Development Team

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Development Team

Paper Coordinator: Prof. Namita Agrawal

Department of Zoology, University of Delhi Principal Investigator: Prof. Neeta Sehgal

Department of Zoology, University of Delhi

Content Writer: Mr. Raj Kumar, Deshbandhu College, University of Delhi Dr. Kiran Bala, Deshbandhu College, University of Delhi

Miss. Charu Tripathi, Department of Zoology, University ofDelhi Content Reviewer: Dr. Surajit Sarkar

Department of Genetic, South Campus, Delhi University Co-Principal Investigator: Prof. D.K. Singh

Department of Zoology, University of Delhi Paper : 16 Molecular Genetics

Module : 04 Structural organization of genome: Sequence organization of genome.

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Description of Module

Subject Name ZOOLOGY

Paper Name Molecular Genetics; Zool 016 Module Name/Title Structural organization of genome Module Id M04: Sequence organization of genome

Keywords Genome, Microsatellite DNAs, Minisatellite DNAs, DNA Fingerprinting, Dynamic Genome, Prokaryotic Genome, Eukaryotic Genome and Gene Density

1. Learning Objectives

The following module explains:

 How genome is organized in prokaryotes and eukaryotes.

 The difference in sequence of organized genome in prokaryotes and eukaryotes.

 Complexity of genome in both prokaryotes and eukaryotes.

 The mechanism that leads to changes in genome size.

 The dynamic nature of genome, role of transposons and other transposable elements.

 Gene density and its relation with G+C content and repeat DNA sequences.

2. Introduction

DNA is a macromolecule formed by nitrogenous bases, phosphorus and pentose sugar arranged in such a way that gives DNA a three dimensional structure suitable for analysis through X-ray crystallography. DNA is the source of all information in a cell. Information on DNA is present in the form of genes. A gene is defined as a segment or stretch of DNA responsible for coding a particular protein. Thus, genetic information possessed by an organism is the sum total of all the genes possessed by it. Therefore, a genome can be defined as the sum total of all the genes possessed by an organism. For a diploid individual it is the entire chromosomal content, whereas, for a haploid individual, the genome is only one set of chromosomes.

3. Analysis of Complexity of Genome

Complexity of genome is usually studied by the denaturation and renaturation processes.

Denaturation of DNA is defined as its property to separate into the two constitutive individual strands from the double helical structure. When a saline solution containing DNA is warmed slowly, it leads to the separation of the double stranded DNA into two single strands. As the temperature reaches boiling point, the two strands separate out completely. This change can be examined by increase in U.V. absorption by the dissolved DNA. This is caused by the decrease in hydrophobic interactions that result from base stacking. This changes the nature of bases and results in increase in absorbance.

Half of the maximum absorbance is called melting temperature (Tm). A higher value of Tm indicates a

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high GC content. A high GC content provides more stability to DNA due to extra hydrogen bonding between these base pairs than AT pairs.

DNA renaturation is defined as a process that results in the reunion of the single strands of DNA into double helix due to lowering of temperature. Initially, the concept of renaturation appeared to be a non-feasible process but the same was proved in 1960 by Julius Marmur and co-workers while working in Harvard University, during their study on bacterial DNA denatured by heat. They found that lowering of temperature slowly results in regaining of the properties of double helix after which it starts behaving as genetic material and retains the ability to transform bacterial cells. Studies thus conducted prove that complementary single-stranded DNA molecules are capable of reassociation and this event is defined as renaturation or reannealing.

3.1. How Complex is the Bacterial or Viral Genome?

The renaturation event depends upon several factors:

1. The length of molecule involved;

2. Concentration of DNA;

3. Duration of incubation;

4. Strength of interaction of ions in solution; and 5. Temperature at which the incubation is done.

Figure 1. Reassociation Kinetics

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Source:https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fimage.slidesharecdn.com%2Fgenomestructu re-medics-140816181407-phpapp02%2F95%2Fgenome-structure-32-638.jpg%3Fcb%3D1408212950&imgre furl=http%3A%2F%2Fwww.slideshare.net%2FNickmwangi%2Fgenome-structure-medics&docid=c5qSxDxBG iLGPM&tbnid=pMcQpFapBc7mBM%3A&w=638&h=479&bih=780&biw=1440&ved=0ahUKEwjd3riPnPHP AhWJrlQKHdcXBb0QMwgdKAAwAA&iact=mrc&uact=8

When DNA from different organisms but of the same size (1000 base pairs) and equal concentration mg/ml was allowed to undergo renaturation, the following observations were recorded: DNA annealing from plant and animals shows three more or less steps when plotted graphically in the form of a curve. These curves represent three broad classes of DNA sequences. These three classes are different in the number of repeats of their nucleotides. These three classes are termed as highly repeated sequences, moderately repeated sequences and non repeated sequences.

