GENOME ORGANIZATION IN EUKARYOTES

What is Genome ?

Genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA.The genome includes both the genes and the non-coding sequences of the DNA.

‘’Genome is thus the entire collection of genes and all other functional and non functional DNA

sequences in an organism in a haploid set of chromosomes. It includes structural genes,

regulatory genes and non functional nucleotide sequences ’’

Structural genes- DNA segments that code for some specific RNAs or proteins. Encode for mRNAs, tRNAs, snRNAs, scRNAs.

Functional sequences- Regulatory sequences- occur as regulatory elements (initiation sites, promoter sites,operator sites,etc.)

Nonfunctional sequences- Introns and repititive sequences. Needed for coding, regulation and replication of DNA. Much more in no than functional sequences.

Genome of all living organisms represents their hereditary material and is formed of DNA.

In Prokaryotic cells- Genomic DNA forms a single circular chromosome, without basic proteins , lies in the cell cytoplasm in

nucleoid region

In Eukaryotic cells- DNA is associated with basic proteins(histones),

form long chromatin fibers. Chromatin fibers form a network, enclosed in a double layered nuclear

envelop, condenses into chromosomes during cell division

comparative genome sizes of organismsorganism Size (bp) gene

numberaverage gene density chromosome

number

Homo sapiens(human) 3.2 billion ~25,000 1 gene /100,000 bases 46

Mus musculus (mouse) 2.6 billion ~25,000 1 gene /100,000 bases 40

Drosophila melanogaster(fruit fly)

137 million 13,000 1 gene / 9,000 bases 8

Arabidopsis thaliana(plant) 100 million 25,000 1 gene / 4000 bases 10

Caenorhabditis elegans(roundworm) 97 million 19,000 1 gene / 5000 bases 12

Saccharomyces cerevisiae(yeast)

12.1 million 6000 1 gene / 2000 bases 32

Escherichia coli(bacteria) 4.6 million 3200 1 gene / 1400 bases 1

H. influenzae (bacteria) 1.8 million 1700 1 gene /1000 bases 1

EUKARYOTIC GENOME‘The nucleus is heart of the cell, which serves as the main

distinguishing feature of the eukaryotic cells. It is an organelle submerged in its sea of turbulent cytoplasm which has the genetic information encoding the past history and future prospects of the cell. Nucleus contains many thread like coiled structures which remain suspended in the nucleoplasm which are known as chromatin substance’

Chromatin is the complex combination of DNA and proteins that makes up chromosomes.

The major proteins involved in chromatin are histone proteins; although many other chromosomal proteins have prominent roles too.. The functions of chromatin is to package DNA into smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and to serve as a mechanism to control gene expression and DNA replication.

ORGANIZATION OF CHROMATINIn resting non-dividing eukaryotic cells, the genome is in the form of nucleoprotein-complex- the chromatin.

(randomly dispersed in the nuclear matrix as interwoven network of fine chromatin threads)

The information stored in DNA is organized, replicated and read with the help of a variety of DNA-binding proteins:

Structural Proteins- Histones(Packing proteins): main structural proteins found in eukaryotic cells low molecular weight basic proteins with high proportion of positively charged amino acids, bound to DNA along most of its length, the positive charge helps histones to bind to DNA and play a crucial role in packing of long DNA molecules.Functional Proteins- Non- Histones: associated with gene regulation and other functions of chromatin.

• Nucleosomes are condensed several times to form the intact chromatids.

o Chemical composition of chromatinDNA= 20-40 %- most important chemical constituent of chromatin

RNA=05-10 %-associated with chromatin as;Ribosomal RNA-( rRNA)

Messenger RNA- (mRNA)Transfer RNA- (tRNA)

PROTEINS=55-60%-associated with chromatin as;Histones: very basic proteins, constitute about 60% of total protein,

almost 1:1 ratio with DNA.

FIVE TYPES: H1, H2a, H2b, H3 and H4Non-Histones: They are 20% of total chromatin protein:

50% structural (actin, L & B tubulin and myosin)-contractile proteins, function during chromosome condensation and in the movement of

chromosomes during mitosis and meiosis.50% include all enzymes and co-factors –involved in replication,

transcription and regulation of transcription.

