Name: dna packing inside the nucleus
Uploaded: 2020-11-23T11:47:35.000Z
Duration: 2 min 21 s
Channel: JoVE

K12 Standards

Pennsylvania State Academic Standards

9-12

Life Science

Inheritance and Variation of Traits

3.1.9-12.P

Chromatin Packaging

Every human diploid cell contains about 2 meters of DNA compressed inside a tiny nucleus of just a few microns in diameter. The arrangement and coiling of DNA inside the nucleus is therefore highly organized, and tightly regulated.
First, the chromosomal DNA is associated with histone proteins to form a structure called the chromatin. The basic structural and functional unit of chromatin is called a nucleosome. The association of the DNA into nucleosomes shortens the DNA length sevenfold.&#160;
Next, a non-core histone protein called H1 binds to each nucleosome. The H1 histone changes the DNA path as it exits the nucleosome, helping to further compact the complex.
These nucleosomes are then stacked on top of each other, generating a shorter and thicker fiber with a diameter of 30 nm, known as 30-nm fibers.&#160;&#160;
The arrangement of nucleosomes into the 30-nm fiber is explained by a widely accepted Solenoid model. The model proposes that nucleosomes are arranged in a left-handed helical conformation with six or more nucleosomes per turn. This shortens the DNA length by a further 50-fold.
Any chromatin region that is not being actively transcribed or replicated exists in the 30-nm fiber form.

chromatin 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?&#160;
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 highest level of compaction is achieved during the cell cycle&#39;s metaphase, where the chromatin condenses to form the chromatids of a chromosome.
Nucleosomes
Nucleosomes are the basic functional and repeating unit of chromatin. A nucleosome consists of 8 histone proteins wound around by 147 base pairs of DNA. Under electron microscopy, the chromatin appears as a structure resembling beads on a string due to nucleosomes&#39; presence along its length. This packaging shortens the fiber length by seven-fold.
Solenoid model
The nucleosomes are further coiled into 30 nm fibers, so-called because of their diameter of approximately 30 nm. Such a compaction is explained by a widely accepted hypothesis - the solenoid model. A solenoid refers to the structure of a wire coiled on a central axis. This model proposes that nucleosomes are arranged in a left-handed helical conformation with six or more nucleosomes per turn. One of the non-core histone proteins, H1, plays an essential role in nucleosome compaction; in its absence the chromatin fiber turns into irregular clumps of nucleosomes.
Chromatin packaging is an active area of research. The new emerging data has allowed scientists to view chromatin and nucleosomes not as highly defined structures, but rather as a continuum of various inter-convertible conformations at all chromatin packaging stages.

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 ...

Education

JoVE Core

Molecular Biology

Unit 1

DNA and Chromosome Structure

KEY TERMS AND CONCEPTS

dna packing inside the nucleus

DNA packing inside the nucleus depends on chromatin and histones. Each human somatic cell contains about 6 billion base-pairs of DNA. Because each base-pair is 0.34 nm long, a diploid cell holds about 2 meters of DNA. That long strand must fit inside a nucleus that is only 10 to 20 microns wide.

Chromatin is the compact DNA-protein complex formed when the DNA double helix combines with specialized DNA-binding proteins called histones. Chromatin is then packed even further into higher-order structures. The most condensed form appears during metaphase, when chromatin tightens into the chromatids of a chromosome.

Nucleosomes are the basic repeating units of chromatin. Each nucleosome contains 8 histone proteins wrapped by 147 base pairs of DNA. Under electron microscopy, chromatin looks like beads on a string because nucleosomes sit along its length. This level of packing shortens the fiber by about seven-fold.

The nucleosomes are coiled again into 30 nm fibers, which are named for their approximate diameter. A widely accepted idea that explains this step is the solenoid model. In this model, nucleosomes form a left-handed helix with six or more nucleosomes per turn.

One non-core histone protein, H1, is important for nucleosome compaction. When H1 is missing, the chromatin fiber becomes irregular clumps of nucleosomes. Chromatin packaging is still an active area of research. New findings suggest that chromatin and nucleosomes may exist as a continuum of inter-convertible forms across all stages of packaging.

