GENOME ORGANISATION IN EUKARYOTES

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GENOME ORGANISATION IN EUKARYOTES

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GENOME ORGANISATION IN EUKARYOTES 1

CONTENTS:

CONTENTS Introduction Chemical composition DNA RNA Protein Chromosome structure Molecular model Multistranded model General Chromosome model Folded fibre model Organisation of chromatine fibre Nucleosome -Solenoid model 2

INTRODUCTION:

INTRODUCTION EUKARYOTIC genome is rather complex and is enclosed by a typical nuclear membrane which forms a true nucleus. The amount of DNA in the haploid genome of eukaryotes is quite variable ; it is usually expressed in terms of C-value. The C-value is characteristic for all living species, but some variation in C-value may occur within the species. There are two main reasons for the C-value variations : (1) the organization of eukaryotic genes and (2) repetitive DNA. 3

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In eukaryotes, the actual coding sequence of a gene is much smaller than the average size of the gene due to the presence of introns . Such genes are called split genes or interrupted genes since their coding or expressed sequences ( exons ) are divided by introns (intervening sequences) which are non-coding sequences. Therefore, the size of mature eukaryotic mRNA is about 1/5 of the size of the gene coding for it (Table 1). Further the actual number of genes per genome is much lower than the number estimated on the basis of haploid DNA content; this is mainly due to the presence of variable amounts of repetitive DNA. This situation is called the C-value paradox. 4

TABLE -1: Relation b/w gene size & length of mature mRNA:

TABLE -1: Relation b/w gene size & length of mature mRNA Species Average number of Exons Average size of gene (kb) Average size of mRNA ( kb) Gene size/ mRNA size ( Ratio) mRNA as % of gene size Nematode ( Caeno - rhabditis elegans ) 4 4.0 3.0 1.3 75.0 Drosophila Melanogaster 4 11.3 2.7 4.2 23.9 Chicken 9 13.9 2.4 5.8 17.3 Mammals 7 16.6 2.2 7.5 13.2 5

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The eukaryotic genome is distributed into several linear chromosomes. The chromosomes are made of DNA (nucleic acid) and proteins which together form the nucleoprotein called chromatin. 6

CHEMICAL COMPOSITION:

CHEMICAL COMPOSITION Chromatin is composed of DNA (30-40%), RNA (1-10%) and proteins (50-60%). These constituents vary in different organisms and even in the different tissues of the same species (Table 2). Even in the same cell, the proportions of DNA, RNA and proteins vary with the stage of cell cycle. For example, tie proportion of DNA in metaphase chromosomes is lower than that in interphase chromosomes. As opposed to this, the proportion of proteins is higher in the metaphase than in the interphase chromosome. The part of DNA active in transcription is also variable in different organisms and in different tissues of a single organism. About 6% of the total DNA is active in transcription in vegetative buds of pea, while 32% of it is involved in transcription in its growing cotyledons (Table 2). 7

TABLE -2: Chemical composition of chromatin:

TABLE -2: Chemical composition of chromatin Organism and cell Source DNA (%) RNA (%) Proteins Proportion of DNA active in transcription (%) His tone (%) Nonhistone (%) Pea Embryonic axis 39 10 40 11 12 Vegetative bud 40 4 52 4 6 Growing cotyledon 43.5 6 34.5 16 32 Sea urchin Blastula 39 1 41 19 10 Larva 33.4 2.6 29 35 20 Rat (Liver) 37 1 37 25 20 Cow (Thymus) 40.2 0.3 46 13.5 15 Human ( HeLa cells) 35.5 3.5 36 25 8

DNA:

DNA The DNA content varies among the cells of different organisms (Table 3 ). The gametes (eggs and sperms) of a species have only one half amount of the DNA present in its somatic tissues. In human, DNA content of egg or sperm is 2.8 picogram (pg) per cell, while in cow it is 3.3 pg per cell. The DNA content per cell also varies during the different stages of cell cycle. The haploid DNA content of a cell is denoted by 2c. DNA content of a somatic cell is 2c in G1, it doubles during the S-phase and becomes 4c in G 2 ; it remains at 4c during prophase and metaphase stages of mitosis, and prophase I and metaphase I of meiosis (Fig.1 ). The 4c DNA of meiotic cells is reduced to half (2c) in the two daughter cells forming the dyad (due to the first meiotic division). Finally, each of the four component cells of the tetrad produced after the completion of meiosis contains 1c DNA which replicates to become 2C DNA of the gametes (Fig.1). 9

