GENE FAMILIES AND

CLUSTERS

D. V. Vidya Lakshmi.

GENE FAMILY A gene family is a set of several

similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions.

A gene family is a set of homologous genes within one organism.

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When a gene is present in two or more copies per genome, the condition is known as “ redundancy”.

The members of a gene family may be either clustered together , dispersed on different chromosomes or present in a combination of both.

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If the genes of a gene family encode proteins, the term “protein family” is often used in an analogous manner to gene family.

One example for such family are the genes for Human haemoglobin subunits.

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GENE CLUSTER A gene cluster is part of a gene

family. A gene cluster is a group of two or

more genes found within an organism’s DNA that encode for similar polypeptides or proteins, which collectively share a generalised function and are located within a few thousand base pairs of each other.

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The size of gene clusters can vary significantly, from a few genes to several hundred genes.

Genes found in a gene cluster may be observed near one another on the same chromosome or on different, but homologous chromosomes.

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Extensive tanden repetition of a gene normally occurs when the gene product is needed in unusually large amounts. E.g., genes for rRNA, histone genes, etc.

Sometimes all the members of a gene family are functional, but often some members are nonfunctional pseudogenes.

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TANDEM REPEAT In a tandem repeat, the nucleotide

sequence is repeated in the same orientation.

For example, the trinucleotide sequence GAA is repeated two times in the DNA segment –GAAGAA-.

GAA GAA CTT CTT tandem repeat

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GLOBIN GENES Genes encoding the various

globin proteins evolved from one common ancestral globin gene, which duplicated and diverged about 450-500 million years ago.

After the duplication events, differences between the genes in globin family arose from the accumulation of mutations.

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ANCESTRAL GLOBIN GENE

Haemoglobin Myoglobin genes genes Plant

globin genes

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REPRESENTATION OF EVOLUTION OF ANCESTRAL GLOBIN GENE

ANCESTRAL GLOBIN GENE

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HAEMOGLOBIN GENES The haemoglobin molecule is a

tetramer and is composed of two similar polypeptides, the alpha and beta chains, encoded by two distinct genes.

Each polypeptide incorporates a hemi-group, that reversibly binds oxygen.

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The genes are co-ordinatedly turned on and turned off during the embryonic, foetal and adult stages of development.

The genes for - globin lie in a cluster on chromosome 16, while those for- globin are located on chromosome 11.

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The- cluster extends over 50 kb and has five functional genes(E ,

, , , ) and one pseudogene ( ) .

The - cluster is smaller, extends over ~20 kb and has four functional genes ( , , , , and ) and two pseudogenes ( , ) .

G A

2 1 2 1

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The two chains, viz., and , differ for a single amino acid i.e; glycine and alanine.

The two genes, namely , code for the same protein; such identical genes present in the same chromosome constitute “non allelic copies” of the gene.

G A

2,1

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VARIOUS GLOBIN GENES EXPRESSED DURING THE EMBRYONIC, FOETAL AND ADULT STAGES OF DEVELOPMENT :-

1. -globins• genes are expressed during the

embryonic development. • genes are expressed during

the foetal and the adult stages of the development.

1,2

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2. - globins • Epsilon genes (E) are expressed

during the embryonic development.

• genes are expressed during the foetal development.

• genes are expressed during the adult stages of development.

AG ,

,

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HUMAN HAEMOGLOBIN GENE CLUSTERS , WITH THE ALPHA AND BETA CHAINS.

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CLUSTERS OF BETA GLOBIN GENES SEEN IN VARIOUS VERTEBRATES.

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MYOGLOBIN GENES Myoglobin is an iron- and

oxygen- binding protein found in the muscle tissue of vertebrates in general and in almost all mammals.

It is related to haemoglobin, which is the iron- and oxygen- binding protein in blood, specifically in the red blood cells.

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In humans, myoglobin is only found in the bloodstream after muscle injury.

Myoglobin is the primary oxygen- carrying pigment of muscle tissues.

High concentrations of myoglobin in muscle cells allow organisms to hold their breath for a longer period of time.

