Chromatin - Analysis, Structure and Functions

Aug 03, 2023, 16:45 IST

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The topic “Chromatin” will be covered in this article. DNA, RNA, and related proteins make up the genetic material or macromolecule known as chromatin, which is what eukaryotic cells' chromosomes are made of. When viewed via an extended light microscope, the structure of chromatin, or the so-called nucleosomes, resembles how the string is strung up on beads. DNA is contained within each nucleosome, containing eight proteins known as histones. Later, these nucleosomes are coiled into a solenoid of 30 nm in diameter. Histone proteins exist to support the chromatin structure.

This article will discuss the factors involving the functions and structure of Chromatin, methods to analyze Chromatin, and Chromatin composition and packaging.

Introduction

The DNA and protein mixture that makes up the chromosomes found in the cells of humans and other higher species is known as "chromatin." Numerous proteins, most notably histones, wrap the massive amount of DNA in a genome into a form that can fit inside the cell nucleus.

The length of all the DNA in a cell, which ranges from 5 to 6 feet, must fit neatly inside the nucleus of a cell. DNA molecules initially wrap the histone proteins to form nucleosomes, which are structures that resemble beads on a string.

Further nucleosome assembly results in the fibrous substance known as chromatin. For DNA transcription and replication, chromatin fibers can unwind. When cells divide into daughter cells, replicated chromatins further condense to resemble chromosomes, which are visible under a microscope and are separated during cell division.

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Functions of Chromatin

• DNA Packaging

Compactifying lengthy DNA strands is chromatin's primary function. The compartment in which DNA is housed in the nucleus is much smaller than the length of the DNA itself. The DNA needs to be compressed to fit into this compartment. The packing ratio measures the degree of DNA condensing. DNA is not directly packaged into the structure of chromatin to obtain the overall packing ratio. Instead, it has numerous organizational structures.

The winding of DNA around the nucleosome results in the first level of packing, which has a packing ratio of roughly 6. All chromosomes' euchromatin and heterochromatin include the same structure. Beads are wrapped in a 30 nm fiber at the second level of packing, which is present in both mitotic and interphase chromatin.

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• Transcription Regulation

The transcription process involves proteins reading the genetic data encoded in DNA, converting it into RNA, and then translating the RNA into valuable proteins. No transcription happens if the chromatin becomes stronger and prevents access to the read proteins. Transcription can be carried out by euchromatin, an expanded kind of chromatin. While heterochromatin, a condensed form of chromatin, is crammed too closely together for proteins to read DNA.

Transcriptional bursting, also known as discontinuity of transcription, may be influenced by fluctuations between open and closed chromatin. The attachment and dissociation of transcription factor complexes with chromatin are likely additional variables that play a role.

• Chromatin and DNA Repair

All DNA-based processes are hindered by how DNA is wrapped up in chromatin. Chromatin can easily change its shape and structure because of the very dynamic way that proteins and DNA are arranged. At the site of DNA damage, chromatin relaxes quickly, allowing repair proteins to connect to the damaged DNA and repair it.

Structure of Chromatin

Numerous factors influence the chromatin structure. Phases of the cell cycle play a major role in determining the overall design. They experience several structural alterations during cell division. During metaphase, when the DNA is replicated and split into two cells, the form of the chromosomes changes and is visible under a light microscope.

The chromatin group has three stages:

• Nucleosomes are formed by wrapping DNA around histone proteins.
• The nucleosome is a 30 nm fiber wrapped in many histones.
• The 30 nm fiber's higher level DNA packing into the metaphase chromosome.

Methods to Analyze Chromatin

• ChIP-seq

The widely used chromatin identification technique (Chromatin Immunoprecipitation Sequencing) relies on antibodies that actively choose, recognize, and combine with proteins such as "histones, histone remodeling, transaction factors, and cofactors." Cutting "oligonucleotides" that are unbound has been able to provide information about the state of chromatin and the transaction of a gene.

• DNase-seq

(DNase I hypersensitive sites Sequencing) maps open or accessible areas of the genome by exploiting the sensitivity of accessible regions to the DNase I enzyme.

• FAIRE-seq

(Formaldehyde-Assisted Isolation of Regulatory Elements sequencing) extracts nucleosome-depleted sections of the genome using a two-phase separation technique and the chemical characteristics of protein-bound DNA.

• DNA footprinting

A process called DNA footprinting is used to spot DNA that is bonded to proteins. It combines labeling and fragmentation with gel electrophoresis to pinpoint regions of the genome where proteins have connected.

• ATAC-seq

The Tn5 transposase is used in (Assay for Transposable Accessible Chromatin Sequencing) to integrate (synthetic) transposons into accessible sections of the genome, highlighting the localization of nucleosomes and transcription factors across the genome.

• MNase-seq

The micrococcal nuclease enzyme is used in (micrococcal nuclease sequencing) to pinpoint the locations of nucleosomes across the genome.

• MACC profiling

(Micrococcal nuclease ACCessibility profiling) determines chromatin accessibility. It maps nucleosomes and non-histone DNA-binding proteins in both open and closed regions of the genome using titration series of chromatin digests with micrococcal nuclease.

