203.341!Module 3!

Genome Evolution: Patterns and Mechanisms!

Austen Ganley, 2015

203.341!Genome Variation!

Lectures 19-20!

Austen Ganley, September 28th, 2015

The Genome The complete genetic material of an

organism!

All of the hereditary material possessed by an organism!

The entire genetic complement of an organism!

The total genetic makeup of an organism!

1977:!First genome

(X174 - virus)!

1995:!First bacterium (H. influenzae)!

1996:!First eukaryote

(S. cerevisiae)!

2001:!Human genome!

2016?:!$1000 human

genome!

Chromosome structure

In most eukaryotes, the genome is organised into several chromosomes!

The basic structure of chromosomes is broadly similar for most species!

Whats in the genome?

Genomes are undergoing continuous change, fuelled obviously by mutation!

Basically, we can divide the mutations into substitutions, small indels, structural changes (insertions, deletions, duplications, copy number variations, inversions, translocations), and chromosomal changes (aneuploidy, fusion, fission)!

Should be aware of the general mechanisms by which substitutions occur (and what they are)!

Will deal with transposon mutations in week 12!

Genome Dynamics - Mutation

Problem with multicellularity..

Dont forget somatic mutations: not heritable, but still important!!

Most structural changes (insertions, deletions, duplications, copy number variations, inversions, translocations) result from double strand break (DSB) repair!

You know recombination from meiotic recombination, but most homologous recombination is a DSB repair mechanism!

Structural Changes

DSBs in the DNA are always occurring! Cell cannot grow if not repaired: checkpoint

arrest because of DNA damage!!

DSB Repair

0.9% of cells

Thus, repair of DSBs is essential!

How do they do this? There are two main pathways:!Non-homologous end-joining!Homologous recombination!

Simple way to repair DSBs: find the two ends and join them back together!

Ends are recognised by the Ku70 and Ku80 protein complex!

These recruit other enzymes that trim the broken ends and ligate them together!

NHEJ is the dominant pathway in mammalian cells!

Non-homologous end joining (NHEJ)

Homologous recombination can repair DSBs without losing genetic information!

Occurs using the other sister chromatid as the template (meiotic recombination is a special exception). If so, when in the cell cycle must repair occur?!

Homologous recombination

Classical DSB repair model First step is resection of the ends: this

is the degradation from the 5 end of one strand of DNA!

Single-stranded DNA ends find a homologous target to invade, forming a D-loop!

The 3 ends can act as primers for DNA synthesis!

This forms double-Holliday junction structures: Holliday junctions are cross over structures between two DNA molecules!

Once all the degraded DNA has been re-synthesised and ligated, the structure is resolved!

Both homologous recombination and NHEJ can join the wrong things up!

Depending on what is joined and how, this can result in:! Insertion/deletion!Duplication/copy number variation! Inversion!Translocation!

Homologous recombination is less prone to this, except for repeat sequences!

Structural Changes Redux

Recombination and duplication

Recombination and inversion

Segmental Duplications

Usually defined as at least 1kb and at 90% sequence identity!

Cancer is characterised by genome instability, including aneuploidy (resulting from nondisjunction)!

HeLa is a cancer cell line isolated from an African-American woman, Henrietta Lacks, in the 1950s!

Aneuploidy