MOL GEN Final: Ch 18 Bioinformatics, proteomics, and genomics

genome

complete set of DNA

shotgun method

a sample of entire genomic DNA cut with restriction enzymes

then sequenced using Sanger dideoxy sequencing

then computers identify overlaps/contigs to assemble

gene annotation

dna sequences analyzed and interpreted

compare with other sequences in genbank

reveals functional elements of gene (exons, introns, promoters, ORF)

homologous

highly conserved

eukaryotic ORF

may be interrupted by introns so best to compare with mature cDNA

ORF function and confidence level

level 1 - gene w funct. known

level 2 - strong homology to genes w/ known funct.

level 3 - proposed. funct. based on encoded motifs / limited homology to known genes

level 4 - worst

functional genomics

study/assign gene funct. based on rnas or proteins they encode; analyze regulatory elements

T2T human genome

used long dna reading to complete human genomes; includes gapless telomere-to-telo assemblies for 22 autosomes and chromo X

19969 genes = protein coding

human genome project

revealed important aspects of genome organization

variations in humans

ex: eye color

genomic seq is 99.9% same

differences from snps = single base changes

copy number variants

segments dna duplicated or delted

proteomics

all proteins in cell

glycomics

all carbs in cell/tissue

metagenomics

analysis genomes from environ.

transcriptomics

analysis of expression of genes

genome mosaicism

in somatic cells; cells in indiv. do not all contain identical genomes

somatic mosacism

result of error in dna rep., aneuploidy, cnvs, and snps

pangenome

single reference genomes; visualize all genomic segments and variations in a species

whole exome sequencing (wes)

seq only 180,000 exons in person’s genome; revels mut. focusing on protein-coding

fails to identify gene regulatory regions that influence expression

encode project

encyclopedia of dna elements; identify all functional genetic elements in genome

2% encode proteins

80% functional / transcribes to rna but not encode protein

70,000 promoter regions and 400,000 enhancer

snps associated w disease

enriched in non-coding parts of genome

comparative genomics

reconstruct phylo. trees; analysis of genomes from diff. species; study evol. and relationships b/w org. and environ.

euk. genome organization

larger genomes

• low gene density

• introns few in yeast)

• repetitive seq. = dominant feat.; transposable elements

• large range genome size but not gene number

neanderthals and humans

99% identical

78 proteins

FOXP2 gene = speech

sea urchin genome

model org. for development

25-30% genes are pseudogenes

1000 gene for sensing light and odor

share 7000 orthologs (funct. conserved) w/ humans

metagenomics aka environmental genomics

whole genome sequencing to seq. from communities of microbes in environ. samples

isolate dna without cultures of microbes and viruses

transcriptome analysis

studies expression of genes

qualitatively and quantitatively

microarrays - gene chips; spot ssdna mol attatched to glass slide using arrayer then hybridized and expression measured (brightness)

mrna-seq = directly seq. all mrna in sample

rna-seq

in situ analysis; whole transcriptome shotgun seq.

quantitative analysis of rnas expressed

proteome

complete set proteins expressed in cell

inteins

internal sequences that are removed in proteins; not introns

2-d gel analysis for protein seperation

cells exposed to 2 diff conditions ( ex growth, drugs, hormones)

then proteins extracted then seperated by isoelectric focusing

then seperated by size in sds-polyacrylamide gel = determine which proteins have changed in gene expression

spots of interest analyzed by maldi then mass spectrometry

sythetic/artificial genomes

375 genes min. to support life

synthetic biol.

make synth. org. that can sythesize biofuels, bioremedication, pharma products, etc.