1 Eukaryotic chromosomes BacterialEukaryotic DNA is in a nucleoid bodyDNA is in chromosomes There is one large DNA moleculeThere are many molecules CircularLinear The DNA in the diploid nucleus is ~2 meters long. It is present in a nucleus that is a 1000 cubic microns. Function of chromosomes Packaging Regulation Total human DNA is 3x10 9 bp Smallest human chromosome is 5x10 7 bp The DNA in this chromosome is 14 mm long The chromosome is 2um long 7000 fold packaging!

2 C-value How do we account for the differences in DNA content/nucleus No of genes Gene size Distance between genes

3 Junk DNA Amount of DNA varies in eukaryotes Salamander genomes are 20 times larger than human genomes Barley genome is 10 times larger than the rice genome Barley and rice are related. Measurements of DNA length Amount of DNA/nucleus = C value SpeciesDNA content (pg or g) haploid Sponge0.05 Drosophila0.2 Human3.5 Lungfish102 Locust46 Frog4.2 Yeast0.03 This is often called the C value paradox. There is no phylogenetic relationship to DNA content There are sibling amphibian species - they look morphologically identical but have 4-fold difference in DNA content

4 Junk DNA 2)Size of genes could increase as genomes increase Does increase in DNA content = Increase in gene content? 1)Number of genes could vary in these organisms

5 Intergenic DNA 3Amount of DNA between genes increases

6 Genome Vertebrates 46% Eukaryote & Prokaryote 21% Eukaryotes 32% Human specific <1% Human Gene catalog Human Genes are categorized according to their function, as deduced from the protein domains specified by each gene.

7 Repetitive DNA

8 Chromatin The single chromosome of the prokaryote Escherichia coli is about 1.3 mm of DNA. A human cell contains about 2 m of DNA (1 m per chromosome set) The human body consists of approximately cells and therefore contains a total of about 2 × m of DNA. Distance from the earth to the sun is 1.5 × m The DNA in your body could stretch to the sun and back about 50 times. The diameter of the nucleus is 5x10 -6 meters How is the DNA packaged? Chromatin= DNA+histones +non-histones 1g+1g+1g

9 Chromatin

10 2 mol H2A 2 mol H2B 2 mol H3 2 mol H4 1 mol H1 ~200 bp DNA Nucleosomes Four histone proteins H2A H2B H3 H4 Very highly conserved There are two copies of each core histone DNA is wrapped around the outside of the histone octamer 166 bp of DNA wraps around the histones Linker DNA connects nucleosomes 1 mol of linker Histone H1

11 10 nm [ 30 nm [ 10 nm fiber folds into the 30 nm filament

12 30nm fiber folds into Chromatin Loop Domains

13 Nucleus DNA needs to be compacted in chromosomes 200 nm fiber 700 nm fiber

xxxxx 14

Different types of chromatin 15 heterochromatin Constitutive heterochromatin: constitute ~ % of nuclear DNA highly compacted, transcriptionally/Recombinationally inert Euchromatin + facultative heterochromatin: constitute ~ 80% of nuclear DNA less condensed, rich in genes, however, only small fraction of euchromatin is transcriptionally active the rest is transcriptionally inactive/silenced (but can be activated in certain tissues or developmental stages) these inactive regions are also known as “facultative heterochromatin” Euchromatin

Gene Silencing and its importance 16 In any given cell, only a small percentage of all genes are expressed Vast majority of the genome has to be shut down or silenced Knowing which genes to keep on and which ones to silence is critical for a cell to survive and proliferate normally Repetitive DNA tends to recombine expanding/contracting repeats. Preventing repetitive DNA from recombination is critical for cell survival

17 Properties of active/inactive domains

18 Facultative heterochromatin Regions of genome, rich in genes that are condensed in specific cell types or during specific stages of development It includes genes that are highly active at a particular stage of development but then are stably repressed. X-chromosome inactivation in mammals. Dosage compensation No. of transcripts are proportional to no. of gene copies Diploid- 2 copies of a gene XXXY 21 Measuring transcript levels for genes on the X chromosome in female and male show that they are equivalent. Dosage imbalance is corrected! In nematodes there is a decrease in transcription from both X chromosomes- dpy27 binds the 2X chromosomes and causes chromosome condensation which reduces transcription. In Drosophila in the males there is an increase in transcription from the single X chromosome. A inhibitor of transcription is turned off in males allowing for full expression from the one X chromosome In mammals, X chromosome inactivation occurs in females by formation of heterochromatin.

19 Dosage compensation

20 Mammalian X-chromosome inactivation (epigenetics)

21 X-inactivation

22 X-inactivation The inactivation of one of the two X-chromosomes means that males and females each have one active X chromosome per cell. X-chromosome inactivation is random. For a given cell in the developing organism there is an equal probability of the female or the male derived X chromosome being inactivated.

23 Barr bodies ·The inactive X-chromosome in normal females is called the barr body.XXX individuals have 2 Barr Bodies leaving one active X ·XXXX individuals have 3 Barr Bodies leaving one active X ·XXY individual have one Barr Body leaving one active X (Klinefelter's syndrome) ·X0 individuals have no Barr Bodies leaving one active X (Turner's syndrome) Given X-chromosome inactivation functions normally why are they phenotypically abnormal? Part of the explanation for the abnormal phenotypes is that the entire X is not inactivated during Barr-Body formation (Escape loci) Consequently an X0 individual is not genetically equivalent to an XX individual. XX female XXX female XY male XXY male

24 Mosaic expression

25 Tortoise shell cats The O gene changes black pigment into a reddish pigment (orange). The O gene is carried on the X chromosome. Female cats heterozygous for the O gene on the X- chromosome have a particular pattern called Tortoise shell. According to Mendel’s rules the cats should be either orange or black. But the cats are neither! They are Tortoise shell.

26 Tortoiseshell cats

27 Tortoise shell cats The O gene changes black pigment into a reddish pigment (orange). The O gene is carried on the X chromosome. Female cats heterozygous for the O gene on the X- chromosome have a particular pattern called Tortoise shell. According to Mendel’s rules these cats should be either orange or black. But the cats are neither! They are Tortoise shell. OOx oY F1 females are Oo

Tortoise shell cats The O gene changes black pigment into a reddish pigment (orange). The O gene is carried on the X chromosome. Female cats heterozygous for the O gene on the X- chromosome have a particular pattern called Tortoise shell. According to Mendel’s rules these cats should be either orange or black. But the cats are neither! They are Tortoise shell.

29 Calliphyge 40% more muscle 7% less fat 20% increased profit

30 Calliphyge

31

32

33 Callipyge Normal femaleMutant male * mutant femaleNormal male * Normal femaleNormal male

34 Imprinting A=off A=on A=off A=on Somatic cell Gamete

35 Imprinted loci

36 War of the sexes