Genome Organisation II Eukaryotic genomes are completely different in their organisation compared to prokaryotic, and also much bigger Their genes are mostly split into exons and introns It is not certain which came first in evolution - genes with introns/exons or genes without Exons may allow evolution of proteins in a modular way

Eukaryotic chromosomes In metaphase of mitosis, chromosomes can be seen under microscope - they have a compact rod-like structure The ends of chromosome are called telomeres, function is to protect the ends of the DNA Near the middle is the centromere, function is to attach to spindles during cell division and ensure correct segregation Telomeres and centromeres contain special DNA sequences and associated proteins Telomeres are replicated differently from the rest of the genome - see figure in Lehninger Different regions of the chromosome can be stained with dyes (e.g. Giemsa) giving a characteristic banding pattern

Eukaryotic chromosome structure (Figure 24-3 Lehninger) Telomeres (heterochromatin) Centromere (heterochromatin) Genes, repeated sequences, replication origins (mostly euchromatin)

The problem of telomere replication

Telomere replication

Centromeres The centromere is essential for correct segregation of chromosomes during cell division, by attachment to spindles Centromere consists of a small, core DNA sequence (AT rich) and specific proteins In many species (e.g. humans) this is flanked by 100s of copies of a tandemly-repeated sequence

Unique and repeated DNA If eukaryotic DNA is melted and allowed to re-anneal, it does so in 3 distinct phases The explanation is that there is highly repetitive DNA (which re-anneals quickly), moderately repetitive DNA (intermediate) and unique or single copy DNA (re-anneals slowly)

DNA melting

Classes of DNA Mammalian DNA contains 3 main classes of DNA sequence, as measured by Cot curves: Highly repeated DNA (up to 1 million copies) Moderately repeated DNA (up to 100,000 copies) Unique sequence DNA (strictly speaking 1 copy, but in practice this also includes sequences with only a few copies)

Origins and function of DNA classes Highly repetitive: –Bits of old virus genomes –Simple sequence repeats e.g. CACACA…. –Special sequences such as centromeres Moderately repetitive: –Other old virus genomes –Multi-gene families, e.g. ribosomal RNA Single-copy: –Most normal genes

Types of repeated DNA

Ribosomal RNA genes

DNA fingerprinting An application of repeated DNA sequences found in mammalian genomes Highly variable between individuals No 2 people are the same, except identical twins

Disease caused by a repeat DNA sequence Mutations in the low-density lipoprotein receptor gene (LDLR) are a common genetic cause of heart disease due to hypercholesterolemia. The LDLR gene is 45kb long with Alu (highly- repetitive class) repeats in its introns. Recombination between 2 of these leads to a truncated gene and defective protein.

CpG islands Vertebrate DNA has not much …CG… because it is mostly methylated and mutates to …TG... 5-methyl-cytosine Thymine But there are short (1-3kb) stretches rich in C, G, …CG… without methylation

CpG islands CpG islands are found at 5 ends of many genes Unlike rest of genome they do not bind the MeCP2 protein MeCP2 acts as a general repressor of transcription