PowerPoint Presentation

Chapter 5: The Organization of the Eukaryotic Genome

structure of the chromosome heterochromatin and gene inactivation the gene concept and eukaryotic gene structure variations in gene structure repetitive sequencesReference: p. 179-192, 241-242, 279

1

Human chromosomes

If members of these two species interbreed: mitotic divisions of the zygote may generate a viable adult due to the presence of 2 copies of each relevant gene, but: the hybrid adult will be sterile due to meiotic failureClosely related species have similar number of genes but may have very different chromosome numbers

Meiotic failure and sterility in hybrid individuals

Meiosis fails in organisms that do not contain a chromosomecomplement consisting of an even number of homologoushaploid sets (i.e. multiples of the diploid number). Suchorganisms do not produce offspring because some chromosomes cannot pair during ________ of meiosis.

Mules are the result of a cross between a female horse(2n = 64) and male donkey (2n = 62) giving rise tooffspring with an odd number of chromosomes (63).Seedless watermelons occur if a tetraploid (4n) plant(which produces 2n gametes) is crossed with a diploid (2n) plant (which produces n gametes) giving rise to triploid (3n) plants. These hybrids are sterile and hence their fruits contain no seeds.Meiotic failure and sterility in hybrid individuals

Important regions of eukaryotic chromosomesCentromere: the point of junction between sister chromatids.(it is also the attachment site for mitotic spindle proteins)Telomeres: the stable ends of linear chromosomes.

Replication origins: sequences where DNA replication begins.

Important regions of eukaryotic chromosomes

During interphase most DNA (~90%) is decondensed into long thin strands called euchromatin (true chromatin).

decondensation is necessary for transcription decondensed DNA is still associated with histones

Some DNA (~10%) remains condensed as heterochromatin which is tightly packed as it is in mitotic chromosomesInterphase chromatinThe nucleolus is the region of the nucleus where _____ genes are transcribed and ________ are assembled.

Interphase chromatin

Decondensed vs. Condensed ChromatinDecondensed euchromatin and associated proteinsspilling out of a lysedinterphase nucleus

Condensed mitoticchromosome

The structure of the eukaryotic chromosomeLevels of organization of DNA in chromosomes:NucleosomesChromatinChromatin fibersCondensed chromosome

The nucleosome DNA (two turns, 147 bp) wrapped around a cluster of histone proteins: two of each H2A, H2B, H3, and H4(= core histone particle) held together by a single histone H1 proteinNucleosomes are thebasic units of DNAorganization.

Isolation of a nucleosomeDigestion of all the linker DNA sectionsby micrococcal nuclease:only DNA sections that are associated with the histone nucleosome cores are protected from nuclease digestion (~147 bp).

Separation of thenucleosome components

Chromatin (11-nm)Chromatin fibers (30-nm)Condensed chromosome

Human mitoticchromosomesHuman karyotypeFully Condensed Chromosomes

The condensed chromosome is the highest level of DNAorganization. DNA is at is maximum condensation stateduring ________.

Interphase Euchromatin

(A) 30-nm chromatin fiber(B) 11-nm chromatin (linked nucleosomes)

The remodeling of interphase chromatin ATP-dependent enzyme complexes can displace nucleosomalDNA to expose specific sequences that can then berecognized by DNA-binding proteins.

chromatin-remodeling complexes use energy from ATP hydrolysis to push the histone-bound DNA along the histone core, thereby exposing the underlying DNA

the exposed DNA can then be recognized and bound by transcription factors that are necessary for gene expression

The remodeling of interphase chromatin

The remodeling of interphase chromatin Multiple rounds of ATP hydrolysis and DNA sliding candecondense the chromosome to make the DNA accessible toother nuclear proteins.

