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Related Concept Videos

The Nucleosome02:33

The Nucleosome

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DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
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The Nucleosome Core Particle01:12

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
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Nucleosome Remodeling02:54

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Histone Modification02:32

Histone Modification

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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...
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Heterochromatin02:38

Heterochromatin

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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.
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Structures of +1 nucleosome-bound PIC-Mediator complex.

Xizi Chen1, Xinxin Wang1, Weida Liu1

  • 1Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.

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Summary

The +1 nucleosome organizes the preinitiation complex (PIC) and Mediator on eukaryotic promoters, facilitating transcription initiation. This nucleosome acts as a barrier, but its specific binding patterns are key to coordinating PIC-Mediator assembly.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Gene Regulation

Background:

  • Eukaryotic transcription initiation involves preinitiation complex (PIC) assembly at core promoters.
  • The +1 nucleosome, positioned downstream of the transcription start site (TSS), is recognized as a transcriptional barrier.
  • Understanding the interaction between nucleosomes and transcription machinery is crucial for deciphering gene regulation.

Purpose of the Study:

  • To elucidate the molecular mechanism of PIC-Mediator organization on chromatin.
  • To investigate the structural role of the +1 nucleosome in coordinating PIC-Mediator assembly.
  • To reveal how the +1 nucleosome influences transcription initiation.

Main Methods:

  • High-resolution structural analysis of PIC-Mediator bound to the +1 nucleosome.
  • Biochemical assays to determine binding preferences and interactions.
  • Chromatin immunoprecipitation to study in vivo organization.

Main Results:

  • PIC-Mediator preferentially binds the T40N nucleosome, located 40 base pairs downstream of the TSS.
  • Specific contacts were observed with T50N but not T70N nucleosomes.
  • The +1 nucleosome facilitates PIC-Mediator organization by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26.

Conclusions:

  • The +1 nucleosome plays a significant role in regulating transcription initiation.
  • Multiple nucleosome-binding patterns of PIC-Mediator highlight its structural role in assembly coordination.
  • This study reveals the intricate molecular mechanisms governing PIC-Mediator organization on chromatin.