A review on human chromosomes

An Introduction to chromosomes:

The ability of the chromosomes in getting stained reveals the true nature of the chromosome (derived from the Greek work word. The word chroma indicates color). These stainable bodies appear like threads under a microscope. They contain the genetic material, mainly the DNA coiled around the proteins. Human chromosomes are visible with when the cell is undergoing mitotic or meiotic cell division. There are total 46 chromosomes in each human cell.

·    Autosomes: There are total 44 autosomes or 22 pairs. Each pair consists of homologous chromosomes. In a pair, one chromosome comes from the father and the other chromosome comes from the mother.

·        Sex Chromosomes: There are two different types of sex chromosomes, X and Y respectively.

The average size of the human metaphase chromosome is 5 millimeters. Chromosomes tightly coil and get condensed during metaphase. Chromosomes appear in different shapes during each phase of the cell cycle. They appear thread-like during interphase. During metaphase, chromosomes look like rod-shaped. They look like V, J or rod-shaped during anaphase. Von Hartz coined the term chromosome. The scientists who first discovered the structure of chromosomes were Schleiden, Virchow, and Bütschli. Walter Sutton and Theodor Boveri independently developed the chromosome theory of inheritance in 1902.

An interphase nucleus contains strands of a material called chromatin. There are two regions in the chromatin, mainly coiled and extended regions.

·    Heterochromatin: It is the dark staining area of the chromatin. There are two types of heterochromatin. Constitutive heterochromatin contains repetitive sequences. It is present near the centromere. Constitutive heterochromatin never expresses itself. There is one more type of heterochromatin, known as facultative heterochromatin, which expresses itself.

·        Euchromatin: It is the light staining area of the chromatin.

The chief constituent of chromatin is DNA, the blueprint of life. At the time of cell division, chromatin strands coil into compact structures, so that they easily fit into the cell nucleus. Chromosomes appear as thick rods only during the cell division. They uncoil and form chromatin at the end of cell division.

Image: Human chromosomes revealed through karyotyping

Structure of the chromosome:

Metaphase chromosome appears clearly under the microscope. Following are the principal point to be discussed:

·        Chromatids: Each metaphase chromosome consists of two symmetrical halves parallel to each other. They are called chromatids. These chromatids are present in the form of chromonema during prophase. There are two types of chromatids mainly, sister and non-sister chromatids. Two chromatids are present on a single chromosome. Thus they are called sister chromatids. The concept of dyad describes a pair of sister chromatids. These structures join with the help of a centromere.  Non-sister chromatids are either of the two chromatids of a chromosome pair.

·        Centromere: A centromere is a light staining constricted area to which both the chromatids are attached. A centromere divides the chromatids into short and long arms respectively. The short arm is known as “p” arm. The long arm is known as “q” arm. Centromere produces a primary constriction. It is the position of the centromere. It is different for different chromosomes. Secondary constriction is also known as nucleolar organizer region. It is involved in the formation of the nucleolus. Human centromere consists of several hundred kilobases of repetitive DNA. Centromeres are the sites where spindle fibers are attached. Thus, centromere helps in the movement of the chromosome.

·     Satellite: A satellite is a region that is attached to the chromosome by a thread of chromatin. It is present at the distal region of the arm of the chromosome.

·        Telomere: A special DNA-protein complex is present at the ends of the chromosomes. This complex is known as a telomere, with tandem repeats of TTAGGG-3’ sequences between 3-20 kilobases in length. Telomeres are not genes since they do not code for any functional molecule. Telomeres provide structural stability to the chromosomes by sealing their ends. Telomeres protect the chromosomes from damage. They also protect the chromosome from fusing into a ring or binding to other DNA.

Classification of chromosomes:

1.     Classification based on the position of the centromere:  

·     Metacentric: The two arms are almost equal in their lengths. The location of the centromere is at the center of the chromosome.

·   Submetacentric: The two arms of the submetacentric chromosomes are unequal in length. The location of the centromere is slightly away from the center.

·   Acrocentric: One arm of an acrocentric chromosome is short. Whereas, the other arm is long.

·      Telocentric: A telocentric chromosome has only one arm.

