14 Genomics

14 4. GENOMICS 5.  Application of DNA sequencing and genome mapping to the study, design and      manufacture of biologically important molecules is known as genomics. It is comparatively more recent branch in the field of biology. The term genomics was introduced by Thomas Roderick. In genomics, function of gene is identified by using the technique of reverse genetics. Genomics study may be classified into three classes: (i) Structural genomics : It involves mapping and sequencing of genes. (ii) Functional genomics : It involves the identification of function of a particular gene. (iii) Application genomics : It involves use of genomics information for crop improvement etc. Complete genomics of Arabidopsis and rice have been worked out and they are having 130 and 430 million base pairs respectively. Human Genome Project (HGP)  The Human genome project was the international, collaborative research program whose goal was the complete mapping and understanding of all the genes of human beings.   All genes together are known as "genome". The Human Genome Project as "Mega project" was a 13 year project co-ordinated by the U.S. Department of Energy and the National Institute of Health.  An International Human Genome project was launched in the year 1990 and completed in 2003. The International Human Genome sequencing consortium published the first draft of  the human genome in the journal Nature in February 2001 .  Human genome is said to have approximately 3 × 109 bp, and the cost of sequencing required is US$ 3 per bp. The total estimated cost of the project would be approximately 9 billion US dollars. In human genome 20,000 to 25,000 genes are present, out of them smallest gene is TDF gene with 14 bp and largest gene is Duchenne Muscular Dystrophy gene with 2400 × 103 bp. Organisms and the number of bp and genes in them Organism 1. E. coli Base pairs 4.7 million No. of genes 4,000 2. Saccharomyces cerevisiae 12 million 6,000 3. Coenorhabditis elegans 97 million 18,000 4. Drosophila melanogaster 180 million 13,000 Goals of HGP  (i) (ii) Following are the important goals of HGP : Identication of all the approximately 20,000 -25,000 genes in human DNA. To determine the sequence of the 3 billion chemical base pairs that make up human DNA. (iii) To store this information in databases. (iv) To improve tools for data analysis. (v) Transfer related technologies to other sectors, such as industries. (vi) Bioinformatics, i.e., close association of HGP with the rapid development of a new area in biology. (vii) Sequencing of model organisms -Complete genome sequence of E.coli, Saccharomyces cerevisiae, Coenorhabditis elegans; Drosophila melanogaster, D. pseudoobscura, Oryza sativa and Arabidopsis was achieved in April, 2003. (viii) Adress the ethical, legal and social issues (ELSI) that may arise from the project. Methodologies The HGP techniques include: (i) (ii) Sequence tagged site: It is a short DNA segment that occurs only once in a genome and whose exact location and order of bases is known. STSs serve as landmarks on the physical map of a genome. It is also called as Expressed Sequence Tags (ESTs). The genes that are expressed as RNA are referred to as ESTs. Sequencing the whole set of genome that contained all the coding and non-coding sequences, and later assigning different regions in the sequence with functions, known (iii) as Sequence Annotation. The Employment of Restriction Fragment Length Polymorphism (RFLP) (iv) (v) (vi) Yeast Artificial Chromosomes (YACs) Bacterial Artificial Chromosomes (BACs) Polymerase chain reaction (PCR) (vii) Electrophoresis  For sequencing, the total DNA from a cell is isolated and converted into random fragments of relatively smaller sizes (recall DNA is a very long polymer, and there are technical limitations in sequencin very long pieces DNA) and cloned in suitable host  using specialised vectors. The cloning resulted into amplification of each piece of DNA fragment so that it subsequently could be sequenced with ease.   The commonly used hosts were bacteria and yeast, and the vectors were called as BAC (bacterial artificial chromosomes), and YAC (yeast artificial chromosomes). The fragments were sequenced using automated DNA sequencers that worked on the principle of a method developed by Frederick Sanger. These sequences were then arranged based on some overlapping regions present in them. This required generation of overlapping fragments for sequencing. Alignment of these sequences was humanly not possible. Therefore, specialised computer based programs were developed. These sequences were subsequently annotated and were assigned to each chromosome. The sequence of chromosome 1 was completed only in May 2006 (this was the last of the 24 human chromosomes -22 autosomes and X and Y -to be sequenced). Salient Features of Human Genome  (i) Some of the salient observations drawn from human genome project are as follows : The human genome contains 3164.7 million nucleotide bases. (ii) The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases (iii) The total number of genes is estimated at 30,000-much lower than previous estimates of 80,000 to 1,40,000 genes. Almost all (99.9 percent) nucleotide bases are exactly the same in all people. (iv) The functions are unknown for over 50 per cent of discovered genes. (v) Less than 2 percent of the genome codes for proteins. (vi) Repeated sequences make up very large portion of the human genome. (vii) Repetitive sequences are stretches of DNA sequences that are repeated many times, sometimes hundred to thousand times. They are thought to have no direct coding functions, but they shed light on chromosome structure, dynamics and evolution. (viii) Chromosome 1 has most genes (2968), and the Y has the fewest (231). (ix) Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs -single nucleotide polymorphism, pronounced as 'snips') occur in humans. This information promises to revolutionise the processes of finding chromosomal locations for disease-associated sequences and tracing numan history. Classes of DNA sequences found in Human Genome Class Frequency Description 1 Introns 24% Non-coding DNA that comprises the great majority of each human gene 2 Protein encoding genes < 2% Transcribed portion of the 30,000 genes (exons) scattered about the chromosomes 3 Structural DNA 20% Constitutive heterochromatin, localised near centromeres and telomres Future Thrust of Human Genome Project  Francis Collins, director of the public funded genome project predicts the following progress in the next thirty years: By 2010 1. Scientists will have developed accurate predictive tests for atleast a dozen common diseases so that preventive measures may be taken in advance. 2. Infertility specialists will be using the sophisticated techniques of pre-implantation genetic diagnosis to screen embryos for genetic disorders and designer babies. 3. Medicines will be making use of gene therapy. By 2020 1. Doctors will have "designer drugs" to treat almost every disease. 2. Doctors will test patient's genetic make-up before prescribing drugs. 3. Doctors could change the genetic make-up of a living person by germ-line therapy. 4. Treatment of diseases like cancer, schizophrenia, depression etc. will have transformed. By 2030 1. 2. 3 Genetic-based health care will have completely developed. Most medical researches will be carried out using computer models rather than living tissues of animals. Average life-span will rise up to 90 years  In translation, ribosomes are often found in clusters linked together by a strand of mRNA. This complex (polyribosome or polysome) enables several molecules of the same polypeptide to be produced simultaneously. Memories Some Other Important Contributions of Scientists 1) Zacharis - Called nuclein as DNA and proved that chromatin is rich in DNA DO YOU KNOW 2) Fuelgen - DNA is located in nucleus where chromosomes are found, nucleus is fuelgen positive 3) Behrem - Nucleic acid is of two types DNA and RNA. 4) Fischer - Identified purines and pyrimidines in nucleic acid. 5) Levene - Studied chemistry of DNA and found that DNA has deoxyribose sugar and four types of nucleotides. 6) Sanger - Determined base sequence in nucleic acid. 7) Hedges and Jacob -Term "transposon"