Name: histone tail modifications in nucleosomes
Uploaded: 2020-11-23T11:47:35.000Z
Duration: 2 min 10 s
Channel: JoVE

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Pennsylvania State Academic Standards

9-12

Life Science

Inheritance and Variation of Traits

3.1.9-12.P

The Nucleosome Core Particle

The nucleosome core particle consists of an octamer containing four kinds of histones encircled by a left-handed coil of DNA. Nucleosome core particles play an important role in DNA function by controlling DNA compaction and chromatin structure.&#160;
This role is so essential that histones are some of the most highly conserved proteins in eukaryotes - from peas to cows and other organisms. For example, there are only two different amino acids out of 102 between the H4 histones of a pea plant and a cow.&#160;
The four kinds of histones that make up the nucleosome core particle, H2A, H2B, H3, and H4, share some characteristics. First, they are each small - only containing up to 135 amino acids.&#160;
Second, they share a common structural motif: the histone fold. The histone fold consists of three &#945;-helices connected by two loops.&#160;
When nucleosome core particles are assembled, histone folds bind to each other first in an interaction described as a &#8216;handshake,&#8217; forming two H2A-H2B dimers and two H3-H4 dimers.&#160;
After this, the H3-H4 dimers form a tetramer, which goes on to form the octamer of the nucleosome core particle with the H2A-H2B dimers.&#160;
The structure of this histone octamer begets extensiv

the 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 bound to the histones for replication and transcription. The mechanism by which nucleosomes solve these two problems is via partial unfolding of the DNA from the nucleosomes or histone protein modifications.
Core structure
The histone core proteins share a common structurally conserved motif called the &#8220;histone fold&#8221; and have a mobile extended tail region. The histone fold is made up of alpha-helices and loops. During the histone dimerization, loops of two histone proteins align together, forming a histone dimer.
Each histone binds to the three consecutive minor grooves of DNA. The alpha-helix and the N-terminal tail of each histone protein play a crucial role in binding to the DNA. Hence, any chemical modifications to the histone tail can modify the chromatin assembly and function. Some of the most common histone modifications include acetylation, methylation, and phosphorylation.
Histone variants
Histone proteins have various isoforms or variants like H2A.1, H2A.2, H2A.X, H3.3, or CENP-A. These variants differ in their amino acid sequences and perform distinct functions. The nucleosomes with histone variants are significantly more mobile than ordinary nucleosomes. For example, incorporation of H2A.Z into the nucleosome is shown to activate the transcription.

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 ...

Education

JoVE Core

Molecular Biology

Unit 1

DNA and Chromosome Structure

KEY TERMS AND CONCEPTS

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 handle this by allowing partial DNA unfolding or by using histone protein modifications.

The histone core proteins share a conserved structural feature called the histone fold. This fold contains alpha-helices and loops, and the proteins also have a mobile extended tail region. During histone dimerization, loops from two histone proteins align to form a dimer. Each histone binds to three consecutive minor grooves of DNA, and the alpha-helix plus the N-terminal tail help with this binding.

Changes to the histone tail can alter chromatin assembly and function. Common histone modifications include acetylation, methylation, and phosphorylation. These chemical changes can influence how tightly DNA is packaged and how accessible it is to cellular enzymes.

Histone proteins also exist as variants, or isoforms, such as H2A.1, H2A.2, H2A.X, H3.3, and CENP-A. These variants differ in amino acid sequence and carry out different roles. Nucleosomes with histone variants are often more mobile than ordinary nucleosomes. For example, adding H2A.Z to a nucleosome is linked to transcription activation.

Histone Tail Modifications in Nucleosomes

histone-tail-modifications-in-nucleosomes

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...

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...

chromatin packaging

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...

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

Learn how nucleosomes package DNA, how histone tail changes affect chromatin, and how histone variants like H2A.Z can support transcription.

Histone Tail Modifications in Nucleosomes | JoVE K12

molecular biology

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High School

Life Sciences

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Heredity: Inheritance And Variation Of Traits

HS-LS3-1

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South Carolina College and Career Ready Science Standards

Biology

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From Molecules to Organisms: Structures and Processes

B-LS1-1.

What is the Cell Cycle?

The cell cycle refers to the sequence of events occurring throughout a typical cell&#8217;s life. In eukaryotic cells, the somatic cell cycle has two ...

Interphase

The cell cycle occurs over approximately 24 hours (in a typical human cell) and in two distinct stages: interphase, which includes three phases of the ...

