ORGANISATION OF GENOME 

• Chromatin is compact organisation of DNA sequences are structurally inaccessible and functionally inactive. 

• Within a cell the DNA is associated with proteins is called chromosomes. 

• The organisation found in both prokaryotic and eukaryotic cell. 

• The organisation of DNA is essential to fit a DNA of 2metre length (atypical human cell)into a nucleus that is only 10-15µm in diameter.

ADVANTAGES OF ORGANISATION:

Packaging of DNA into chromosomes hold several functions 

• First chromosome is a compact form of DNA that readily fits inside cell. 

• Second packaging DNA into chromosome serve to protect the DNA from damage. Naked DNA molecules are relatively unstable in cells. In contrast chromosomal DNA is extremely stable.

• Third only packed DNA can be transmitted efficiently to both daughter cells during cell division.

• Fourth chromosomes confers an overall organisation of DNA , that helps in gene expression and recombination.

PROTEINS INVOLVED IN ORGANISATION 

• Half of the molecular mass of eukaryotic chromosome is protein. 
• They are two major types of proteins that was found associated with DNA 

• Histone proteins 
• Non-histone proteins

HISTONE PROTEINS 

• The majority of proteins associated with DNA are small basic proteins are called histones. 

• It has high content of positively charged aminoacid which help them in their association with negatively charged DNA 

• It consists of aminoacids like arginine and lysine.

TYPES OF HISTONE PROTEINS 

• They are five types of histone proteins 

• 1.𝐻_1 2. .𝐻_2𝐴 3. .𝐻_2𝐵 4. .𝐻_3  5. .𝐻_4 

• These proteins assemble into a disc-shaped structure with a central (H3-H4)2 tetramer flanked by two (H2A-H2B) dimers on top and bottom. 

• 𝐻_2𝐴, 𝐻_2𝐵 , 𝐻_3 , 𝐻_4  forms core protein or core histone around DNA wrapped. 

• 𝐻_1 binds to linker DNA , it is called linker histones. 

Function 

• It determine structure of chromatin. 

• It plays regulatory role in repression activity of gene

NON-HISTONE PROTEINS 

• The non-histone varies from 12-20. 

• The non-histones differ in different time of same organism regulate action of specific genes. 

• The non-histones of chromatin are structural protein include actin,myosin and 𝛼𝛽-tubulin. 

Functions 

• It involves in chromosome condensation and movement of chromosomes during mitosis and meiosis.

ORGANISATION OF CHROMOSOME –HYPOTHESIS 

• The section of chromosomes studied in electron microscope with fine fibrils having thickness of 2nm-4nm. 

• They are 2 hypothesis 

1. Single stranded and multistranded hypothesis 
2. Folded fibre model and nucleosome concept

1.SINGLE STRANDED AND MULTISTRANDED HYPOTHESIS 

When chromsomes compared to related species they differ in one of 2 causes. 

1.LATERAL MULTIPLICATION- 

• It is of chromanemata lead to multistrandedness. 

2.TANDEM DUPLICATION- 

• It is of chromanemata where lengthen with duplication differ. 

• The multiple strandedness is demonstrated in several plants. 

• There is also evidence against this hypothesis, many evidence support single strand nature of chromatin confirm by pulse field electrophoresis

2. Folded fibre model and nucleosome concept 

• The single chromatid has been long, DNA is coiled or folded 

• This folding manner proposed by E.J.Dupraw 

• The bulk of chromosomes composed of tightly folded fibre which has homogenous diameter of 200-300𝐴 ̇ 

• Histones are outside the DNA 

Nucleosome concept 

• The DNA has histone helix on supercoiled condition. 

• Nucleosome concept A nucleosome concept universally accepted, histones inside the DNA. 

• It was proposed by P.Oudet and R.D.Kornberg.

LEVELS OF ORGANISATION OF GENE 

1. FIRST LEVEL OF ORGANISATION 
2. SECOND LEVEL OF ORGANISATION 
3. THIRD LEVEL OF ORGANISATION 
4. FOURTH LEVEL OF ORGANISATION 
5. FIFTH LEVEL OF ORGANSATION

1.FIRST LEVEL OF ORGANISATION 

• The first level of Organisation of DNA is also called Nucleosome formation. 

• It is also called Bead on string structure. 

• The DNA is associated with histone proteins to form Nucleosome. 

• Nucleosome are fundamental packaging unit of chromatin as a bead and string model in electron micrograph. 

• It is wound about 1.65 times around core protein. 

• Nucleosome beads are removed from long DNA string by digestion with bacterial enzyme micrococcal nuclease

DNA is divided into two region 

Core DNA 

• It has length 146bp 

• It is resistant to digestion of nucleases 

Linker DNA 

• DNA of rest repeating unit 

• It has length of 8 to114 bp /Nucleosome 

Core protein 

• It is disc shaped octomeric protein of 6nm hight and 11nm diameter. 

• The histone proteins has two molecules of 𝐻_2𝐴, 𝐻_2𝐵 , 𝐻_3 , 𝐻_4 𝐻_3 and 𝐻_4 tetramer with molecule of 𝐻_2𝐴, 𝐻_2𝐵  dimer stacked on each face of disc

Turns 

• They are two turns around nucleosome 

• One turn of 80bp of DNA. 