DNA Packing Inside the Nucleus

dna packaging

DNA Packaging in Chromosomes

DNA packaging in chromosomes helps cells fit long DNA molecules into a compact space. The DNA must be organized so it can be stored and used by the cell. This packaging also supports chromosome structure. In eukaryotic cells, DNA wraps around histone proteins. Histones help form chromatin, which is the DNA-protein material that makes up chromosomes. This arrangement packs DNA more tightly while still keeping it organized. The way DNA is packaged affects how a cell manages its genetic material.

dna as a genetic template

DNA Replication Proved by Meselson-Stahl

DNA replication was confirmed by the Meselson and Stahl experiment, which tested how DNA copies itself. The experiment also connects to the Watson-Crick model of DNA, first proposed in 1952. That model was built from X-ray crystallography work by Rosalind Franklin and Maurice Wilkins, and Watson, Crick, and Wilkins later shared the 1962 Nobel Prize in Physiology or Medicine. Franklin was not included, and that decision remains debated. The Watson-Crick model describes DNA as two strands of...

organization of genes

Genes on Chromosomes: DNA Organization

Genes are organized within DNA and packed into chromosomes. This structure helps keep genetic information arranged and readable inside the cell. A gene is a segment of DNA that carries instructions for a specific trait or product. In many genes, the coding sequence is broken into exons, which are the parts that remain in the final message, and introns, which are removed before the message is used. The order of these parts is part of how genes are organized. Genes also include regulatory...

chromosome structure

Chromosome Ends, Centers, and Replication

A functional eukaryotic chromosome needs three key parts: a centromere, telomeres, and many origins of replication. These regions help the chromosome stay organized, copy its DNA, and move correctly during cell division. The centromere is a DNA sequence that holds sister chromatids together. After the chromosome is replicated, this region is where kinetochores are built. Kinetochores are protein complexes that bind spindle microtubules, which help move chromosomes within the cell during...

chromosome replication

Origins of Replication in Chromosomes

Chromosome replication starts at many origins of replication during the S phase of the cell cycle. Each chromosome copies its DNA at the same time. The process also includes the histone and non-histone proteins attached to the DNA. By the time the cell reaches M phase and is ready to divide, its chromosomal mass has effectively doubled. Replication begins at nucleotide sequences called origins of replication. These sites work with specialized initiator proteins that start DNA separation and...

the nucleosome

How DNA Is Packed into Nucleosomes

DNA in a human cell is almost 2 m long, yet it fits inside a nucleus that is only a few microns wide. To make this possible, DNA is packed into several higher levels of compaction. The most compact form is a chromosome, which can be seen under a microscope in a dividing cell. A key step in this packing process is the nucleosome. In a nucleosome, DNA winds twice around a histone core made of 8 histone proteins. This DNA and histone protein complex is the fundamental and functional unit of DNA...

the nucleosome core particle

Histone Tail Modifications in Nucleosomes

Nucleosomes are DNA wrapped around a histone core. The core is an octamer, or eight-protein complex, made of two copies each of H2A, H2B, H3, and H4. This DNA-histone structure helps package DNA while still keeping it organized inside the cell. Nucleosomes have to balance two opposite jobs. They protect delicate DNA from physical damage and help create a higher level of compaction. At the same time, they must let polymerase enzymes reach the DNA for replication and transcription. Nucleosomes...

nucleosome remodeling

How Chromatin Opens for DNA Access

Chromatin must open at the right time so proteins can reach DNA. Nucleosomes, the basic units of chromatin compaction, wrap DNA tightly around a histone core. This packing makes DNA less accessible to proteins such as DNA polymerase and RNA polymerase. Eukaryotic cells use ATP-dependent nucleosome remodeling enzymes to solve this problem. These enzymes bind to histones and the wrapped DNA. They can shift nucleosomes along DNA, a process called nucleosome sliding, or replace part or all of the...

DNA packing inside the nucleus depends on chromatin and histones. Each human somatic cell contains about 6 billion base-pairs of DNA. Because each base-pair is 0.34 nm long, a diploid cell holds about 2 meters of DNA. That long strand must fit inside a nucleus that is only 10 to 20 microns wide. Chromatin is the compact DNA-protein complex formed when the DNA double helix combines with specialized DNA-binding proteins called histones. Chromatin is then packed even further into higher-order...

karyotyping

Chromosome Pairing and Karyotypes

Chromosome pairing and karyotypes help scientists study the number and structure of chromosomes in a cell. A karyotype is a visual display of chromosomes arranged in matching pairs. It can reveal large-scale changes that affect chromosome shape or count. To make a karyotype, chromosomes are first collected when they are most condensed and easiest to see. They are then stained and photographed so the pairs can be organized. The finished image gives a clear view of the full chromosome set in one...

position-effect variegation

Chromatin Spreading and Gene Silencing

Chromatin spreading can silence a gene when it moves near heterochromatin. This effect is called position-effect variegation, or PEV. It happens because the gene’s location changes, not because the gene itself changes. Emil Heitz first noticed that some chromatin in moss nuclei spread out during interphase, while other regions stayed compact. He named the open form euchromatin and the compact form heterochromatin. He suggested that heterochromatin marked a part of the genome that was...

histone modification

Histone Marks and Gene Control

Histone marks help control how tightly DNA is packed and how genes are turned on or off. Histone proteins have a flexible N-terminal tail that extends out from the nucleosome. These tails can be modified after the protein is made. Common modifications include acetylation, methylation, phosphorylation, and ubiquitination. Different combinations of these changes create a histone code. This code influences chromatin folding and tissue-specific gene expression. In other words, the same DNA can...

