9: Genomics and Systems Biology Flashcards
What is genomics?
Study of genomes as a whole, rather than one gene at a time.
Uses experimentation or data analysis
What is sequence tags, and how do they contribute to large-scale mapping?
Sequence tagged sites (STSs) and expressed sequence tags (ESTs) are unique regions of DNA seq that can be easily detected, usually by PCR.
STSs and ESTs are mapped relative to each other using linking analysis after cloning into yeast artificial chromosome (YACs) or in radiation hybrid cells.
The number of times two STS seq are found on the same fragment indicates how close they are to each other.
What is shotgun sequencing?
The genome is broken down into many random short fragments for sequencing.
The complete genome is then assembled by computerized searching for overlaps between individual seq.
Overlapping seq are assembled to generate contigs; continuous stretches of DNA that lacks gaps.
Need large number of fragments to assemble a complete genome seq.
Disadvantageous if the genome contains repeated seq.
The gaps between contigs can be closed by:
- using library clones that hybridize to probes from the ends of previously identified contigs
- PCR amplifying with primers that anneal to the ends of two known contigs.
What is the estimated size of the human genome? How many percent of human DNA consists of genes?
3200 million (3.2x10^9) bp
- 2 gigabase pairs
- 95 gb is euchromatin
~28% consists of genes (ca. 20000 genes), but since primary transcripts from genes include introns, only 1.5% encodes proteins
G/C regions have higher density of genes and the introns are shorter.
What is a polymorphism?
A difference in DNA sequences between to related organisms (i.e., two individual humans).
Two categories:
- Base changes
- Difference in length of the corresponding DNA region
What is a SNP?
Single nucleotide polymorphism.
Single base change between two individuals. Prevent restriction enzymes from cutting the recognition sequence.
Often detected by use of hybridization using DNA chips, by (quantitative) PCR or by sequencing multiple genomes.
Different human individuals differ by ca. 1 base change every 1000-2000 bases => 2.5 mill SNPs in genome.
60 000 in exons
What is a SSLP?
Simple sequence length polymorphism. Any DNA region consisting of tandem repeats that vary in number from individual to individual.
VNTR, microsatellites…
What is exon trapping? How is it performed?
Experimental procedure for isolating exons by using their flanking splice recognition sites.
DNA must first be cloned into a vector that can replicate in E.coli and animals. DNA containing the exons are cut and inserted into the multiple cloning site (flanked by introns and exons on both sides).
Cloned fragment contains exon => spliced mRNA longer.
Isolation of trapped exon:
- mRNA -> cDNA
- PCR: amplify region with exon
What are the contents of an exon-trapping (pSPL) vector?
- Bacterial and eukaryotic origins of replication.
- Multiple cloning site within mini-gene; intron flanked by two exons.
Insertion of DNA fragment.
Has eukaryotic promoter and -polyA tail. - Selection marker, i.e., antibiotic resistance
- Tail recognition site
What is pharmacogenomics?
Field of research that correlates individual genotypes relative to the person’s reaction to a pharmaceutical agent.
What is the transcriptome?
The sum of RNA transcribed in a cell (or an organism) under any particular conditions.
What is the proteome?
The sum of the proteins encoded by an organism or the total protein complement of an organism at a given time.
What is systems biology?
The integration of many different types of research on an organism with the goal of defining the biological state of an organism within a certain environment.
What is metagenomics?
The genome level study of whole biological communities.
DNA/RNA from environment is sequenced and analyzed without isolating, culturing, or individual identifying, the organisms from their habitat.
What is a microbiome?
The total complement of microorganisms found in a particular habitat.
About 10 times as many microbial cells as human cells (if counting that about 90% of human cells are red blood cells and platelets that lack nuclei).
If only counting the total number of cells: ~1:1 ratio