3.2. Highly Repeated Sequences

They are usually present in 10⁵ copies per genome. They are short in nature and present in clusters.

The same sequence is repeated again and again. Such highly repeated sequences fall into satellite DNAs, minisatellite DNAs and microsatellite DNAs.

3.3. Microsatellite DNAs

Shortest possible sequences (1-5 bp long) which have even distribution throughout the genome.

Enzymes involved in DNA replication face difficulty in copying them and are responsible for changing their length in the subsequent generations. The microsatellite DNA sequences are used to establish the relationship between different individuals in a human population due to their differences in length among the population. For example, the evidence that clearly indicates that modern humans arose in Africa is predicted by their longer microsatellite DNA sequence than the human population from other countries. Validation of this can be made by comparison of 60 different microsatellite loci which show a greater difference in African population than in Asian or European populations.

3.4. Minisatellite DNAs

These sequences range from 10-100 base pairs. These sequences can have more than 3000 repeats.

They occupy short stretch of the genome. They are unstable and the number of repeats of a particular sequence can increase or decrease from one generation to another due to crossing over. They are used for DNA fingerprinting.

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3.5. DNA Fingerprinting

DNA fingerprinting is used to identify an individual from a sample of DNA. In this technique, DNA is digested by enzymes called restriction endonucleases and the digested fragments of DNA are subjected to gel electrophoresis for separation. These fragments are identified by using labeled probes whose sequences are complementary to the fragment to be identified. There are 13 different VNTR (Variable number of Tandem Repeats) loci that are used as probes in case of DNA fingerprinting. The length of the VNTR loci varies from person to person. There is no chance of similarity between two loci of VNTRs between two different individuals.

The eukaryotic genome contains copies of short DNA sequences, however, it is difficult to identify the exact location of these sequences on the chromosome. The answers for these questions are obtained through nucleic acid hybridization technique. For such analysis, a new technique called in situ hybridization methodology was developed in 1969 by Mary Lou Pardue and Joseph Gacl of Yale University and it was used to determine the position of satellite DNA. It is a type of hybridization that uses a labeled complementary RNA or DNA probe to identify a specific DNA or RNA sequence in a cell, tissue, seed or early embryonic stage cells. It is also used in medical diagnostics to assess chromosomal integrity.

3.5.1. Moderately Repeated DNA Sequences

These can comprise 20 to more than 80 percent of the total DNA based on the type of organism under study. Within the genome, these sequences can be repeated few to tens of thousand times. These sequences are composed of coding and non coding functions.

3.5.2. Moderately Repeated DNA Sequences without Coding Function

Majority of repeated DNA do not code for any product. They are not present in tandem repeats, instead they are interspersed within the genome as individual elements. These elements are divided into two categories: LINES (long interspersed elements) and SINES (short interspersed elements).

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Figure 2. DNA Finger Printing

Source:https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fcdn.yourarticlelibrary.com%2Fwp-content%

2Fuploads%2F2013%2F10%2Fimage_thumb88.png&imgrefurl=http%3A%2F%2Fwww.yourarticlelibrary.com

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3.5.3. Repeated DNA with Coding Functions

These sequences encode for ribosomal RNAs and also for chromosomal proteins called histones.

These sequences are usually identical to each other and present in a tandem array. These sequences are present in multiple numbers because RNAs are required in large amount.

4. Dynamic Genome

Although the genome sequence of an organism is static, but changes are brought about by evolutionary forces acting via the environment. We have a general idea that genes are occupying a fixed loci on the chromosome and their position remains unchanged. However, we are also familiar with the phenomenon of crossing over between homologous chromosomes during meiosis, that results

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in the formation of new allelic combinations. The stability of the genome is due to linkage relationships. There exists a difference between the generation time of prokaryotes and eukaryotes, which suggests that their evolutionary scales might be different in terms of real time.