TABLE -3: DNA content/cell in diff. organism:

TABLE -3: DNA content/cell in diff. organism Organism DNA content per cell (pg) Length of DNA double helix (cm) Chicken 2.5 78 Man 5.6 174 Cow 6.4 198 Rat 6.6 205 Drosophila ( salivary gland) 293 9083 Trillium 120 3700 10

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The eukaryotic genome is composed of the following two types of base sequences : ( i ) unique or nonrepetitive DNA and (ii) repetitive DNA. Unique DNA : These are the sequences which are present in a single copy, in each genome. The base sequences of unique DNA are not repeated in the genome. The proportion of unique DNA varies in different eukaryotic organisms (Table 4). It constitutes 8% of the rye genome, 25% of pea, 40% of snail and 70% of human genome. A large number of genes, e.g., most of the structural genes, are present in single copy in the genome. Bacterial genome is considered to be composed of unique DNA ; it contains only 0.3% repetitive DNA which, in fact, is rDNA and codes for ribosomes . 12

TABLE – 4: Proportion of repetitive and unique (nonrepetitive) base sequen ces in the genomic DNA of some plant and animal species.:

TABLE – 4: Proportion of repetitive and unique ( nonrepetitive ) base sequen ces in the genomic DNA of some plant and animal species. Organism RepetiUve DNA (%) Unique DNA (%) Ratio (Unique/Repetitive) DNA ANIMAL Human {Homo sapiens) 30 70 2.33 Calf ( Bos Taurus) 45 55 1.22 Mouse 40 60 1.50 Toad ( Xenopus laevis ) 45 55 1.22 Sea urchin ( Arbacia punctulata ) 38 62 1.63 PLANT Rye ( Secale cereale ) 92 8 0.09 Bread wheat ( Triticum aestivum ) 83 17 0.20 Maize , ( Zea mays ) 78 22 0.28 Barley ( Hordeum vulgare ) 76 24 0.31 Pea ( Pisum sativum ) 75 25 0.33 13

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Repetitive DNA : DNA sequences present in more than one copy per genome are called repetitive DNA. They consist of families of sequences that are not exactly similar but are related. However, the members of each family consist of a set of base sequences which are sufficiently similar to reassociate with one another. Differences among individual sequences occur due to deletion, insertion and substitution. Unequal crossing over plays a role in changing the size of these sequences. Repetitive DNA sequences are classified into two main groups : ( i ) moderately repetitive sequences, and (ii) highly repeti­tive sequences. 14

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Moderately repetitive sequences : In the case of moderately repetitive sequences, the number varies from 2 to less than 10 5 copies of genome. The proportion of these sequences is variable in different species. Drosophila melanogaster has 12% of its DNA in the form of moderately repetitive sequences, while in man, 13% of the DNA is of this type. In Nicotiana tabacum , these sequences constitute 65% of the genome. Several genes are present in the form of moderately repetitive DNA sequences, e.g., genes for ribosomal RNA, genes for ribosomal proteins, genes for histones and several others. Several families of transposable elements are also grouped under this class of DNA. 15

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Highly repetitive DNA : Highly repetitive DNA constitutes a smaller proportion of the genome. Generally, it consists of very short sequences which are repeated tandemly in large clusters. Highly repetitive DNA is also called simple sequence DNA due to its short repeating units. They may be present in more than 10 5 copies, even upto millions of copies per genome. These sequences are located in the constitutive heterochromatin, present mostly in the centromeric and telomeric regions of chromosomes. In mammalian genomes, the proportion of highly repetitive DNA is generally below 10%, while in Drosophila melanogaster , it is 17%. Another Drosophila species, D. virilis , contains more than 40% highly repetitive DNA sequences per genome. The short tandemly repeated DNA sequences are identical in some cases but are related in the others. There exists a great variation among different individuals of a single species regarding the size of the tandem clusters ; therefore, they can be used in "DNA finger printing", for characterization of individual genomes. 16

RNA:

RNA RNA constitutes a very small proportion of chromatin; it is 3.5% in human, 0.3% in cow and 10% in pea. Most of the RNAs are ribosomal RNA, mRNA and tRNA . But part from these, a special class of RNAs called "chromosomal RNA" is associated with the chromosomes. Chromosomal RNA constitutes about 5% of the total chromosome weight. These RNAs are small molecules containing 40 to 60 nucleotides. They may be involved in the structural organization of chromatin fibres and gene regulation. 17

