Genomics and proteomics ppt
- 1. GENOMICS AND PROTEOMICS SUBMITTED BY: P.SUPRIYA, MSC AG FIRST YEAR, DEPT OF GENETICS AND PLANT BREEDING
- 3. GENOMICS:AN OVERVIEW • It is the subdiscipline of genetics that focuses on the structure and function of entire genomes • Genomics is the subdiscipline of genetics devoted to the mapping,sequencing and functional and comparative analyses of genomes
- 4. • The word genomics appears to have been coined by Thomas Roderick in 1986 to refer to genetics subdiscipline of mapping,sequencing and analysing the function of entire genomes and to serve as the name of a new journal genomics dedicated to the communication of new information in this subdiscipline
- 6. SUBDISCIPLINES OF GENOMICS: • Structural genomics:The study of genome structure • Functional genomics:The study of genome function • Comparative genomics:The study of genome evolu- -tion
- 7. STRUCTURAL GENOMICS: • Structural genomics is quite advanced with the complex nucleotide sequences available for many organisms • Structural genomics seeks to describe the 3 dimensional structure of every protein encoded by agiven genome • Structural genomics emphasizes high throughout determination of protein structures.This is performed in dedicated centers of structural genomics
- 8. FUNCTIONAL GENOMICS: • Functional genomics includes analyses of transcriptome,the complete set of RNAs transcribed from a genome and proteome • Indeed functional genomics has spawned an entirely new discipline ,proteomics,which has its goal the determination of the structures and functions of all proteins in an organism
- 9. COMPARATIVE GENOMICS: • The comparative genomics is afield of biological research in which the genomic features of different organisms are comapared • The genomic features may include the DNA sequence,genes,gene order,regulatory sequences,and other genomics structural genomics
- 11. CORRELATED GENETIC,CYTOLOGICAL AND PHYSICAL MAPS OF CHROMOSOMES • The choromosomal locations of genes and other molecular markers can be mapped based on recombination frequencies,positions relative to cytological features,positions relative ,or physical distances
- 13. POSITIONAL CLONING: • It can be used to identify and clone any gene with a known phenotypic effect in any species • Positional cloning has been extensively used in many species,including humans • This positional cloning depends on the availabilty of detailed map of regions of choromosomes where genes of interest reside • Major efforts focused on developing detailed maps of human genome and genomes of important model organisms such as Drosophila,C.elegans and A.thailana
- 14. • In case of human and Drosophila genomes,the genetic and physical maps can be correlated with cytological maps of the choromosomes • Physical maps of achromosome can be correlated with the genetic and cytological maps in various ways : • 1.PCR • 2.Southern blotting • 3.Insitu hybridisation
- 15. MAP POSITION BASED CLONING OF GENES: • The first eukaryotic genes to be cloned were genes that are expressed at very high level in specialised cells and tissues • About 90% of proteins synthesized in mammalian reticulocyte is haemoglobin • Detailed genetic,cytogenetic,physical maps of choromosomes allow scientists to isolate genes from the chromosome
- 16. CHOROMOSOME WALKS AND CHOROMOSOME JUMPS • Choromosome walks are intiated by the selection of the molecular marker close to the gene of interest and use this clone as a hybridisation probe to screen a genomic library for the overlapping clones identified in library screen • Repeat the procedure of isolating overlapping genomic clones allow a researcher to walk along choromosome to gene of interest • It is easier in organisms such as A thaliana,C elegans which have small genome and less repetitive DNA
- 17. CHOROMOSOME JUMPS • When the distance from the closest molecular marker to gene of interest a large technique called choromosome jumping can be used to speed up an otherwise long walk • Each jump covers 100kb or more • It has proven especially useful in work with large genomes such a human genome • If molecular marker such as RFLP,VNTR,STR map close to gene,the gene can be usually isolated by choromosome walks or choromosome jumps