Figure 3. Different types of repetitive DNA

Source:https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fimage.slidesharecdn.com%2Fgenomestructu re-medics-140816181407-phpapp02%2F95%2Fgenome-structure-14-638.jpg%3Fcb%3D1408212950&imgre furl=http%3A%2F%2Fwww.slideshare.net%2FNickmwangi%2Fgenome-structure-medics&docid=c5qSxDxBG iLGPM&tbnid=XDbcV64dLYwC8M%3A&w=638&h=479&bih=780&biw=1440&ved=0ahUKEwi0sa_TnfHP AhVJxlQKHdPuCKwQMwhSKCowKg&iact=mrc&uact=8

There is good amount of difference between individual genomes at the molecular level because of polymorphic variations provided by transposable elements or transposons. Transposons are defined as discrete sequences showing mobility in the genome. They are capable of transferring themselves to other locations within the genome. However, they do not behave like phage or plasmid DNA.

In eukaryotes, majority of elements have lost their function but they retain the capability of transposition due to enzyme from functional transposons. Therefore transposable elements can cause rearrangement of genome, directly or indirectly.

 Transposition can lead to deletions or inversions or lead to change in position of host sequence to a new location.

 They serve for cellular recombination. This is possible due to the region of homology on different locations. Two copies of transposons on different chromosomes or at different locations may

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provide sites for reciprocal recombination. Such changes lead to insertion, deletion, inversions or translocations. Transposons can also be regarded as “selfish DNA”, concerned only with their own propagation. Thus, transposons can be considered as independent entities that are present in the genome. Sometimes, a transpsoson can lead to a selective advantage that can be beneficial for the survival of the genome carrying the transposon.

 IS-elements- These are simple transposition modules. Insertion (IS) elements were discovered from the bacterial genome. They were first thought to be responsible for prevention of transcription and translation. They are the simplest transposons.

Changes in genome are possible by rearranging existing sequences and acquiring new sequences.

New sequences are acquired via vectors which carry information horizontally by mediating the transfer of short length of DNA. Transposons are DNA sequences coding for proteins. Transposons from retroviruses are capable of making DNA copies of their RNA transcripts, thus propagating themselves. The DNA copies of RNA transcript become integrated at new sites. So, the prokaryotes and eukaryotes exhibit transposons that mobilize via DNA. Bacterial transposons carry information for their transposition, but in addition to this they require the help of the genome in which they reside (for enzymes such as DNA gyrase and DNA polymerase).

In eukaryotes, the enzyme involved in transposition is not well characterized and the genome contains both functional and defective elements. Each IS element is named by adding a prefix IS. IS elements are a part of plasmids and bacterial chromosomes. To justify their position, double colon is used; thus lambda::ISI can be explained as an ISI element inserted into phage lambda. An IS element can be defined as an autonomous unit capable of causing its own transposition by producing its own protein required for transposition. Each IS element is different in its composition but they share similarity in organization (Figure 4) of generic transposons and IS elements. The ends of IS elements have short similar inverted repeats. During transposition of IS elements, a sequence of host DNA is duplicated at the site of insertion, that is shown by the presence of direct repeat sequence on either side of the insertion element. The frequency of transposition varies at a rate of 10^-3-10^-4 per element and it is different as per generation time.

Transposons are also responsible for drug resistance in addition to their transposition activity. Larger transposons are called composite elements. Composite elements carry a drug marker in the central

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region flanked on either side by arms that consist of IS elements. The arms mostly have an inverted orientation, however, sometimes, they can have a simple orientation.

Figure 4. Representation of the integration of an IS elements into chromosomal DNA.