• The histone has N-terminal extension called a tail for nucleosome accessible 

The degree of supercoiling in mini chromosome 

• The free supercoils of mini chromosome is relaxed and forms a circular string with Unconstrained superhelical density of zero 

• Every negative supercoil was present but constrained in nucleosome as deprotonised DNA. 

• The DNA follow a path of nucleosomal surface as –ve turn when proteins are removed ,the path has -1.67 supercoil turn this is called this linking number paradox 

• Torsional strain in nucleosomal DNA lead to increasing number of base pairs /turn, only rest of them was supercoiled

2.SECOND LEVEL OF ORGANISATION 

• It formed 30nm fibre formation 

• It consists of approximately 6 nucleosomes for every turn 

• The formation needs intranucleosomal contact which needs a histone tail 

• The histone proteins 𝐻_1 required positively charged protein for compaction 

• 𝑯_𝟏  interact with linker DNA between nucleosome 

• It lead to further tightening association of DNA with a nucleosome

• About H1 protein has property of binding two distinct regions of DNA duplex 

• 1.Linker DNA -114bp 

• 2.In middle of Associated 146 bp[Core DNA] 

• They are two model employed in 30nm fibre formation 

• 1.Solenoid model 

• 2.Zigzag model

SOLENOID MODEL 

• This model has 6 nucleosomes / turn forms super Helix. 

• The 30nm fibre has a helical pitch of approximately 11 nm. 

• The approximate diameter of nucleosome discs stacked in edge in form of Helix . 

• In this model the flat surface on either face of histone 

• Octomer disc are adjacent to each other DNA surface of nucleosome forms outside accessible surface of super helix. 

• The linker DNA Buried in Centre of the Super Helix but it never passes through the axis of the Fibre 

• The solenoid is of 2types 

1. Single linear array(Single start) 

1. Two start (Double row nucleosome) 

• This solenoid can pack 40 to chromosomes.

Zigzag model 

• This model based on zig-zag pattern of nucleosome is formed. 

• The zigzag conformation require linker DNA to pass through central axis of fibre in straight form. 

• The 30nm fibre compact to length of DNA by 40 folds.

THIRD LEVEL OF ORGANISATION 

• It is also called rosette structure. 

• The nucleus is about 5µm in diameter. 

• The packaging of DNA int0 30nm chromatin fibre leaves human chromosome of 0.1cm long, higher folding is found. 

• The folding contains looped domains. 

• The looped region of chromatin maintain by binding protein clamp 2regions of 30nm fibre by recognising specific sequence forms neck of each loop.

• The 30nm fibre convert to loop by non-histone proteins. 

• The looping folded to 80nm fibre.

• The loops has 80-90kb that held base at non-histone proteins. 

• This is called nuclear scaffold proteins. 

• The loop arranged on helically coiled path. Each chromosome has 2 scaffold regions. 

• Two classes of nonhistone proteins involved in scaffold formation. 

• 1.Topoisomerase 

• It is found in scaffold preparation and purified mitotic chromosomes. 

• It make DNA to 50kb in size. 

• 2.SMC proteins 

• These protein of machinery condenses and holds daughter chromosomes after chromosome duplication.

• The association of these proteins enhance their function by providing foundation for interaction with chromosomal DNA. 

• DNA has specific sequence called SAR1(Scaffold Association Region 1)MAR(Matrix Associated Region). 

• 1Rosette forms 6loops with 50kb.

FOURTH LEVEL OF ORGANISATION 

• The rosette structure organised into a coil 

• It is known as coiled coils. 

• Each coil consist of 30 rosettes.

FIFTH LEVEL OF ORGANISATION 

• This organisation is known as chromatids 

• The coils organised into chromatids 

• The chromatids contains 10coils 

• The condensed metaphase chromosome the DNA packaged into highly compact manner to 10000 folds. 

• The compaction level of interphase chromosome not completely uniform.

They are 2 types of chromatin 

i)EUCHROMATIN 

• It is less condensed region of chromosome. It is region where 30nm forms radial loops.

ii)HETEROCHROMATIN 

• Tightly compacted region of chromosome. 

• 1.Constiutive heterochromatin 

• 2.Facultative heterochromatin

Constitutive Heterochromatin 

• It is region which is permanently heterochromatin. 

Facultative Heterochromatin 

• Region with interconversion between euchromatin and heterochromatin.

Compaction of DNA in Eukaryotic Chromosomes 

Packaging of DNA into chromosome has several function. 

1. Chromosomes as compact form of DNA that readily fits into cells. 
2. Packaging DNA into chromosome protect DNA from damage. As DNA is unstable in cell. But chromosomal DNA stable in cell. 
3. Packaged DNA transmit efficiently to both daughter cells during cell division. 
4. The overall organisation of DNA involve gene expression and recombination.

References

1.Lewin's Genes twelve

2.Molecular Biology of the Gene by Watson,Baker,Bell,Gann,Levine&Losick