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

Marwal, Avinash, Anurag Kumar Sahu, and R.K. Gaur. "Molecular Markers." Animal
Biotechnology (2014): 289-305. Web. 25 Oct. 2017. •

https://www.ncbi.nlm.nih.gov/probe/docs/tec hsts/