The Cell Cycle Control System

Positive Regulator Molecules

Inhibition of CDK Activity

Mitosis and Cytokinesis

In eukaryotes, the cell division cycle is divided into distinct, coordinated cellular processes that include cell growth, DNA replication/chromosome ...

Chromosome Duplication

Cohesins

Condensins

The Mitotic Spindle

Centrosome Duplication

Spindle Assembly

Attachment of Sister Chromatids

Forces Acting on Chromosomes

Separation of Sister Chromatids

The Spindle Assembly Checkpoint

Anaphase A and B

Anaphase Promoting Complex

The Contractile Ring

Determining the Plane of Cell Division

The Phragmoplast

Distribution of Cytoplasmic Content

An Introduction to Cell Division

Cell division is the process by which a parent cell divides and gives rise to two or more daughter cells. It is a means of reproduction for single-cell ...

Cell Cycle Analysis

Cell cycle refers to the set of events through which a cell grows, replicates its genome, and ultimately divides into two daughter cells through the ...

Live Cell Imaging of Mitosis

Mitosis is a form of cell division in which a cell&#8217;s genetic material is divided equally between two daughter cells. Mitosis can be broken down into ...

Fertilization

During fertilization, an egg and sperm cell fuse to create a new diploid structure. In humans, the process occurs once the egg has been released from the ...

Cleavage and Blastulation

After a large-single-celled zygote is produced via fertilization, the process of cleavage occurs while zygotes travel through the uterine tube. Cleavage ...

Gastrulation

Gastrulation establishes the three primary tissues of an embryo: the ectoderm, mesoderm, and endoderm. This developmental process relies on a series of ...

Neurulation

Neurulation is the embryological process which forms the precursors of the central nervous system and occurs after gastrulation has established the three ...

Cell Migration

Cell migration, the process by which cells move from one location to another, is essential for the proper development and viability of organisms ...

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An Introduction to Developmental Genetics

Development is the complex process through which a single-celled embryo transforms into a multicellular organism. Developmental processes are guided by ...

An Introduction to Organogenesis

Organogenesis is the process by which organs arise from one of three germ layers during the later stages of embryonic development. Researchers studying ...

Fate Mapping

Fate mapping is a technique used to understand how embryonic cells divide, differentiate, and migrate during development. In classic fate mapping ...

Students who demonstrate understanding can use a model to illustrate the role of cellular division (mitosis) and differentiation in producing and maintaining complex organisms.  Assessment Boundary: Assessment does not include specific gene control mechanisms or rote memorization of the steps of mitosis.

3.1.9-12.D

DNA Packaging

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The ...

Organization of Genes

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the ...

Chromosome Structure

A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA ...

Chromosome Replication

Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone ...

The 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 ...

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA ...

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 ...

Karyotyping

Proteins: From Genes to Degradation

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA ...

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between ...

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations ...

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Genome Size and the Evolution of New Genes

Gene Families

Students who demonstrate understanding can ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring. Assessment Boundary: Assessment does not include the phases of meiosis or the biochemical mechanism of specific steps in the process.

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the ...

Binary Fission

Fission is the division of a single entity into two or more parts, which regenerate into separate entities that resemble the original. Organisms in the ...

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the ...

What is Meiosis?

Meiosis is the process by which diploid cells divide to produce haploid daughter cells. In humans, each diploid cell contains 46 chromosomes, half from ...

Meiosis I

Meiosis is a carefully orchestrated set of cell divisions, the goal of which&#x2014;in humans&#x2014;is to produce haploid sperm or eggs, each containing ...

Meiosis II

Meiosis II is the second and final stage of meiosis. It relies on the haploid cells produced during meiosis I, each of which contain only 23 ...

Crossing Over

Unlike mitosis, meiosis aims for genetic diversity in its creation of haploid gametes. Dividing germ cells first begin this process in prophase I, where ...

Nondisjunction

During meiosis, chromosomes occasionally separate improperly. This occurs due to failure of homologous chromosome separation during meiosis I or failed ...

Base-pairing and DNA Repair

The DNA Replication Fork

Lagging Strand Synthesis

The Replisome

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template ...

Replication in Prokaryotes

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the ...

Replication in Eukaryotes

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before ...

Students who demonstrate understanding can make and defend a claim based on evidence that inheritable genetic variations may result from (1) new genetic combinations through meiosis, (2) viable errors occurring during replication, and/or (3) mutations caused by environmental factors. Assessment Boundary: Assessment does not include the phases of meiosis or the biochemical mechanism of specific steps in the process.

3.1.9-12.Q

Histone Tail Modifications in Nucleosomes

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