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Mesoscale simulations of two nucleosome-repeat length oligonucleosomes
Tamar Schlick1, Ognjen Perisić
1Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, USA. schlick@nyu.edu
Physical Chemistry Chemical Physics : PCCP
|February 11, 2010
Summary
Chromatin fiber compaction depends on nucleosome repeat length (NRL) and ionic strength. Longer NRL fibers show varied structures and are better for packing, with linker histones aiding compaction alongside counterions.
Area of Science:
- Structural biology
- Biophysics
- Computational modeling
Background:
- Chromatin structure is essential for genome organization and regulation.
- Understanding chromatin compaction is key to deciphering cellular processes.
- Factors influencing chromatin folding remain an active area of research.
Purpose of the Study:
- To investigate how nucleosome repeat length (NRL), linker histone presence, and ionic strength affect chromatin fiber compaction.
- To elucidate the structural heterogeneity and folding patterns of chromatin fibers.
- To provide insights into the interplay of internal and external factors governing chromatin structure.
Main Methods:
- Coarse-grained modeling of chromatin fibers.
- Computer simulations to analyze folding patterns.
- Systematic variation of NRL, linker histone presence, and ionic strength.
Main Results:
- Linker histone influence is minimal on short NRL fibers but significant on longer ones.
- Linker histones act synergistically with concentrated counterions to condense longer NRL fibers.
- Longer NRL fibers display structural heterogeneity, supporting both solenoid-like and zigzag conformations.
- Chromatin compaction is sensitive to both intrinsic (NRL) and extrinsic (ionic strength, linker histone) factors.
Conclusions:
- Longer NRL fibers are more adaptable for achieving diverse levels of chromatin compaction.
- The findings offer a framework for interpreting structural dependencies of chromatin fibers.
- These insights are crucial for understanding chromatin dynamics throughout the cell cycle.
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01:32Chromatin Packaging
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
02:21Chromatin Packaging
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
02:10The Nucleosome Core Particle
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.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
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01:12The Nucleosome Core Particle
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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01:19The Nucleosome
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can 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.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
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02:33The Nucleosome
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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