Lecture 6 Flashcards
Genome
The whole hereditary information of an organism that is encoded in the DNA
Human Genome Project
- Identify 100,000 genes
- Determine sequence of the 3B bases human DNA
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Heterochromatin
Condensed Chromatin
Euchromatin
More diffuse chromatin, corresponds to regions where most most genes and functional elements reside
Benefits of Human Genome Research
- improvements in medicine
- microbial genome research for fuel and environmental cleanup
- DNA forensics
- improved agriculture and livestock
- better understanding of evolution and human migration
- more accurate risk assessment
-omics Science
- Structural genomics: mapping and sequencing
- Functional genomics: how genes function
- Proteomics: how proteins and encoded and function
- Metabolomics: how small molecules are metabolized and function
Hierarchical shotgun sequencing
Break DNA into smaller fragments, sequence each with Sanger seq, assemble contigs to find the whole sequence
Sanger Sequencing
- DNA is fragmented and cloned to a plasmid vector
- Sequencing reaction using dideoxynucleotides
- Separation of molecules by electrophoresis
- Detection of dye-labelled fluorescent tags
Sequence detection technologies
- Sanger sequencing
- 454 pyrosequencing
- Illumina sequencing
- SOLiD sequencing
- Ion Torrent sequencing
Type of information gleaned from sequencing genomes
- A-T and G-C Content
- Number of protein coding genes
- Number of non-coding RNAs
- Frequency and types of repetitive elements
- Comparison between physical and genetic distance
- Homology to other organisms, evolution of genes
- New genes
- Duplicated genes
- Deleted genes
- Degree of conservation
Syntenic regions
Same gene structure between species
Homologs
Orthologs or Paralogs
Orthologs
Similar genes in two organisms that arose in a common ancestor
Paralogs
Similar genes which arose by duplication in the same organism
What is in the human genome
- Protein coding regions (exons)~1.5%
- Regulatory regions (promoters, enhancers)~5%
- Repetitive elements (LINEs, SINEs, transposons)~50%
- Non-coding RNAs ???
Mitochondrial genome unique region
Control region (at 12 o’clock)
Which pathway are the mtDNA encoded proteins into
Electron Transport Chain
Classes of interspersed repeats in the human genome
- LINEs
- SINEs
- Retrovirus-like elements
- Transposon
Categories of Genetic Variants
- Single Nucleotide Polymorphism
- Insertion/Deletion
- Simple Sequence Repeat
- Copy Number Variation/Copy Number Polymorphism
- Complex variant
How SNPs can be detected by microarrays
With differential hybridization (if mismatch, raising temperature denature)
Types of Human DNA Variation
Insertion-Deletion polymorphisms: - Minisatellites - Microsatellites (STRs) Single Nucleotide Polymorphisms (SNPs) Copy Number Variations (CNVs) Others: Chromosomal or large scale variations, rearrangements, translocations, ...
Minisatellite
Tandemly repeated 10-100bp blocks of DNA => VNTR (Variable Number of Tandem Repeats)
Microsatellite
Short Tandem Repeat: di-, tri-, tetra-nucleotide repeats
Single Nucleotide Polymorphism
Frequency of 1 in 10^3 bp, PCR-detectable marker
Copy Number Variation
Variation in segments of genome from 200bp to 2Mb, once to many copies, detected by array comparative genomic hybridization
Gene family
Genes with high sequence similarity (>85%) that may carry out similar but distinct functions.
Arise through gene duplication => Mechanism behind evolutionary change
Date of shift in sequencing technology
2006-2007
NGS technology
massive parallelization of sequencing reactions producing orders of magnitude more sequence data than capillary-based seq
Why sequence more human genomes
- Genetic variation at individual, family and population level
- Discovery: Heritability of most disease not understood, individual rare variation important
- Advance medical treatment
GINA
Genetic Non-Discrimination Act (2008): Research DNA not release to health insurance and workplace (but life insurance, disability and long-term care insurance)
