prevalent in these regions, which are depleted for nucleosome-excluding poly-A sequences.

Conclusions:

  • Unlike yeast, human regulatory DNA sequences possess an inherent preference for nucleosome binding.
  • This high nucleosome preference is likely encoded within the DNA sequence itself.
  • The findings suggest a regulatory strategy in the human genome to restrict access to regulatory information, enabling cell-type-specific utilization.