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Diving mammals such as whales and seals have muscles with particularly high abundance of myoglobin.

In humans, myoglobin is encoded by the MB gene.

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MEAT COLOUR

Myoglobin contains hemes, pigments responsible for the colour of red meat.

The colour that meat takes is partly determined by the degree of oxidation of the myoglobin.

The higher the degree of oxidation of myoglobin, the richer the meat colour.

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ROLE IN DISEASE

Myoglobin is released from damaged muscle tissue, which has very high concentrations of myoglobin.

Myoglobin is a sensitive marker for muscle injury, making it a potential marker for heart attack in patients with chest pain.

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DIAGRAM REPRESENTING THE POSITION OF MYOGLOBIN GENE ON THE CHROMOSOME.

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HISTONE GENES Histones are highly alkaline

proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called “nucleosomes”.

They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation.

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Without histones, the unwound DNA in chromosomes would be very long.

Histones are found in the nuclei of the eukaryotic cells and in certain Archaea, but not in bacteria.

The unicellular algae known as dinoflagellates are the only eukaryotes that are known to completely lack histones.

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Histone proteins are among the highly conserved proteins in eukaryotes, emphasizing their important role in the biology of the nucleus.

Histone genes are of five types namely, H1, H2A, H2B,H3 and H4.

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Large quantities of histones are required during the S phase of cell cycle to package the newly synthesised DNA.

To meet this demand multiple copies of each of the five histone genes are present per genome in clusters of tandemly repeated units.

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A repeat unit contains one copy each of five histone genes seperated from each other by non transcribed spacer regions.

The histone genes don’t have intron sequences. All the exon sequences (coding sequences) are highly conserved.

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The variation in the length of repeated units in different organisms is due to the variation in the lengths of their non transcribed spacer regions.

The arrangement of histone genes is same in all species, but variation is observed in the orientation of genes on the chromosome.

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TYPES OF HISTONE GENES1.Histone H1:-• H1 is one of the five main histone

protein families which are components of chromatin in eukaryotic cells.

• Unlike other histones, H1 doesn’t make up the nucleosome bead. It sits on top of the stucture, keeping in place the DNA that has wrapped around the nucleosome.

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2. HISTONE H2A:-• Histone H2A is one of the five

main histone proteins involved in the structure of chromatin in eukaryotic cells.

• H2A is important for packaging DNA into chromatin.

• H2A plays a major role in determining the overall structure of chromatin.

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3. HISTONE H2B:-• Histone H2B is one of the five

main histone proteins involved in the structure of chromatin in eukaryotic cells.

• H2B is involved with the structure of the nucleosomes of the ‘beads on a string’ structure.

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4. HISTONE H3:-• Histone H3 is one of the five

main histone proteins involved in the structure of chromatin in eukaryotic cells.

• H3 is involved with the structure of the nucleosomes of the ‘beads on a string’ stucture.

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5. HISTONE H4:-• Histone H4 is one of the five main

histone proteins involved in the structure of chromatin in eukaryotic cells.

• H4 is a structural component of the nucleosome, and is subjected to some modifications including acetylation and methylation, which may alter expression of genes located on DNA associated with its parent histone octamer.

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Ex- histone genes in sea urchin• In sea urchins, histone genes are

classified into 2 classes. They are:-

1.Early genes-• Genes which express in the early

stages of embryogenesis. They are present upto around ~300 copies per genome.

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2. Late genes:-• Genes which are expressed later

in embryonic development.• They are present upto around

~10 copies per genome.

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. Types of histone gene organization in sea urchins

Top: The organization of the 5.6-kb S. purpuratus α-histone gene repeat Bottom: The organization of the late histone H3-H4 and the histone H2a-H2b gene pairs.

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Ex- histone genes in Drosophila melanogaster.

• The orientation of histone genes on the chromosome :-

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• The variations in length are due to the no. of repeated units, the non-transcribed space.

• The ends of the histone genes have attachment regions seen in the non-transcribed space.

• These attachment sites may help in the packing of DNA, in form of nuclear scaffolds.