Source:https://www.google.co.in/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0a hUKEwjP_Iy7nvHPAhXIPo8KHcMLA_8QjRwIBw&url=http%3A%2F%2Fwww.biologydiscussion.com%2Fc ell%2Fprokaryotes%2Ftransposable-genetic-elements-in-prokaryotes-2%2F12001&bvm=bv.136593572,d.cG w&psig=AFQjCNEoiEEI0UDayaCN0ACWKVAgaKR9Zg&ust=1477322799056559

Arms with inverted repeats have the following structure:

----ArmL---Central Region---ArmR----

The arrow shows the orientation of arms. L and R indicate the left and right region in the genetic map of the transposons. The similarity in module between two transposons provides the basis of transposition in which one module can favor the movement of the other.

4.1. Transposition Mechanism (Replicative and Non Replicative)

The common mechanism of transposon insertion into new site can be replicative or non replicative. It occurs through staggered breaks in the target site followed by plugging the ends of transposons to the end of the target DNA site, followed by filling the gaps. The formation of staggered ends and their filling explains how the direct repeats are produced at the ends of target DNA sites. Type of cut is the

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property of the enzyme involved and it also confirms the property of the repeat and length of the repeat. These are three possible mechanisms through which a transposon moves (Figure 6).

4.1.1. Non Replicative Transposition

In this kind of transposition, the element moves from one position to another as a physical entity directly. It involves a connection between donor and target DNA. Transposons like Tn5 and Tn10 utilize this mechanism.

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Figure 5. Representation of (a) transposon Tn10 (b) transposon Tn5

Source: (a) https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fimages.slideplayer.com%2F25%2F7868579%2 Fslides%2Fslide_23.jpg&imgrefurl=http%3A%2F%2Fslideplayer.com%2Fslide%2F7868579%2F&docid=VSu7KK6oI8 9iZM&tbnid=cSf69IdPRJxJAM%3A&w=960&h=720&bih=780&biw=1440&ved=0ahUKEwjriu6vn_HPAhXny1QKH cWDBukQMwglKAgwCA&iact=mrc&uact=8

(b) https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fwww.pnas.org%2Fcontent%2F97%2F16%2F8 944%2FF1.medium.gif&imgrefurl=http%3A%2F%2Fwww.pnas.org%2Fcontent%2F97%2F16%2F8944.figures-only

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In this mechanism, the sequence is released from the flanking region of the donor DNA during transfer. There is a loss of sequence from one site and gain at the recipient site. All these processes raise questions about the fate of the donor DNA. The possible explanation for this is that the donor DNA is destroyed that is possible in bacteria because more than one chromosome is present. The host DNA repair mechanism recognizes the double stranded break and repairs it.

4.1.2. Replicative Transposition

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In this case, the sequence is duplicated before transposition and followed by transposition of other copy. During this process, one copy remains on the original site but the other one is shifted at a new position. This type of transposition increases the number of the transposons. The enzymes involved in this type of transposition include transposases that act on the end of the original DNA sequence and resolvase that act on the duplicate copies, for example TnA.

Figure 6. Transposition mechanism

Source:https://www.google.co.in/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0a hUKEwjP8LmyoPHPAhVLqI8KHVdGDO8QjRwIBw&url=https%3A%2F%2Fwww.studyblue.com%2Fnotes

%2Fnote%2Fn%2Fchapter-14-objectives%2Fdeck%2F2246187&bvm=bv.136593572,d.cGw&psig=AFQjCNG OpX3GhIPYfK2EQFUkZ42kQZdJeA&ust=1477323314875827

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Figure 7. Difference between replicative and non replicative transposition.

Source: https://www.google.co.in/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0 ahUKEwjrkJHLoPHPAhUKp48KHYCICegQjRwIBw&url=http%3A%2F%2Ffemsre.oxfordjournals.org%2Fco ntent%2F21%2F2%2F157&psig=AFQjCNH0xDYgisFwiPKnmLcAiU1sH2i0eQ&ust=1477323367622079

4.1.3. Conservative Transposition

It is a kind of non replicative event. During this process, the element is removed from the donor site and inserted on the target site through a complex mechanism, that preserves the nucleotide bond (Figure 8). The element involved in this is capable of transferring not only to itself but also to the donor DNA from one bacterium to another. They resemble episomes. Although transposition can occur via one mechanism but there are transposons that use both the mechanisms.

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Figure 8. Mechanism of conservative transposition.