PROTEINS:

PROTEINS Proteins constitute more than half of the total mass of chromosomes. They belong to two classes : ( i ) histones or basic proteins, and (ii)non histones protiens . Another class of proteins called “ protamines ” are found associated with chromosomes in sperms of certain animals. Protamines are acidic proteins with molecular weights ranging from 1000 to 5000 ; they replace histones from the chromatin of the sperms. 18

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Histones proteines : Histones are basic proteins or acid soluble proteins and have a net positive charge. These proteins are of 5 types namely, HI, H2A, H2B, H3 and H4. These proteins have low molecular mass . The amino acid compositions of different histone types in pea bud histone are given in Table 5. The histones are divided into three classes. 19

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Very rich in lysine : They are the largest histone molecules. They possess little or no α -helix and are relatively weakly bound to DNA e.g., H1 histone . The H1 histone accounts for 20-25% of calf thymus whole histones and 15% of pea bud histones . The proportion of lysine is 25.5 per 100 moles of amino acids in pea bud H1 histone (Table 5). Moderately rich in lysine : H2A and H2B are the histones of this type. H2B has lysine/ arginine ratio of about 2.5, while H2A has a lysine/ arginine ratio of about 1.2. Therefore, H2A histone is also called "lysine- arginine rich " histone . In pea, moderately lysine rich histones constitute about 50% of total pea bud histones . Arginine rich histone : The two types of arginine rich histones are designated as H3 and H4. The H3 histone is larger than H4. Molecular weight of H4 histone is 11000 and it is the smallest histone molecule. The proportion of arginine as moles per 100 moles of amino acids is 13.1 in H3 histone , while 15.6 in H4 histone of pea bud (Table 5). 20

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Amino acid Histone types H1 H2A H2B H3 H4 Lysine 25.5 16 .1 10.6 8.6 8.5 Histidine 1.1 1 .1 1 .6 2 .1 2.4 Arginine 2.8 6.5 9.0 13.1 15.6 Aspartic acid 2.3 6.0 6.1 4.5 5.6 Threonine 4.0 4.8 4.1 6.6 7.3 Serine 4.9 6.7 5.6 4.1 2.2 Glutamic acid 7.3 8.0 6.6 10.8 6.2 Proline 9.9 6.7 7.1 4.5 1.4 Glycine 2.3 8.8 11.4 6.6 17.2 Alanine 22.8 12.3 12.8 12.9 7.5 Valine 5.3 6.7 7.9 5.2 6.6 Methionine 0.0 0.5 - trace trace Isoleucine 1.9 4.5 3.1 5.1 6.3 Leucine 4.1 7.9 10.6 9.4 7.6 Tyrosine 0.4 1 .7 1 .9 1.0 3.0 Phenylalanine 0.4 1.9 1.6 3.9 2.7 Table 5. Amino acid composition of the various kinds of histones found in pea bud (moles per 100 moles of amino acids) 21

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Nonhistone proteins : Nonhistone proteins occur in much lower proportion than histones , and their proportion in the total chromosome mass varies considerably in the different organisms. These proteins make up about 4% in pea vegetative bud, 16% in growing pea cotyledon, while 25% in human HeLa cells (Table 2). Nonhistone proteins consist of various enzymes involved in different metabolic functions, e.g., DNA polymerase, RNA polymerase, nucleases, polynucleotide ligase , DNA methylase , proteases, histone methylases , histone actylases , histone deacetylases , histone kinases etc. Apart from these enzymes, certain nonhistone proteins are found that have high electrophoretic mobility ; they are called HMG (high mobility group) proteins. Some of the HMG proteins form association with chromatin fibres during transcription. 22

CHROMOSOME STRUCTURE:

CHROMOSOME STRUCTURE Proteins and DNA are complexed together to form nucleoprotein fibres called chromatin. The chromatin fibres coil and fold to form the chromosome. Very long DNA molecules are packaged into chromosomes of much smaller sizes. The amount of DNA is measured in picogram (pg), one pg being equal to 10 -12 g. One pg DNA corresponds to 31 cm of DNA double helix which contains 10 9 base pairs. In man, 5.6 pg DNA is found in each cell ; this DNA is equivalent to 174 cm of DNA double helix (Table 3), and is distributed into 46 chromosomes which together measure only about 220 um during metaphase of mitosis. Therefore, such a long DNA molecule must be packaged in some way to be accommodated within the short dimensions of the 46 chromosomes. To account for this, several models have been proposed. 23