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GENES FOR RIBOSOMAL RNA’S• Ribosomal RNA (rRNA) constitutes 80-

90% of the total cellular RNA in both prokaryotes and eukaryotes.

• Both rRNA’s and tRNA’s are present in multiple copies per genome.

• In eukaryotes, these copies are present in clusters either confined to a single chromosome, eg., in X. laevis, or they spread on more than one chromosome, eg., in humans and mouse.

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• In D. melanogaster, rRNA genes are present in X and Y chromosomes, the cluster in X being much larger than that in Y chromosome.

• The region containing rRNA genes is often called rDNA (ribosomal DNA).

Prokaryotes vs Eukaryotes• Both prokaryotic and eukaryotic

ribosomes can be broken down into two subunits.

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• In prokaryotes, a small 30S ribosomal subunit contains the 5S ribosomal RNA.

• The large 50S ribosomal subunit contains two rRNA species (the 16S and 23S ribosomal RNAs).

• Bacterial 16S rRNA, 23S rRNA and 5S rRNA genes are typically organised as a co-transcribed operon.

• There may be one or more copies of the operon dispersed in the genome. Eg., Escherichia coli has seven).

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• Archaea contains either a single rDNA operon or multiple copies of the operon.

• The 3’ end of the 16S rRNA (in a ribosome) binds to a sequence on the 5’ end of mRNA called the Shine-Dalgarno sequence.

• In eukaryotes, many copies of the rRNA genes are organised in tandem repeats.

• In humans, ~300-400 repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22).

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• The 5S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5.8S, 18S and 28S in mammals, 25S in plants).

• In eukaryotes, the 5S RNA is transcribed independently.

• In higher eukaryotes, 5S RNA genes are organised in separate clusters and their numbers are far in excess of those coding 18S-28S rRNA.

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• The number of copies of tRNA genes is difficult to estimate and most likely the numbers given in the following table.ORGANISM rRNA

genes tRNA genes

18S/23S rRNA(16S/23S rRNA)*

5S rRNA

E.Coli 7 7 60Yeast 140 140 250DrosophilaX chromosome 250Y chromosome 150Human 280 2,000 1,300Xenopus laevis 450 24,000 1,150

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• The repeating unit of rRNA gene clusters in eukaryotes consists of the following:

1. a transcribed region containing, a) a 5’ leader, followed by b) 18S rRNA , c) a transcribed spacer and d) 28S rRNA &2. Non transcribed spacer.• After trancription, the leader and the

transcribed spacer are cleaved to generate the 18S and 28S rRNA sequences within the same transcription unit, while the non transcribed spacer seperates different transcription units.

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• The transcribed spacer contains some shorter and useful sequences that are released by cleavage.

• In bacteria, it contains tRNA sequences, in mammals and amphibians one short sequence cleaved from this region forms 5.8S RNA, which forms H-bonds with 28S rRNA in ribosomes.

• The remaining transcribed spacer and the leader are presumably degraded.

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Organisation of rDNA in eukaryotes.A. General organisation of the repeating unit of

rDNAB. Organisation of the nontranscribed spacer in

X.laevis.

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• The non transcribed spacer varies widely. The nontranscribed spacer in yeast is short (1.75 kb) and is constant in length.

• In drosophila and X. laevis, this region is much larger and shows a variation in length between different copies of the repeating unit.

• Mammals represent the extreme case, where the non transcribed spacer is ~30 kb long.

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• Each nontranscribed spacer is internally repetitious, variation in length arises from changes in number of repeats of some of the sub units.

• In case of Xenopus , it contains 3 repetitious regions each comprised of a variable number of repeats of a rather short sequence.

• At the start of each nontranscribed region is a ~500bp long unique sequence. In addition, there are 3 sequences called Bam islands.

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• They are termed as bam islands because they are isolated following the digestion of spacer with BamH1 restriction enzyme.

• Two of the Bam islands separate the (each ~300 bp) 3 repetitious regions, while the third one lies at the end of the spacer.

• The 60/81 repeats of the NTS are involved in transcription initiation in a manner comparable with the enhancer sequences in relation to RNA polymeraseII.

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THANK YOU

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