Ultrastructure and organizationMulti-strand modelFolded fiber modelNucleosome model-( R.D.Kornberg & O. Thomas-1974widely accepted)NUCLEOSOME MODEL: DNA is tightly bound to histone proteins which serve to form a repeating array of DNA- Protein particles called nucleosomes.THREE LEVELS OF ORGANIZATION:DNA wrapping around “Nucleosomes”- The string on beads structure.

A 30 nm condensed chromatin fiber consisting of nucleosome arrays in their most compact form- The solenoid structure.

Higher levels of packing into metaphase chromosome- The loops, domains and scaffold structure.

Fig.. Nucleosome with histone H1

Fig. Histone Octamer (a nucleosome)

from Jiang and Pugh, Nature Rev.Genet. 10, 161 (2009)

Nucleosomes contain 2 copies of H2A, H2B, H3 and H4

147 bp of DNA is wrapped around nucleosome

Histone tails emanate from core

Some nucleosomes contain histone variants

H1 is a linker histone

Nucleosome Structure

Hierarchy of Chromatin Organization in the Cell Nucleus: Nuclear Matrix Associated Chromatin Loops

TYPES OF CHROMATINEuchromatin Lightly packed form of chromatin that is rich in gene concentration takes up light stain and represent most of the chromatin, that disperse after mitosis has completed. Consists of structural genes which replicate and transcribe during G1 and S phase of the interphase.Considered genetically active chromatin, since it has a role in their phenotypic expression of the genes. DNA is found packed in 3-8 mm fibre.During metaphase it takes up dark stain.

HeterochromatinTightly packed form of chromatin that takes up deep stain during interphase and prophase but metaphase takes up light stain. Chromomeres, centromeric regions, and knobs also take up dark staining, of which centromeric regions and knobs are the true Heterochromatic. (chromomeres are transcribed so not true H.C.). IN the chromosomes all the centromeres fuse to form a long Heterochromatic mass called chromocentre. Heterochromatin consists of highly repetitive DNA sequences. It is late replicating during the s-phase of the cell and is not transcribed.

•Euchromatin is uncoiled and active, whereas heterochromatin remains condensed and is inactive.

• Eukaryotic Chromosomes Demonstrate Complex Organization Characterized by Repetitive DNA

• Repetitive DNA sequences are repeated many times within eukaryotic chromosomes.

• Satellite DNA is highly repetitive and consists of short repeated sequences.

Centromeres• are the primary constrictions along

eukaryotic chromosomes• mediate chromosomal migration during

mitosis and meiosis

• Telomeric DNA sequences consist of short tandem repeats that contribute to the stability and integrity of the chromosome.

• Moderately repetitive DNA includes: – variable number tandem repeats (VNTRs)– minisatellites– microsatellites

• Short interspersed elements (SINES) and long interspersed elements (LINES) are dispersed throughout the genome rather than tandemly repeated, and constitute over 1/3 of the human genome.

• These transposable elements are generated via an RNA intermediate and are referred to as retrotransposons.

• The Vast Majority of a Eukaryotic Genome Does Not Encode Functional Genes

• Only a small portion of the eukaryotic genome (2%–10%) constitute protein-encoding genes.

• There are also a large number of single-copy noncoding regions, some of which are pseudogenes.

FUNCTION OF CHROMATIN

“The function of the chromatin is to carry out the genetic information from

one generation to another, by encoding the past history and future prospects of the cell. DNA, being the only permanent

component of chromatin, is the sole genetic material of eukaryotes. It never

leaves the cell, thus maintaining heredity of the cell”

CONCLUSIONChromatin is the complex combination of DNA and proteins that organizes chromosomes which appear as many thread like coiled and elongated structures suspended in the nucleoplasm. So the chromatin contains genetic material instructions to direct cell function.

The first level of packing in Chromatin involves the binding of DNA to histones into fundamental packing unit particles called nucleosomes.

The second level of packing involves packing of nucleosomes into 30 nm thick chromatin fibre.

The highest level of packing of chromatin in the chromosome is found at the metaphase stage of cell division.

There are two distinct types of chromatin- euchromatin and heterochromatin which differ on their staining properties.

In the chromatin, DNA and basic proteins called histones are present in about equal amounts.

DNA is the permanent component of chromosomes and is the sole genetic material of eukaryotes.

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