Source:https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fimage.slidesharecdn.com%2Fbacterial- transposons-1235039960223797-2%2F95%2Fbacterial-transposons-28-728.jpg%3Fcb%3D1235018415&imgre furl=http%3A%2F%2Fwww.slideshare.net%2Fguest06ad101%2Fbacterial-transposons&docid=xeIoEbWlD6 lW_M&tbnid=dI8QqvwpUhXLGM%3A&w=728&h=546&bih=780&biw=1440&ved=0ahUKEwiY-MTfoPH PAhUBN5QKHaGeDK0QMwgdKAAwAA&iact=mrc&uact=8

5. Structure of Prokaryotic Gene

The remarkable characteristics of bacterial gene organization is that they are always present in a clustered group, involved in a biochemical pathway. They are often found adjacent to each other and are translated together as single polycistronic mRNA. This type of arrangement can be studied in E.

coli. Although there are few genes in E. coli that are expressed individually but majority of them are

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transcribed in a single large transcriptome unit. Thus, control of transcription process regulates the expression of these gene clusters. This mechanism of coordinate expression is achieved by control elements in combination with regulator proteins. Jacob Monod proposed the operon model for metabolism of lactose. The operon is composed of a whole unit of genes including regulator genes, structural genes and control elements. In the operon model, expression of genes are controlled in such a way that they are turned off and on together with their control elements. In prokaryotes, the majority of DNA consists of genes and the intermittent non coding DNA is called intergenic DNA.

Figure 9. Prokaryotic gene structure.

Source:https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fimage.slidesharecdn.com%2Fgeneidentifica tionanddiscovery-110901054918-phpapp01%2F95%2Fgene-identification-and-discovery-6-728.jpg%3Fcb%3 D1314858134&imgrefurl=http%3A%2F%2Fwww.slideshare.net%2FAmitRuchiYadav%2Fgene-identification- and-discovery&docid=oIj_fJzIJkzkcM&tbnid=PHv-CnnbzH921M%3A&w=728&h=546&bih=780&biw=1440

&ved=0ahUKEwirtsqZofHPAhXFkJQKHUCDCh4QMwggKAUwBQ&iact=mrc&uact=8

A eukaryotic gene is usually comprised of coding and non coding regions. The coding region is expressed in an mRNA and the non coding region is not represented in an mRNA. Transcription results in the production of copies of RNA complementary to the sequence present in gene. To make a functional RNA or mRNA, introns are removed and exons are joined together to form functional mRNA.

5.1. Alternate and Overlapping Genes

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Sometimes a gene sequence can encode for more than one protein. This occurs due to overlapping genes. In this condition, a part of gene represents another gene. Overlapping genes are of common occurrence in bacterial and viral genomes. Some eukaryotes and viruses are capable of alternate expression of genes which is made possible only due to the presence of switch for connecting exons.

6. Characteristics of Structural Genes

A gene can be defined as a stretch of nucleotides that encode for a functional protein that occupies a particular locus. Most genes are identified when their function is missing due to lack of functional protein caused due to alternation in protein structure due to mutation. Therefore, these types of genes are usually present in multiple copies. They either code for related protein or same protein. A gene can also be identified and characterized by its mRNA.

Structural genes have the following organization:

a. Another sequence producing a similar protein may be present.

b. DNA sequences that encode for specific sequence.

c. Multiple copies of a sequence coding for the same protein.

6.1. Structural Gene Organization of Eukaryotes

Figure 10. Representation of structural gene organization in Eukaryotes.

Source:https://www.google.co.in/imgres?imgurl=https%3A%2F%2Fclassconnection.s3.amazonaws.com%2F57 9%2Fflashcards%2F997579%2Fjpg%2F151323425424778.jpg&imgrefurl=https%3A%2F%2Fwww.studyblue.

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6.2. The Genome of Eukaryotes

In eukaryotes, the genetic material is present inside the nucleus and is separated from the surrounding cytoplasm by the porous nuclear membrane. In eukaryotes, the genome is organized into chromosomes. The number and size of chromosomes varies from species to species. The organelles like chloroplast and mitochondria contain a small amount of genomic material. Genes can have interruptions, multiple copies and large nucleotide sequences that do not encode for any protein. In eukaryotes, the differential expression of genes is regulated through compartmentalization of the nucleus and the cytoplasm.

