This document discusses gene expression analysis using sequence tagged sites (STS). It explains that STS are short, easily amplified DNA sequences that serve as landmarks in genome mapping. Several types of STS markers are described, including microsatellites, SCARs, CAPs, and ISSRs. STS can be used to construct genetic maps, detect gene deletions, and identify genes for evolutionary studies. The document provides details on how STS are mapped by determining which cloned DNA fragments contain overlapping sequences.
This document discusses gene expression analysis using sequence tagged sites (STS). It explains that STS are short, easily amplified DNA sequences that serve as landmarks in genome mapping. Several types of STS markers are described, including microsatellites, SCARs, CAPs, and ISSRs. STS can be used to construct genetic maps, detect gene deletions, and identify genes for evolutionary studies. The document provides details on how STS are mapped by determining which cloned DNA fragments contain overlapping sequences.
This document discusses gene expression analysis using sequence tagged sites (STS). It explains that STS are short, easily amplified DNA sequences that serve as landmarks in genome mapping. Several types of STS markers are described, including microsatellites, SCARs, CAPs, and ISSRs. STS can be used to construct genetic maps, detect gene deletions, and identify genes for evolutionary studies. The document provides details on how STS are mapped by determining which cloned DNA fragments contain overlapping sequences.
This document discusses gene expression analysis using sequence tagged sites (STS). It explains that STS are short, easily amplified DNA sequences that serve as landmarks in genome mapping. Several types of STS markers are described, including microsatellites, SCARs, CAPs, and ISSRs. STS can be used to construct genetic maps, detect gene deletions, and identify genes for evolutionary studies. The document provides details on how STS are mapped by determining which cloned DNA fragments contain overlapping sequences.
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PRESENTATION ON
GENE EXPRESSION ANALYSIS - STS BY IDA NANCY K LS19013 IV YEAR MSc LIFE SCIENCES GENE ANALYSIS Genome analysis tells us what genes are present, but before we can determine the organism’s phenotype, we need to know how those genes are expressed: under what conditions, in what tissues, how much gene product is made, etc.
Also, understanding and curing diseases is tied to the analysis of what genes are expressed in disease states. STS – SEQUENCE TAGGED SITES STS is a relatively short, easily PCR-amplified sequence (200 to 500 bp) which can be specifically amplified by PCR and detected in the presence of all other genomic sequences and whose location in the genome is mapped.
STSs can be easily detected by the polymerase chain reaction (PCR) using specific primers.
For this reason they are useful for constructing genetic and physical maps from sequence data reported from many different laboratories.
serve as landmarks on the developing physical map of a genome.
MAPPING OF STS A collection of overlapping DNA fragments
And "molecular cloning" is carried out by recombinant DNA technology
After introduction into a suitable host, the DNA fragments can then be reproduced along with the host cell DNA
An unordered set of cloned DNA fragments iscalled a library
the clones, or copies, are assembled in the order they would be found in the original chromosome by determining which clones contain overlapping DNA fragments.
This assembly of overlapping clones is called a clonecontig Mapping Process of STS
TYPES OF STS MARKERS STS include such markers as –
microsatellites (SSRs, STMS or SSRPs)
SCARs
CAPs
ISSRs. MICROSATELITES Polymorphic loci present in nuclear DNA and organellar DNA that consist of repeating units of 1-10 base pairs, most typically, 2-3 bp in length, also called Simple Sequence Repeats (SSR), Sequence-Tagged Microsatellite Sites (STMS) or Simple Sequence Repeats Polymorphisms (SSRP).
SSRs are highly variable and evenly distributed throughout the genome. This type of repeated DNA is common in eukaryotes.
These polymorphisms are identified by constructing PCR primers for the DNA flanking the microsatellite region.
The flanking regions tend to be conserved within the species, although sometimes they may also be conserved in higher taxonomic levels. SEQUENCE CHARACTERIZED AMPLIFIED REGION DNA fragments amplified by the Polymerase Chain Reaction (PCR) using specific 15-30 bp primers, designed from nucleotide sequences established in cloned RAPD (Random Amplified Polymorphic DNA) fragments linked to a trait of interest.
By using longer PCR primers, SCARs do not face the problem of low reproducibility generally encountered with RAPDs. Obtaining a co-dominant marker may be an additional advantage of converting RAPDs into SCARs. CLEAVE AMPLIFIED POLYMORPHIC SEQUENCE STS polymorphisms that can be detected by differences in restriction fragment lengths caused by SNPs or INDELs that create or abolish restriction endonuclease recognition sites in PCR amplicons produced by locus-specific oligonucleotide primers.
In other words this technique aims to convert and amplified band that does not show variation by length of PCR product into a polymorphic one. INTER SIMPLE SEQUENCE REPEATS (ISSR) STS polymorphisms that are found between microsatellite repeats.
Primers can be designed based on a microsatellite repeats exclusively, in which case
this technique will target multiple loci due to known abundance of repeat sequences in the genome.
Alternatively, primers can be extended outside or inside the ISSR in which case a unique region most likely will be amplified. APPILCATIONS detecting microdeletions in some genes. For example, some STSs can be used in screening by PCR to detect microdeletions in Azoospermia (AZF) genes in infertile men.
Identification of genes in elephants could provide additional information for
evolutionary studies and for evaluating genetic diversity in existing elephant populations. REFERENCE