spreading of chromatin modifications

Histone Marks and Chromatin Boundaries

Histone marks help control how tightly DNA is packed in chromatin. These post-translational modifications, or PTMs, happen on histone proteins in nucleosomes and can increase or decrease access to DNA. Common PTMs include methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone marks carry specific meaning for the cell. For that reason, they are often called the histone code. The protein complex that helps place and read...

lampbrush chromosomes

Lampbrush Chromosomes in Oocyte Meiosis

Lampbrush chromosomes are large chromosomes found in oocytes during meiosis. They are best known from lower vertebrates, invertebrates, and birds. Their unusual shape and size make them a useful model for studying chromosome structure and gene activity. Flemming first observed lampbrush chromosomes in salamander eggs in 1882. Later, in 1892, Rückert saw them in shark egg cells and gave them their name. He chose the term because they looked like the brushes used to clean kerosene lamps. These...

polytene chromosomes

Polytene Chromosomes in Salivary Glands

Polytene chromosomes are giant interphase chromosomes made of many DNA strands aligned side by side. They were first described by Balbiani in 1881. They are often called salivary gland chromosomes because they are regularly seen in salivary gland cells, especially in Drosophila. These chromosomes are found in insects of the order Diptera and Collembola. They also appear in certain organs of mammals and in synergids and antipodes of flowering plants. In larvae of Chironomus plumosus, they were...

histone variants at the centromere

CENP-A and Centromere Identity

CENP-A is a specialized histone H3 variant found in centromeric chromatin. It has about 60% similarity to canonical histone H3. This histone variant helps build the kinetochore, the protein structure that links chromosomes to microtubules during cell division. CENP-A is also thought to act as an epigenetic mark. An epigenetic mark is a signal that helps cells keep centromere identity without changing the DNA sequence. The centromere-targeting process depends on the CENP-A targeting domain, or...

inheritance of chromatin structures

Epigenetic Memory in Chromatin

Epigenetic memory in chromatin helps cells keep their identity without changing the DNA sequence. Epigenetics is the study of inherited changes in cell phenotype that do not alter DNA. This kind of memory helps maintain cell lineage, position-effect variegation, dosage compensation, and chromatin structures such as telomeres and centromeres. Centromeres are a clear example of this process. Their structure and location on chromosomes can be inherited epigenetically. Centromere function is not...

euchromatin

Euchromatin and DNA Packaging

Euchromatin is the less compact form of chromatin. Chromatin can be studied by staining DNA with specific dyes, because dense regions take up more dye and appear darker under the microscope. Lighter-staining areas are less compact, and euchromatin is one of these regions. This open chromatin state is linked to histone changes. Histone H3 in euchromatin is extensively acetylated on lysine 9. In promoter regions, histones can also carry methylated lysine 4 and phosphorylation at position 10.

chromatin position affects gene expression

chromatin-position-affects-gene-expression

Chromatin Folding Shapes Gene Activity

Chromatin folding inside the nucleus shapes gene activity in eukaryotic cells. Chromatin is the large complex of DNA and proteins packed into the nucleus. How it is arranged affects how easily genetic information can be reached. In general, the nucleus periphery is linked with lower transcription, while the cell interior is linked with more active transcription. Gene promoters are often kept physically separate from regulatory DNA elements such as enhancers. To turn on gene expression, these...

heterochromatin

Heterochromatin Staining and Chromatin Packing

Heterochromatin is the tightly packed form of chromatin, and it can be seen by staining DNA with specific dyes. Under the microscope, these dense regions take up more dye than less compact chromatin. Heterochromatin is usually divided into constitutive heterochromatin and facultative heterochromatin. Constitutive heterochromatin is a highly compact part of chromatin. It is mostly found at centromeres and telomeres. In this form, the amino acid at position 9 on the histone H3 tail is di- or...

key terms and concepts

See how 2 meters of DNA fit inside a tiny nucleus through chromatin, nucleosomes, histones, and the solenoid model in high school biology.

DNA Packing Inside the Nucleus | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

Louisiana Student Standards for Science

High School

Life Sciences

heredity-inheritance-and-variation-of-traits

Heredity: Inheritance And Variation Of Traits

HS-LS3-1

Alabama Course of Study Science

Biology

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

9-12.B.1.2.b

Next Generation Science Standards

Heredity: Inheritance and Variation of Traits

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South Carolina College and Career Ready Science Standards

B-LS1-1.

new-york-state-science-learning-standards

New York State Science Learning Standards

HS-LS3-1.

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3.1.9-12.D

DNA Packaging

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3.1.9-12.Q

DNA Packing Inside the Nucleus

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