Figure 11. Difference in gene structure of prokaryote and eukaryote.

Source:https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fimage.slidesharecdn.com%2Ftranscriptiona ndsplicing-111019134351-phpapp01%2F95%2Ftranscription-and-splicing-38-728.jpg%3Fcb%3D1319031926

&imgrefurl=http%3A%2F%2Fwww.slideshare.net%2Far_shad%2Ftranscription-and-splicing&docid=ldie9np NZWAVAM&tbnid=Ddl5voiNJl_btM%3A&w=728&h=546&bih=731&biw=1440&ved=0ahUKEwjQy9yeo_

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A eukaryotic gene is composed of interrupted regions called introns. A transcribed RNA consists of both introns and exons. Introns are removed from the primary transcript leading to the formation a

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mature mRNA. A large gene consists of exon sequence at its starting point and end point. The length of introns varies from 14 bp to 46 bp in different genes. Introns consist of non repeat sequences.

6.3. Structure Gene Relation

The exon sequences in a gene are related to the other sequences present. This has been validated experimentally by DNA hybridization experiments. The extra sequences have sometimes been shown to possess functional activity. Such genes, without any function, but which were once functionally active are known as pseudogenes. Pseudogenes have been known to have become inactive due to accumulation of mutations during the course of evolution. Sometimes these exons are brought together to form a functional gene or they can be duplicated.

7. Gene Density

Each organism exhibits a large number of genes and their number can vary from few thousand to tens of thousands. The variation in the number of genes depends upon the complexity of the organisms under consideration. The number of genes per Mb of the genome or a chromosome depicts the gene density of an organism. As the eukaryotic genome is organized into chromosomes, the gene density will vary on different chromosomes. Thus, there can be few genes on one chromosome and a large number of genes on another chromosome. For example, in case of yeast genome, a 50 Kb region on chromosome 3 contains 20 genes. On the other hand, a 50 Kb region on chromosome 16 of the human genome contains only 6 genes. This variation is due to the varying number of introns. The entire yeast genome contains 230 introns, while even single genes in the human genome contain over 100s of introns.

C. elegans (a free living nematode) consists ~100 Mb of DNA forming the entire genome and is organized into six chromosomes harboring a total of ~20,000 genes. Although C. elegans contains 8 times the DNA content and 3 times the number of genes as compared to yeast, but the gene density is much lower. This is due to the fact that half of the C. elegans genome consists of introns. Also, the C.

elegans genome consists of tens of thousands of ATAT repeats spanning the entire genome. A unique feature of the C. elegans genome organization is that 25% of the genes are arranged into polycistronic units or operons showing a close resemblance to bacterial genome structure.

The human genome contains about 30,000 genes previously estimated to be around 50,000 to 100,000. Human genes are larger in size due to large introns and more number of introns as compared

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to invertebrate genomes. Dystrophin gene is the largest gene in humans, which when mutated causes muscular dystrophy. The total length of the gene is 2.5 Mb which is even greater than some complete bacterial genomes. There are genes in the human genome that contain upto 30 to 50 introns. To explain the differences in gene density between two chromosomes in humans we can take the example of chromosome numbers 21 to 22. The long arms of these two chromosomes are actually similar in size (chromosome 21 = 33.5 Mb and chromosome 22 = 34.65 Mb), but the number of genes present on chromosome 21 is 225 whereas chromosome 22 contains 541 genes. This difference reflects that chromosome 22 has a higher gene density than chromosome 21. This clearly reflects that genes are not evenly spread on chromosomes even in the same organisms. The upper portion of the long arm of chromosome 21 contains a "G band", a segment that is considerably gene poor as compared to the lower region of the long arm which has a higher gene density. There is a segment of 7 Mb on chromosome number 21 containing only one gene. Three region of 1Mb length in addition to above mentioned region, do not contain any genes. Thus, 10 Mb of DNA contains only one gene.

Chromosome number 22 has a small stretch or segment of DNA towards the telomere, of length 2.5 Mb and 1Mb that does not contain any gene.