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Several models are : Molecular Model : Proposed by Taylor and his coworkers in 1957, 1963. Multistranded Model or Polyneme Chromosome Model : Proposed by Ris & Chandler in 1963. General Chromosome Model : Proposed by Crick in 1971. Folded Fibre Model : Proposed by DuPraw in 1965. 24

Folded fibre model:

Folded fibre model DuPraw in 1965 proposed this model on the basis of electron microscopic studies of human chromosomes. According to this model, each chromatid contains single long nucleoprotein complex (Chromatin fibres ) in which a single DNA double helix forms the main structure of the axis. This model of chromosome has been widely accepted. 25

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Features : Before interphase replication, each chromosome consists of a single chromatid made up of a single 200-500 A thick chromatin fibre ; each fibre contains a single long DNA double helix which is associated with proteins and RNA. The chromatin fibre ( chromatid ) replicates during S phase of cell cycle to produce two sister chromatids which are held together by the unreplicated regions. This pair of sister chromatids folds up to form a visible chromosome at prophase, but sister chromatids are held together by minute unreplicated regions. Exact folding and packing patterns of chromatids of different chromosomes are thought to vary in some specific ways. 26

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Fig. 2 Chromosome replication and structure according to the folded fibre model of DuPraw . A. Unreplicated chromatid is a single 200-500A chromatin fibre containing a DNA double helix in supercoiled configuration (replication is just being initiated). B. Replication of the chromatid begins at several sites. C. The late replicating segment of the fibre at the centromere serves to hold the sister chromatids together. The chromatin fibre is folded to give the chromatid and chromosome structures visible under light microscope. 27

Organization of Chromatin Fibres :

Organization of Chromatin Fibres DNA of eukaryotes is complexed with proteins to form fibrils of 100 A (= 10 nm) diameter which is coiled to give rise to the chromatin fibre of ~ 300 A ( = 30 nm) diameter. The chromatin fibres are dispersed during interphase but they become condensed and visible during cell division. Two models of chromatin fibre organization have been proposed : the coiled DNA model and the nucleo-solenoide model. 28

Nucleosome-Solenoid model of chromatin fibre:

Nucleosome -Solenoid model of chromatin fibre This is the most widely accepted model; it was proposed by Kornberg and Thomas in 1974. According to this model, chromatin fibres consist of discrete particles called nucleosomes which generate a bead-like structure. The thread (string) is made up of the DNA molecules ; wound around the beads but does not pass through the beads. The nucleosome is the basic structural unit of chromatin fibre ; it consists of DNA wound around an " octamer " of histone proteins. A bacterial enzyme, micrococcal nuclease, has the ability to cut DNA between nucleosomes . However this enzyme can not cleave the DNA wound round the histone octamer . Individual nucleosomes , therefore, can be obtained following digestion of chromatin with micrococcal nuclease. The stretch of DNA between two nucleosomes (this DNA is digested by micrococcal nuclease) is called linker DNA or spacer DNA. 29

Composition of Nucleasome:

Composition of Nucleasome A nucleosome consists of about 200 bp DNA associated with the histone octamer . The histone octamer of a nucleosome consists of two molecules each of the histones H2A, H2B, H3 and H4. The associated DNA and the histone octamer together constitute the core particle (Fig. 3 ). Micrococcal nuclease produces nucleosome monomers by cleaving the DNA between the core particles. This enzyme can further cleave the DNA of the nucleosomes , but at least 146 bp DNA remains associated with the protein octamer and is not available for the enzyme. Thus the core DNA (DNA bound to the core particle) is actually 146 bp in length. The remaining part of the DNA is calleld linker DNA which joins neighbouring core particles of the chromatin fibres ; linker DNA varies from 8 to 114 bp in different organisms and tissues. The histone H1 is associated with the linker DNA. 30

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H1=24,000 daltons Fig. 3. Constituents of a nucleosome . The total molecular weight is 2,62.000 daltons (DNA + histone ) ; the DNA and proteins are in approximately equal ratio. DNA 200 bp (67 nm long) H 2 A (2 X 14,000) H 2 B (2X14,000) H 3 (2X15,000) H 4 (2X11,000) 6 nm Histone octamer 31

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Thank you 32