Chromatin in Mitosis

• Prophase: Chromatin fibers wrap into chromosomes during the mitotic prophase. Two chromatids are connected at the centromere of each replicated chromosome.
• Metaphase: Chromatin gets severely compressed during metaphase.
• Anaphase: During anaphase, sister chromatids and paired chromosomes separate and are drawn to the cell's periphery by spindle microtubules.
• Telophase: Each new daughter chromosome is divided into its nucleus during the telophase process. Chromatin fibers loosen up and loosen up. Two daughter cells with the exact same genetic makeup are created following cytokinesis. Chromatin continues to develop as the chromosomes continue to uncoil and lengthen.

Chromatin Composition and Packaging

Histones

• In histones, the fundamental amino acids lysine and arginine are found in significant amounts.
• The histones receive a net positive charge from these positively charged amino acids, facilitating their interaction with the negatively charged DNA.
• According to structural investigations that show the histone classes have a similar tertiary structure, all histones are ultimately related to one another in terms of evolution.
• Positively charged essential proteins called histones attach to DNA's negatively charged phosphate molecules. Chromatin primarily consists of two components. They are the DNA and corresponding proteins of the cell. Histones are the name for the related proteins.

Role of H1

• The next chromatin level condenses due to histone H1.
• H1 attaches to the linker DNA at one end of the nucleosome and the middle of the DNA segment encircling the core histones.
• H1 holds the DNA in place by clamping around the nucleosome octamer.
• The H1 histone that it connects with and the core particle are collectively referred to as the chromatosome.

Nucleosomes

• When chromatin is taken out of a cell's nucleus and observed under an electron microscope, it resembles a string of beads.
• When nuclease enzymes digest DNA and protein, the nucleosome is formed.
• The fundamental structural and functional unit of chromatin, the nucleosome, is the lowest chromatin level.
• A nucleosome is a core component formed when DNA is twice encircled by an octamer of eight histone proteins (2 copies each of H2A, H2B, H3, H4).
• The nucleosomes coil and are gathered to create chromatin fiber, a type of fiber. With the aid of proteins, these chromatins loop and fold back on themselves to form a chromosome.

Genes in Chromatin

It is possible to turn on or off the genes present in chromatin. It denotes that in some cells, one portion of the gene is turned on while the other is turned off. The on-and-off states of the genes in chromatin were examined by the researchers using the fruit fly as a model organism to verify this. Their study revealed five different chromatin types, each uniquely characterized by specific proteins.

Green, Yellow, Black, Blue, and Red were the colors for these five categories. Yellow and red were fully active genes in the chromatin, whereas black was inert. Green and blue were just half active. They discovered that the genes in Yellow chromatin were activated in nearly all cells because they controlled the essential cellular processes. Because they were controlling more specialized tasks, red chromatins were activated in some particular cells.

Key Points of Chromatin

• Eukaryotic cells may include the protein, RNA, and DNA complex known as chromatin. Its key feature is compacting exceedingly long DNA molecules into a denser shape that prevents the strands from tangling.
• The simple organization of the chromatin system is dependent on the cell cycle stage. The chromatin is structurally loosened during the interphase to give DNA and RNA polymerases access to duplicate the DNA.
• The packing of DNA blocks all DNA-based techniques into chromatin. Chromatin can easily change its structure and shape because of the very dynamic arrangement of proteins and DNA.
• Chromatin relaxation unpredictably takes place at the site of DNA damage, allowing the repaired proteins to attach and repair the DNA.

Chromatin: FAQs

Q1. How does chromatin function, and what exactly is it?

Ans. Chromosomes include a material called chromatin, which is made up of DNA and protein. The genetic code for the cell is contained in the DNA. The most significant proteins in chromatin are histones. The nucleosome is the fundamental component of chromatin, which can be either heterochromatin or euchromatin. The nucleosome is a complex made up of eight proteins and 146 base pairs of DNA coiled in two rounds around the outside of a disk-shaped structure (called histones).

Q2. What do the phases of chromatin mean?

Ans. Chromatin is the least dense and seems to be dispersed loosely around the nucleus during interphase (1). Chromosomes become visible during prophase (2) when chromatin condensation starts. Chromosomes stay condensed during the several stages of mitosis (2-5).

Q3. How many chromosomes make up a chromatid?

Ans. Half of the initial 46 chromosomes, or 23 chromosomes, will be present in each daughter cell. The two chromatids that make up each chromosome are sisters. The daughter cells are currently in meiosis II, the third and last stage of meiosis.

Q4. How many DNA molecules can you find in a chromatid?

Ans. How many DNA molecules can you find in a chromatid? Keep in mind that DNA replication occurs during the cell cycle's S phase. As a result, during mitotic metaphase, each chromosome will have two molecules of double-stranded DNA.

Q5. What are non-sister chromatids and allosomes?

Ans. Any pair of chromatids from two homologous chromosomes is a non-sister chromatid. To exchange genetic material, non-sister chromatids of (homologous chromosomes) create chiasma(ta) during prophase I of meiosis I. An allosome is a sex chromosome different from a typical autosome in size, structure, or behavior.

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