Table 1. Characteristics of ten of the most completely studied chromosomes of the human genome. Source:

https://www.google.co.in/imgres?imgurl=http%3A%2F%2Fwww.scielo.br%2Fimg%2Frevistas%2Faabc%2Fv7 7n4%2Fa06tab07.gif&imgrefurl=http%3A%2F%2Fwww.scielo.br%2Fscielo.php%3Fscript%3Dsci_arttext%26 pid%3DS0001-37652005000400006&docid=XF07gR1wOVtC9M&tbnid=Lx1GJxyeJ6lTDM%3A&w=414&

h=407&bih=731&biw=1440&ved=0ahUKEwih8ZaUpPHPAhXFmpQKHWKIDEQQMwgrKA4wDg&iact=mr c&uact=8

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8. Summary

DNA is a macromolecule formed by nitrogenous bases, phosphorus and pentose sugar arranged to give a three dimensional structure. DNA contains information in the form of genes. A gene encodes for a functional protein. Genome consists of the total number of genes possessed by an individual. For a diploid individual, it is encoded by entire sets of chromosomes, whereas, for a haploid individual it is formed by half set of the total number of chromosomes.

Complexity of the genome is studied by denaturation and renaturation kinetics. Warming of DNA is followed by separation of the two constituent DNA strands. This change of double stranded DNA into single stranded DNA can be studied by U.V. absorption. Renaturation is referring to as the reunion of the single strands to form a double stranded DNA due to lowering of temperature. Renaturation also results in resumption of the function of DNA. Complexity of prokaryotic as well as eukaryotic genome can also be studied by denaturation and renaturation process. Renaturation depends upon various attributes including, length of DNA, concentration, duration of incubation, strength of ions in solution and temperature of incubation. DNA renaturation reveals three classes of DNA termed as highly repeated sequences, moderately repeated sequences and non repeated sequences. Highly repeated sequences are usually present 10⁵copies per genome. Mircosatellite DNA, have even distribution throughout the genome. Minsatellite DNAs usually have 3000 copies per genome. DNA fingerprinting is used in forensic sciences and paternity cases it is based on VNTR loci and for humans there are 13 VNTR loci whose length varies from person to person, for identification of which, labeled probes are used. There is no possibility of similarity between two loci of VNTR in two different individuals. Copies of short DNA sequences can be determined by DNA hybridization that uses labeled complementary RNA or DNA. Moderately repeated DNA sequences constitute 20 to 80 percent of total DNA based on the organism under study. These sequence are repeated few to tens of thousand times. These sequences can or cannot have coding function.

Although the genome is static but it changes under the influence of evolutionary processes. Crossing over during meiosis leads to the formation of new allelic combinations. Transposons are a source of genomic rearrangements directly or indirectly. Transposons are regarded as “selfish DNA” as they are only concerned with their own propagation. Some transposons lead to survival of the genome carrying the transposons wheras others may not. Eukaryotes contain both functional and non-functional transposon elements. Transposons are also responsible for drug resistance. Composite elements carry

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drug markers in the central region. Transposition occurs via replicative and non-replicative mechanisms. IS-elements, Tn5 and Tn10 undergo transposition via non-replicative mechanism. There is loss at one site and gain at the recipient site. On the other hand, in case of replicative transposition, sequences are replicated during transposition (Example, TnA undergoes such transposition).

Additionally, in non-replicative transposition, the transposon moves as a physical entity directly. It involves a connection between the donor and target DNA. In replicative transposition the sequence is duplicated followed by transposition of the other copy. It increases the number of transposons. Two enzymes are involved in this process: transposase and resolvase. Conservative transposition is an example of non-replicative transposition.

In prokaryotes, genes are usually arranged in clusters to form a polycistronic mRNA and transcribed in a single large transcriptome unit. Coordinate expression is achieved by control elements in combination with regular protein. It is divided into genic and intergenic DNA. Overlapping genes are prevalent in bacteria and virus. The eukaryotic genome is usually organized into chromosomes. Each chromosome may differ in terms of the number of genes, gene density, interruptions and multiple copies of genes. There are large sequences that do not encode for any protein. mRNA consists of exons (coding) and introns (non coding). After transcription, removal of introns leads to the formation of mature mRNA. Gene density means the number of genes per Mb of the genome or a chromosome.

The gene density varies on different chromosomes of the same organism and for different organisms.

This variation can be due to the presence of introns of different sizes and in different numbers.

Development Team