Chapter 2 The Structure of Genes and Genomes. Electron micrograph of a metaphase chromosome

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1 Chapter 2 The Structure of Genes and Genomes Electron micrograph of a metaphase chromosome

2 Genetic information is stored in double stranded DNA

3 DNA structure, building blocks: (A) Bases

4 DNA structure, building blocks: (B) Pentose sugars

5 DNA structure, building blocks: (C) A ribonucleotide

6 A single stranded DNA (ssdna) chain Representations of DNA

7 The structure of DNA was solved by Watson and Crick 1953

8 minor groove major groove

9 DNA Units of measurement base pair (bp) or nucleotide (nt) kilobase (1kb) megabase (1Mb) Replication: each strand serves as template for synthesis of complement, using rules of base pairing Information: specified by sequence of nucleotides; may be copied into RNA Mutation: replacement, insertion, deletion of nucleotides results in altered sequence

10 dsdna Wasserstoffdonor N - H O δ - δ + δ - Wasserstoffacceptor

11 Sequence specific DNA recognition occurs predominantly via the major groove

12 Generalized eukaryotic gene structure

13 Genome sizes of various organisms

14

15 25,000

16 Arabidopsis Fritillaria times more DNA

17 Genomes Viruses: Prokaryotes: Mitochondria: Chloroplasts: Eukaryontes: DNA, RNA, single and double stranded DNA, mostly circular circular DNA circular DNA Chromosomes with linear DNA

18 Electron micrographs of small genomes: plasmids

19 Electron micrographs of the E. coli genome

20 Prokaryotic genome Usually circular double helix occupies nucleoid region of cell attached to plasma membrane Genes are close together with little intergenic spacer Operon tandem cluster of coordinately regulated genes transcribed as single mrna Introns very rare

21 Eukaryotic Genomes Eukarotic species are haploid or diploid 1n or 2n n = haploid chromosome number Plants are often polyploid

22

23 Visible chromosomal landmarks a) Chromosome size

24 Human chromosomes

25 Visible chromosomal landmarks c) Position of nucleolar organizer A maize microsporocyte nucleus at pachytene stage, showing the 10 chromosomes and the nucleolus.

26 photograph interpretation Chromosome 2 of tomato, showing the nucleolus and the nucleolar organizer

27 The function of the nucleolus in ribosome (and other ribonucleoprotein) synthesis.

28 Message Nucleoli are spherical structures found associated with constrictions of the chromosomes called nucleolar organizers (NO). NOs contain numerous tandem copies of the genes that code for ribosomal RNA. rrna is synthesized in the NO, deposited in the nucleolus, then assembled and matured, and finally transported to the cytoplasm.

29 Visible chromosomal landmarks d) Heterochromatin patterns

30 Message Densley staining regions of chromosomes are called heterochromatin and reflect a high degree of compactness; poorly staining regions are called euchromatin and indicate less tightly packed regions. Most of the active genes are in euchromatin.

31 Eukaryotic chromosomes Heterochromatin densely stained regions of highly compact DNA mostly repetitive sequences Euchromatin: poorly stained, less compact, contains transcribed genes Banding patterns (metaphase chromosomes) differential uptake of dyes G bands, Giemsa stain (A/T rich) R bands, reverse of Giemsa (G/C rich) Polytene chromosomes replicated, unseparated chromosomes present in certain tissues of dipteran insects

32 The structure of chromosomes What is the best way to efficiently pack DNA? 2m of human DNA are packed into 46 chromosomes inside a nucleus of 6x10-6 m The most famous ball of twine resides in Darwin, Minnesota. This behemoth weighs in at 17,400 lbs. and measures 12 feet in diameter. This monument is the lifework of a Mr. Francis A. Johnson, who began work on the twine ball in March of Mr. Johnson dedicated his life to the construction of that twine ball. In fact, Mr. Johnson labored on the twine ball for the next 39 years until his death in 1989.

33 What is the best way to efficiently pack DNA? 2m of human DNA are packed into 46 chromosomes inside a nucleus of 6x10-6 m nucleosomes

34 Regulated chromatin folding directs gene expression A parsimonious model illustrating the transition from a 10-nm "beads-ona-string" open chromatin formation to the next level of chromatin organization: the compacted 30-nm chromatin fiber. Depicted is one possible form of the chromatin fiber produced by a "two-start helix." Folding or unfolding of the chromatin fiber affects the accessibility of DNA to regulatory factors, which control gene expression. Whereas gene silencing factors such as the PCC complex, HP1, and H1 stabilize higher order chromatin folding, gene activators such as the SWI/SNF remodeling complexes and histone acetyl transferases (HATS) initiate chromatin unfolding. Mohod-Sarip, Verrijzer, Science (2004) 306, 1484

35 Nucleosome Arrays Reveal the Two-Start Organization of the Chromatin Fibre Dorigo et al, Science (2004), 306,1571 possible structures Models for the DNA path in the chromatin fiber. Higher order structure models: (A) one-start solenoidal, (B) two-start supercoiled, and (C) two-start twisted. Upper views have the fiber axis running vertically; lower views are down the fiber axis. DNA associated with the nucleosome core is red/blue, and linker DNA running between cores is yellow. These models are idealized, with nucleosome cores in each start contacting each other. The open threedimensional zigzag seen in conditions not fully compacting may be a precursor.

36 Model of a nucleosome, the DNA is wrapped twice around a histone octamer

37 The Nucleosome is stabilized by histone H1.

38 Message A nucleosome consists of DNA wrapped arround an octamer of histone proteins made up of two tetramers, each consisting of H2A, H2B, H3, and H4. A bp spacer intervenes between adjacent nucleosomes. An additional histone, H1, binds outside the nucleosome core; one of its function is to stabilize both the nucleosome array and higher order chromatin structures.

39 Model for chromosome structure The solenoid loops attach to a central scaffold. The scaffold plus loops arrange into a giant supercoil.

40 Scaffold attachment regions (SARs).

41 Modifications of chromatin (= protein and DNA) can influence gene activity by influencing euchromation/heterochromation structure Chromatin remodelling

42 Modification of histones in chromatin affects DNA accessibility Histones can be modified by actetyl transferases and deacetylases to influence the degree of chromatin condensation.

43 Histone Modifications Chromatin chemistry. Chemical modifications - acetylation (Ac) or methylation (Me) - of histone proteins determine whether genes on the surrounding DNA are active. HP1 is a transcription-inhibiting protein.

44 Message In eukaryotic chromosomes histon acetylations correlates with active euchromatin. The histones in condensed heterochromatin are methylated.

45 DNA methylation affects gene expression and developmental regulation Message Many eukaryotic genes exhibit a strong inverse correlation between density of DNA methylation and transcriptional activity. In eukaryotes the 5 position of cytosin is methylated.

46 Cytosine methylation H 3 C

47 CpG-islands Cytosines found in CpG or CpNpG context are possible substrates for methylation. Often CpG-islands occur upstream of promoters. C-methylation is counter selected because it favours C to T mutation by oxidative deamination.

48 Cytosine methylation and inheritance of methylation patterns