- 18. HUMAN GENOME PROJECT: • Goals:1.To map all of human genes 2.To construct a detailed physical map of the entire human genome 3.To determine the nucleotide sequences of all 24 human choromosomesby the year 2005 • Launched in the year 1990 • The amount of information in these 1st draft of human genome was overwhelming including the sequence of over 2650 Mb pairs of DNA
- 19. • The human genome is more than 25times the size of the previously sequenced Drosophila and Arabidopsis genomes and more than 8 times the sum of all genomes sequenced before it • The sequence of human genome provided one surprise there appeared to be only about 25,000 to 30,000 genes • Exons make up 1.1% of genome and Introns 24% with 75% of the genome being intergeneric DNA • Nearly complete sequence of euchromatic DNA in the human genome was released in Oct 2004
- 21. RNA AND PROTEIN ASSAYS OF GENOME FUNCTION • The availability of nucleotide sequence for entire genomes had led to the development of microarray,Gene chip and reporter gene technologies that permit researchers to study the expression of all genes of an organism simultaneously • Microarray:That contain thousands of hybridisation probes on a single membrane or other solid support
- 23. • Gene chips:The thousands of probes are synthesized on silicon wafers 1-2 sq cms in size • These microarray and gene chips help to study transcription of thousand of genes simultaneously • Chimeric genes contain the coding region of green fluroscent protein of jelly fish fused with the coding regions of genes of experimental organismd can be used to study the localisation of proteins in living cell
- 25. COMPARATIVE GENOMICS • Comparative genomics comparing the nucleotide sequences of genomes has provided new information about the realtionships between various taxonomic groups • Bioinformatics is the science of storing,comparing and extracting information from biological sysytems especially DNA and protein sequences
- 27. PROKARYOTIC GENOMES • Haemophilus influenza was the 1st cellular organism to have its entire genome sequence in 1995 • Feb 2011 complete sequences of the genomes of 1412 archea and bacteria were available in data bases
- 28. MITOCHONDRIAL AND CHLOROPLAST GENOME • These are usually circular and range in size from 6 kb to 2500kb whereas chloroplast genomes also are usually circular and are typically 120 to 292 kb in size with more than 100 genes
- 29. EUKARYOTIC GENOME: • As eukaryotic organisms have increased their complexity the proportion of their genomes that encode proteins have decreased • Comparative genomics has revealed remarkable conservation of synteny related eukaryotic species such as mammals and the cereal grasses
- 30. PROTEOMICS • It is the large scale study of proteins ,particularly their structures and functions • Most importantly while the genome is rather constant entity the proteome is constantly changing through its biochemical interactions with the genome • The rate of synthesis of different proteins vary among different tissues and differ cell types and states of activity • Methods are available for efficient anlysis of transcription patterns of multiple genes
- 34. KEY TECHNOLOGIES FOR PROTEOMICS
- 36. MAPS OF HEREDITARY INFORMATION • Linkage maps of genes,mini/micro satellites • Banding patterns of choromosomes • Physical objects with visible landmarks called banding patterns • DNA sequences contig maps , sequence tagged sites, single nucleotide polymorphism
- 37. VARIABLE NUMBER OF TANDEM REPEATS • Regions 8-80 bp long repeated a variable number of times the distribution and size of repeats in the marker • Inheritance of VNTR can be followed in a family and mapped to pathological phenotype
- 38. SHORT TANDEM REPEATS POLYMORPHISM(MICROSATELLITES) • Regions of 2-7 bp repeated many times ,usually to 10-30 consecutive copies
- 40. CONTIG MAPS • Series of overlapping DNA clones of known order along a choromosome from an organism of interest , stored in yeast or bacterial cells as YAC or BAC
- 41. SINGLE NUCLEOTIDE POLYMORPHISM • Single nucleotide polymorphism is a genetic variation between individuals • SNP are distributed throughout the genome average every 2000bp • Provide markers for mapping genes