functional genomics

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Some definition related to genomics :

Some definition related to genomics Gene:- It may be defined as a segment of DNA that contains the information related to a single polypeptide or RNA molecule . Genome: - A complete set of chromosome (hence of genes) inherited as a (haploid) unit from one parent. I.e. The entire compliment of genetic material (genes +intergenal chromosomal segment) present in each cell of an organism . Genomics : - it is the study of how gene and genetic information are organized within the genome and how this organization determines their function.



Why the study of genomics is necessary:

Why the study of genomics is necessary It helps in understanding the sequence of bases would unlock the whole blueprint of the development of an organism. Genome study of crops can ensure a better future with the capability of more perfect and précised genetic manipulation for enhanced yield and survival under adverse conditions. Genomics conducts structural and functional studies of genomes the former deals with the determination of DNA sequences and gene mapping, while the latter is concerned with the attachment of functional information to existing structural knowledge about DNA sequences


APPROACHES TO GENE IDENTIFICATION Sanger techniques. Whole genome shotgun sequencing. Gene identification with INTERNET resources

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Sanger techniques.

Whole genome shotgun sequencing:

Whole genome shotgun sequencing

Gene identification with INTERNET resources:

Gene identification with INTERNET resources Computational analyses of DNA sequences/gene identification can be carried out by the use of Internet resources. The nucleotide sequences can be retrieved from one of the three IC (International Collaboration) nucleotide sequence repositories/databases: SN DATA BASE WEB SITE 1 NCBI Gene Bank 2 EMBL Nucleotide Sequence Database 3 DNA Data Bank of Japan


SOME USEFUL WEBSITE FOR GENOMIC DATABASE SN DATA BASE WEBSITE 1 Arabidopsis thaliana genome 2 Crop plants genome mapping 3 Rice genomic maps and sequences 4 Maize genome 5 Human genes and genomic maps 6 Escherichia coli

organisms whose genome has been sequenced:

organisms whose genome has been sequenced Sn Organisms Genome size (Mb) No. of genes remark 1 Haemophilus influenzae 1.83 1,743 1 st sequenced organism 2 E.coli 4.6 4,288 3 Yeast (S.cerevisae) 13 6,000 1 st eukaryote 4 Drosophila 139 13,601 5 Arabidopsis thaliana 140 27,000 1 st plant 6 Human 3,200 Around 40,000

Why We Need Functional Genomics:

Why We Need Functional Genomics Organism # genes % of genes with known function Completion date of genome E. coli 4288 60 1997 yeast 6,600 40 1996 C. elegans 19,000 40 1998 Drosophila 12-14000 25 1999 Arabadopsis 25,000 40 2000 mouse ~30,000? 10-20 2002 human ~30,000? 40-50 2000

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Genome of Arabidopsis

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FUNCTIONAL GENOMICS:- It involves the function of all specific gene and their expression in time and space in an organism . Once new gene is located and sequenced then the next question is what function it controls.

Goals of functional genomics:

Goals of functional genomics To understand the relationship between an organism's genome and its phenotype. It helps in understanding of the dynamic properties of an organism at cellular and/or organism levels. It provides a more complete picture of how biological function arises from the information encoded in an organism's genome. How a particular mutation leads to a given phenotype has important implications for human genetic diseases Attempt are being made to find out the pattern of gene expression, which genes are switched on and which are switched off in different tissues during different developmental stage.

How to determine the function of unknown genes:

How to determine the function of unknown genes Following approaches are used Experimental analysis Phage display Yeast two hybrid system Computer analysis

Experimental analysis:

Experimental analysis In conventional analysis the gene responsible for a phenotype can be identified by determing which genes are inactivated in organisms that display a mutant version of phenotype. In functional genomics we mutate the gene & identify the phenotypic changes that results. This can be done either by introduction of mutation into genes or silencing the gene families using RNA interference approach. Mutation libraries have been developed by chemical or insertion mutagenesis

TILLING (targeting induced local lesion in genome ):

TILLING (targeting induced local lesion in genome ) In this method we mutate the gene by chemical treatment. The end product of tilling process is a plant that has been identified with a change in a specific gene of interest. The plant line is then useful for determing the effect of the gene on the characteristics of the tilled population that screened as mutant allele in specific gene.


INSERTION MUTAGENESIS It is also known as gene knock out method In this method the activity of a gene has been eliminated due to insertion of a DNA fragment. This DNA fragment may be a T-DNA or a transposon sequences Following methods are employed to inactivate specific gene or over-expressed gene for determination of its function

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GENE INACTIVATION:- To inactivate a specific gene a unrelated segment of DNA is inserted into gene by homologous recombination between the chromosomal copy of gene & a second piece of DNA that share some sequence identity with the target gene.


GENE OVER EXPRESSION:- In this approach the test gene is much more activated than the normal gene to determine what changes it will cause on phenotype. For this purpose special type of cloning vector (multicopy vector) is used which direct the synthesis of as much protein as possible. The vector also contains a highly active promoter so each copy of the test gene is converted into large quantity of m-RNA leading to high amount of protein. EX:- some gene function have been identified in mouse using this approach


PHASE DISPLAY In this approach a special type of cloning vector based on bacteriophage or M13 filamentous bacteriophage is used. The vector is so designed that a new gene that is cloned into it expressed in such a way that its protein product is synthesized on the coat of phage. The phage protein therefore carries the foreign protein into where it is displayed and identified.

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foreign protein


YEAST TWO HYBRID SYSTEM Transcription factor is responsible for controlling and expression of a gene. But in yeast there are two segment of a transcription factor. I.e. DNA binding domine and active domine (activate the RNA polymerase enzyme). DNA binding domine is ligated to the gene for the protein whose interaction we want to study (protein X). The engineering gene will specify synthesis of a fusion protein then the two set of constructions are mixed and co-transformed into yeast. A colony in which reporter gene is expressed contains fusion protein whose segment interact. Then the protein attached to the activation domine of the transcription factor must be one that can interact with protein X.


COMPUTER ANALYSIS It plays an important role in locating genes in DNA . for this the most importance tool is homology searching it locates the gene by comparing DNA sequence under study with all the other DNA sequence in the databases . this is also known as annotation . For this purpose a computer programme BLAST (basic local alignment search tool) has developed by NCBI (National centre of biotechnology information Washington D.C. ) Using BLAST we can compare a segment of genomic DNA to sequences of databases such as Genebank

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