2.     Standard classification: It is also known as Denver classification. It classifies chromosomes into seven groups, depending on the length of the chromosomes.

·  Group A: This group consists of pairs of chromosomes 1, 2 and 3. Chromosome 1 is the largest human chromosome. It represents 8% of the total DNA content.  Chromosome 2 is the second one. The third chromosome represents 6.5 % of the total DNA content.

·       Group B: This group consists of pairs of chromosome 4 and 5.

·    Group C: This group consists of pairs of chromosome 6, 7, 8, 9, 10, 11 and 12.

·        Group D: This group consists of pairs of chromosomes 13, 14 and 15.

·        Group E: This group consists of pairs of chromosomes 16, 17 and 18.

·        Group F: This group consists of pairs of chromosomes 19 and 20.

·        Group G: This group consists of pairs of chromosomes 21 and 22.

·  Sex Chromosomes: There are two types of sex chromosomes. X chromosome and Y chromosome are called sex chromosomes.

3.     Paris nomenclature: According to this method, the long and short arms of the chromosomes have specific regions that get stained. These regions are further stained using banding techniques. Such techniques may not only help to identify specific chromosomes, but also find out the location within the chromosome. Banding techniques may help to detect minor structural abnormalities.

What is sex chromatin?

The nucleus in the interphase is in the resting phase. An interphase nucleus shows a dark stain chromatin mass attached on one side of the nuclear membrane. Sex chromatin is also known as the Barr body. It is observed only in females. However, the chromatin determination using the Barr body is not as accurate as the Karyotyping technique.

What are chromosomal aberrations?

Chromosomal mutations or aberrations are variation in the normal chromosome structure or chromosome number.

A deletion is a chromosomal mutation in which a part of a chromosome is missing. Chromosomal breaks result in deletions. Sometimes an entire chromosome may get deleted. Duplication may lead to doubling of a chromosomal segment. Excision of a chromosomal segment follows reinsertion leading to an inversion. A translocation is a chromosomal mutation in which a chromosome segment gets positioned in a different location in the genome.

Chromosome Analysis:

Chromosome analysis indicates a proper diagnosis of many clinical conditions. It is a microscopic analysis of chromosomes in the dividing cells. Chromosomal analysis can detect chromosome number and structure.

Uses of chromosome analysis are as follows:

·        Detection of congenital malformations, mental retardation, and repeated abortions.

·        Prenatal diagnosis

·        Diagnosis of malignancies

Karyotyping:

Karyotyping is a test to evaluate the number and the structure of the chromosomes. In this procedure, the metaphase chromosomes are obtained and photographed. The procedure of karyotyping is specialized. Peripheral blood lymphocytes, bone marrow cells or amniotic fluid samples are collected and analyzed for chromosomes. A photo-micrograph reveals chromosomes scattered randomly. These chromosomes are arranged into groups, using the software. A karyotype can be sued to detect chromosomal abnormalities.

Chromosome Banding:

Analysis of chromosome becomes precise with the help of banding techniques. There are four types of banding techniques such as G-banding, Q-banding, R-banding, and C-banding. A unique pattern of light and dark bands are obtained using the G-banding technique.

Fluorescence in-situ hybridization (FISH):

FISH is a new diagnostic technique that involves a single-stranded probe annealing to its complementary sequence. FISH can be used to detect minute chromosomal aberrations, malignancies, and study of chromosomes.

References:
[1] Medical genetics, G.P. Pal
[2] Human Genetics, 3/e, Gangane
[3] Vogel and Motulsky's Human Genetics: Problems and Approaches, Friedrich Vogel, Gunter Vogel, Arno G. Motulsky
[4] Biology for the IB Diploma: Standard and Higher Level, Andrew Allott
[5] Principles of Medical Genetics, Thomas D. Gelehrter

© Copyright, 2018  All Rights Reserved

Chromatin remodeling

Chromosome involves the fine design of DNA and protein complex. It also involves few non-histone proteins performing various functions. The compact structure of chromosomes fits them in the nucleus of the cell. The eukaryotic chromatin organization includes an inbuilt system of regulation. Hence, it does not require an additional repressor molecule to control the gene expression. It is the main feature of eukaryotic regulation of gene expression. The prokaryotic gene expression consists of operons such as Lac and the tryptophan operons. They require repressors to bind with the respective operators and prevent the transcription of the structural genes. However, the eukaryotic systems have their own mechanisms independent of the repressors. Hence, they save their machinery and material from making the repressor molecules. 

