Chapter 2The Structure of Genes and Genomes

Electron micrograph of a metaphase chromosome

Genetic information is stored in double stranded DNA

DNA structure, building blocks:

(A) Bases

DNA structure, building blocks:

(B) Pentose sugars

DNA structure, building blocks:(C) A ribonucleotide

A single stranded DNA (ssDNA) chain

Representations of DNA

The structure of DNA was solved by Watson and Crick 1953

minor groove

major groove

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 copiedinto RNA

• Mutation: replacement, insertion, deletion of nucleotides resultsin altered sequence

dsDNA

N - H ------------Oδ- δ+ δ-

Wasserstoffdonor Wasserstoffacceptor

Sequence specificDNA recognitionoccurs predominantlyvia the major groove

Generalized eukaryotic gene structure

Genome sizes of various organisms

25,000

Arabidopsis Fritillaria 10.000 times more DNA

Genomes

Viruses: DNA, RNA, single and double strandedProkaryotes: DNA, mostly circularMitochondria: circular DNAChloroplasts: circular DNAEukaryontes: Chromosomes with linear DNA

Electron micrographs of small genomes: plasmids

Electron micrographs of the E. coli genome

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

Eukaryotic Genomes

Eukarotic species are haploid or diploid1n or 2n

n = haploid chromosome number

Plants are often polyploid

Visible chromosomal landmarksa) Chromosome size

Human chromosomes

Visible chromosomal landmarksc) Position of nucleolar organizer

A maize microsporocyte nucleus at pachytene stage, showing the 10 chromosomes and the nucleolus.

photograph interpretation

Chromosome 2 of tomato,showing the nucleolus and thenucleolar organizer

The function of the nucleolusin ribosome (and otherribonucleoprotein) synthesis.

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, thenassembled and matured, and finally transported to the cytoplasm.

Message

Visible chromosomal landmarksd) Heterochromatin patterns

Densley staining regions of chromosomes are called heterochromatinand reflect a high degree of compactness; poorly staining regions arecalled euchromatin and indicate less tightly packed regions.

Most of the active genes are in euchromatin.

Message

Eukaryotic chromosomes

• Heterochromatin– densely stained regions of highly compact DNA– mostly repetitive sequences

• Euchromatin: poorly stained, less compact, containstranscribed 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

The structure The structure ofof chromosomes 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 inDarwin, Minnesota. This behemothweighs in at 17,400 lbs. and measures 12feet in diameter. This monument is thelifework of a Mr. Francis A. Johnson,who began work on the twine ball inMarch of 1950. Mr. Johnson dedicatedhis life to the construction of that twineball. In fact, Mr. Johnson labored on thetwine ball for the next 39 years until hisdeath in 1989.

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

A parsimonious model illustrating the transition from a 10-nm "beads-on-a-string" open chromatin formation to the next level of chromatinorganization: the compacted 30-nm chromatin fiber. Depicted is onepossible form of the chromatin fiber produced by a "two-start helix."Folding or unfolding of the chromatin fiber affects the accessibility of DNAto regulatory factors, which control gene expression. Whereas gene silencingfactors such as the PCC complex, HP1, and H1 stabilize higher orderchromatin folding, gene activators such as the SWI/SNF remodelingcomplexes and histone acetyl transferases (HATS) initiate chromatinunfolding. Mohod-Sarip, Verrijzer, Science (2004) 306, 1484

Regulated chromatin folding directs gene expression

Nucleosome Arrays Reveal theTwo-Start Organization of theChromatin FibreDorigo et al, Science (2004),306,1571

Models for the DNA path in thechromatin fiber. Higher orderstructure models: (A) one-startsolenoidal, (B) two-startsupercoiled, and (C) two-starttwisted. Upper views have thefiber axis running vertically;lower views are down the fiberaxis. DNA associated with thenucleosome core is red/blue, andlinker DNA running betweencores is yellow. These models areidealized, with nucleosome coresin each start contacting eachother. The open three-dimensional zigzag seen inconditions not fully compactingmay be a precursor.

possible structures

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

The Nucleosomeis stabilized by histone H1.

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 20-200 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.

Message

Model for chromosome structure

The solenoid loopsattach to a centralscaffold.

The scaffold plusloops arrangeinto a giantsupercoil.

Scaffold attachment regions (SARs).

Modifications of chromatin (= protein and DNA)can influence gene activity by influencingeuchromation/heterochromation structure

Chromatin remodelling

Modification of histones in chromatin affects DNA accessibility

Histones can be modifiedby actetyl transferasesand deacetylases to influence the degree ofchromatin condensation.

Chromatin chemistry. Chemical modifications - acetylation (Ac) ormethylation (Me) - of histone proteins determine whether genes onthe surrounding DNA are active. HP1 is a transcription-inhibitingprotein.

Histone Modifications

In eukaryotic chromosomes histon acetylations correlates withactive euchromatin.

The histones in condensed heterochromatin are methylated.

Message

DNA methylation affects gene expression and developmental regulation

Many eukaryotic genes exhibit a strong inverse correlationbetween density of DNA methylation and transcriptionalactivity.

In eukaryotes the 5 position of cytosin is methylated.

Message

Cytosine methylation

H3C

CpG-islands

Cytosines found in CpG or CpNpG context are possiblesubstrates for methylation. Often CpG-islands occurupstream of promoters.

C-methylation is counter selected because it favours C to Tmutation by oxidative deamination.

Cytosine methylation and inheritance of methylation patterns