2.4 bio

Gen-omics

Determine genome sequences.

Epigen-omics

Define epigenetic elements.

Prote-omics

Identify all gene products (proteins).

Interact-omics

Determine interacting molecules.

Metabol-omics

Define the function (metabolic pathways).

Inventor of DNA Sequencing

Fred Sanger (1975).

Sanger Sequencing (Method)

Uses special nucleotides (ddNTPs) missing the 3' hydroxyl (OH) group.

ddNTPs (dideoxy nucleotide triphosphates)

Nucleotides that block DNA polymerase from adding the next base, terminating the chain.

Sanger Sequencing (Summary)

Make complementary DNA strands with labeled terminating bases (ddNTPs), separate them by size (length), and read the fluorescent labels to reconstruct the sequence.

Shotgun Sequencing

DNA is cut many times randomly; each segment is sequenced.

Fragment Assembly

Sequenced fragments are assembled by a computer looking for overlaps (often with 10x redundancy).

NGS (Next Generation Sequencing) Summary

Fragments -> add adaptors -> attach to flowcell -> PCR (cluster formation) -> Sequencing by synthesis -> signal scanning.

Human Genome Project (Goal)

Determine the nucleotide sequence of all DNA in the human genome and identify every human gene.

Human Genome Project (Timeline)

Launched 1988; 1st draft 2000; complete version 2003.

Human Genome Project (Result 1)

~21,000 genes in 3.2 billion nucleotide pairs.

Human Genome Project (Result 2)

As many pseudogenes (inactivated, nonfunctional copies) as functional genes.

Human Genome Project (Result 3)

Only 1.5% of DNA codes for proteins; 98.5% is control regions, noncoding DNA, etc.

Project ENCODE (Goal)

Find the uses of all the functional elements in the human genome (not just genes).

ENCODE Surprise 1

80% of the genome contains elements (active RNA molecules) with biochemical function; NOT JUNK.

ENCODE Surprise 2

Identified 18,400 RNA genes & 20,687 protein-coding genes.

ENCODE Surprise 3

RNA is a major functional unit of the epigenome.

ENCODE Implication (Evolution)

Evolution can occur by selection for RNA sequences that alter gene regulation, not just protein-coding sequences.

The Genome 10k Project (Goal)

Sequence the DNA of 10,000 vertebrate species.

ROADMAP Epigenomics Project (Context)

Follow-up to ENCODE; found 90% of disease-associated DNA alterations lie in gene-switching areas (epigenome).

Epigenome & Disease (Central Result)

It's the combinations of modifications (not single ones) that cause changes in gene expression associated with disease.

Enhancers

Regions in the genome (uncovered by ENCODE) that regulate gene expression and development; activated by transcription factors.

Earth Biogenome Project (Goal)

Sequence all known Eukaryotic Species (1.67 Million) by 2035.

DNA Data Storage

One gram of DNA could (theoretically) back-up the entire internet.

Nondisjunction

The failure of chromosomes or chromatids to separate properly during meiosis.

Nondisjunction in Meiosis I (Result)

All (4) resulting gametes will have an abnormal number of chromosomes (two n+1, two n-1).

Nondisjunction in Meiosis II (Result)

Half (2) gametes will be normal (n); one will have an extra chromosome (n+1); one will be missing a chromosome (n-1).

Down Syndrome (Cause)

Trisomy 21 (inheritance of 3 copies of chromosome 21), usually caused by nondisjunction.

Klinefelter Syndrome

XXY; males have an extra X chromosome. Effects include low testosterone and low fertility.

Turner Syndrome

X0; abnormality in which one of the X chromosomes is absent. Effects include short stature and non-functional ovaries.

Turner Syndrome is an example of…

Monosomy (having only one copy of a particular chromosome).

Huntington's Disease

A dominant autosomal disorder; neurodegenerative, affects muscle coordination, leads to paralysis and dementia.

Galactosemia

A recessive autosomal disorder; inability to fully break down galactose, causing damage to liver, brain, kidneys, and eyes.

X-Linked Disorders

Genes on the X chromosome but not on the Y; affect mostly males.

Why X-linked disorders affect males more

Males (XY) have only one X chromosome, so a recessive allele on that X will always be expressed.

Hemophilia

An example of an X-linked recessive disorder.

Sex Determination (Genetic)

Examples: humans, birds, most mammals (e.g., XX/XY system).

Sex Determination (Environmental)

Examples: Temperature (Turtles), Nutrition (Worms).

Sex Determination (Sequential)

Organism changes sex during its lifetime based on social or environmental cues (e.g., Clownfish).