Chromatin remodeling by chemical modification of histones The covalent modification of histones can regulate theinitiation of transcription.

the methylation of certain arginine and lysine residues nearthe N-tail of histone H3 provides binding sites for proteinsthat repress the initiation of transcription

the acetylation of specific lysines or the phosphorylation ofspecific serines destabilize DNA-histone interactions,decondensing the chromatin to promote the initiationof transcription

Position effectsThe position of a gene on a chromosome relative to heterochromatin may affect its expression.The Drosophila white gene is necessary for normal eye pigmentation. the absence of white gene product results in white eyes

if the white gene is moved close to heterochromatin DNA by a chromosomal inversion, the gene may be silenced in some eye cells = mottled eye

Position effects

One X chromosome is chosen at random to be inactivated at an early stage of embryonic development.

the inactivated X chromosome may be the paternal (Xp) ormaternal (Xm) the inactivated chromosome remains as heterochromatin and(mostly) transcriptionally inert (a Barr body) once inactivation has occurred, all the descendants of thatcell will have the same X chromosome inactivatedX chromosome inactivation

X chromosome inactivationFemales are mosaics for all heterozygous X loci

Calico catTortoiseshell catCoat color is expressed by pigment genes in melanocytes.An X-linked pigment gene has 2 co-dominant alleles: XO = orange coatXB = black coat

(Calico cats have colored patches on a white background because they carry a mutation in an autosomal gene that affects timing of melanocyte migration to skin surface)Mottled coat color phenotype = mosaic cats

Interphase chromatinThe heterochromatic regions of individual interphasechromosomes are well-defined and heritable.What would the condensation pattern for this chromosome look like in a different cell type?

Inheritance of chromatin condensation patternsTissue-specific histone-binding enzymepassed along to daughter cells

Parental histones are distributedrandomly to each daughter cell,then new histones are produced.

The gene conceptGene: a segment of DNA that is transcribed and codes for afunctional product: a polypeptide (protein), or an RNA species as end productSequences within genes: exons: coding sequences & UTRs introns: non-coding DNA (intervening sequences) regulatory regions: control gene transcription levels

The gene concept

promoter

Exons

The dystrophin gene

The dystrophin gene is ~2.6 million nucleotide pairs long. about 0.01% of the human genome: the largest gene known 79 exons code for a ~3600 amino acid protein only about 0.004% of the gene is exons

DMD patients have deletions in the dystrophin gene

Eukaryotic gene expression

Alternative splicing can generate different versionsof a gene product

Genes within genes

One or more genes may be contained within the intron of another gene.

this is a relatively common feature of nuclear genomes

Example: intron 27 of the human neurofibromatosis type I (NF1) gene contains three genes: OGMP, EV12B, & EV12A

Overlapping genesThe coding regions of two genes may overlap.

a single locus can produce more than one product by the use of different reading frames

found in compact genomes such as viruses & mitochondria Example: ATPase-6 and ATPase-8 in human mitochondria

Gene densities In mitochondrial andviral genomes: mostof the DNA encodesa product. In the human nucleargenome: only 1.5%encodes a product.Human mitochondrial genomeThe human mtDNA is16.6 kb and codes for tworRNAs, 22 tRNAs, and 13polypeptides necessary forthe oxidative respiratoryfunctions of the organelle.

Gene densities in four organisms in a typical 50 kb region

Repetitive DNA sequences are noncoding sequences that are present in multiple copies. simple sequence DNA (satellites) are clustered repeats interspersed repeats are repetitive sequences that are notclustered but are scattered throughout the genome(satellites)(SINEs, LINEs)Repetitive DNA sequences

Examination of the human genome

Long interspersed elements (LINEs): example: Line1 in human 6000 bp ~21% of total human DNA some LINEs are transcribed and translated, but their products have no known functionExamples of interspersed repeated sequencesShort interspersed elements (SINEs): example: Alu sequences in mammalian genomes(characterized by an Alu1 restriction enzyme site) 300 bp ~13% of total human DNA some of them are transcribed but not translated function unknownBoth types originatedas retrotranspositions.

Simple sequence repeatsSatellite DNA: tandemly repeated short sequences - repeated 1000s of times

5% of human genome:

a 171bp repeat around centromere makes up 1 million bp