Ch. 14 Flashcards
Genome
refers to all DNA in haploid set of chromosomes
Genomics
study of genomes
Cytogenetic map
highlights only largest cities
ex. like a map of California within US
Linkage Map
like a map the depicts smaller cities and large towns
Physical map
similar to geographical map indicating all towns in an area
Sequence map
equivalent of a Google map showing all buildings in a specific town
Sequencing the Human Genome
US gov funded international consortium: clone-by-clone approach (aligned pieces one chromosome at a time)
Celera Genomics (private company): used whole genome shotgun approach (shattered entire genome then rebuilt it)
Sequencing Genomes
Sequencing then Assembly
Sequencing
DNA “shotgunned” into small fragments using restriction enzymes
DNA sequencer devices sequences small fragments
Route 1 to Sequencing the Human Genome
Chromosome - Shotgun - Fragments (restriction sites) - Derived sequence “contig” (continguous sequence) - Store in BACs - BAC sequence overlapped to derive longer sequence (scaffolds)
Route 2 to Sequencing the Human Genome
Whole Genome - Shotgun - Fragments - Reconstruct scaffolds from overlaps - assign scaffolds to knowon chromosomal “sequence tagged sites” (STSs)
Assembly
software aligns ends of DNA pieces by recognizing sequence overlaps
Similarities between human genome and other species
around 90% genes shared with mouse
Human Genome Content
Only 1.5% of human DNA encodes protein
By the end of the human genome project, 95% of the protein encoding genes had been identified
Exome
Chromosomes now sequenced “telomere-to-telomere”
Includes repeats and reveals structural variants
What is in the rest of the genome?
Viral DNA, noncoding RNAs, introns, promoters and other control sequences, repreated sequences
What are retroviruses?
RNA viruses that makes up 8% of our genome
proof of past infection, increased sequences over time
What is HERVs?
human endogenous retriviruses
the genetic material in the human chromosomes (most HERV sequences have exchanged parts (recombined) and mutated to the extent that they no longer make us sick
ppl w forms of AML, MS, and melanoma have overexpressed HERVs
Noncoding RNAs
transcribed genomes (includes all RNAs other than mRNAs
Pseudogenes
transcribes hundreds of thousands of other ncRNAs (not translated into proteins)
Long non-coding RNAs
another class of RNA molecules (200+ nucleotides)
transcribed from exons, introns, and regions between genes (associated with chromatin and control gene expresion)
1/3 of long noncoding RNAs found in primates (mainly brain)
Transposons
most abudant type of repeat (hold a different type of info than a protein’s amino acid sequence)
sequences that jump about the genome while Alu repeats can copy themselves (2-3% of the genome)
Viral DNA
evidence of past infection
tRNA genes
connect mRNA codons to amino acids