Repression of gene activity:

Image: Chromatin remodeling

The eukaryotic nucleosome organization shows a repressive effect on the gene expression. Hence, it does not include the extra repressors. The eukaryotic genes involve two main types based on the transcription such as the transcriptionally active genes and the transcriptionally inactive genes. The enzymes known as nucleases degrade or interact with the DNA molecules. The transcriptionally active genes show sensitivity to the DNase-I. The transcriptionally inactive genes do not sensitivity to the DNase-I. The transcriptionally active and inactive genes get distinguished by a restriction digest and a southern blot. Process the cells for obtaining the chromatin. Treat the chromatin with the DNase-I enzyme. The process of restriction digestion involves treatment of the DNA with the restriction enzyme. The enzyme cleaves the DNA to form fragments of different sizes. Hence, it targets the restriction sites.

The fragments get separated by gel electrophoresis followed by Southern blotting and autoradiography. The studies reveal two types of genes. One type of genes shows accessibility to the DNase-I. The other type of genes does not allow the DNase-I access. The genes accessible to the DNase-I consists of few fragments or no fragments. These regions involve a less coiled DNA. The less coiled DNA expose more hypersensitive sites near the transcriptionally active sites. These regions show very high sensitivity. They are present upstream of the transcription start site. The non-accessible regions involve more and more coiling. Hence, they show the whole gene. Due to very high coiling, they do not expose the genes to DNase-I.

The histone proteins also repress the gene expression. Suppose DNA gets simultaneously treated with histones and promoter binding protein. In this case, the histones compete more strongly for the promoters. They form nucleosomes at TATA box of the core promoter. The promoter binding proteins do not get a chance to bind with the promoters. Hence, the transcription does not occur. Suppose if the DNA first binds with the promoter binding protein. The proteins get assembled to the TATA box, thereby blocking the nucleosome assembly. Hence, it results in the transcription of the genes. The third possibility involves the treatment of DNA with the promoter binding proteins and activators. The activators bind with the enhancers thereby allowing the promoter binding proteins to bind to the TATA box. Hence, transcription occurs.

Activation of genes by chromatin remodeling:

Gene activation involves a key event related to the chromatin structure. It alters the chromatin structure in the vicinity of the core promoter. It is known as the chromatin remodeling. Two types of chromatin remodelers include nucleosome modifying enzymes and the ATP-dependent nucleosome remodeling complex. The nucleosome modifying enzymes conduct acetylation or deacetylation of the core histones.

Let us consider the nucleosome modifying enzymes. The histone acetyltransferases help in the acetylation process. The histone acetyltransferases get recruited to the chromatin. The activators interact with the DNA binding sites in the presence of the histone acetyltransferases and acetylate the lysine residues. Mainly the amino-terminal tails of the core histones have the lysine residues. Thus, the histones slowly lose the affinity for the DNA. Due to the acetylation, the chromatin structure gets reduced from the 30 nm to the 10 nm. Now the promoters become more accessible for the transcription. The TFIID binds to the site and allows transcription. The acetylated structures get deacetylated by another class of enzymes known as histone deacetylases. These enzymes remove the acetyl groups and restore the 30nm fiber.

ATP-dependent nucleosome remodeling complexes involve a large multiprotein complex. They help in remodeling the chromatin. They use ATP hydrolysis for obtaining energy. The activators interacting with the DNA binding sites recruit nucleosome remodeling complexes. These complexes alter the nucleosome. Thus, the transcription machinery binds to the promoter. An example includes SW1/SNF ATP-dependent nucleosome remodeling complex in yeast.

References:

[1] Epigenetics, Lyle Armstrong
[2] Human Molecular Genetics, Tom Strachan, Andrew Read

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