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Yeast chromosome structure and function
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- 2. Yeast Chromosome Structure andFunction • In eukaryotes, the genetic material is packed in the cell nucleus and divided between a set of different chromosomes. • The DNA had been found to be associated with proteins that packaged the DNA in the cell nucleus. • how the DNA is packaged in the structure collectively called chromatin. • In 1974 the nucleosome discovered and thought to be a fundamental unit for chromatin organization (Kornberg and Lorch, 1999).
- 3. Chromatin Structure • Thenucleus of Saccharomyces cerevisiae contain16 chromosomes. • Each of which carries a centromere and two telomeres. • The repeat unit of chromatin is made from the core nucleosome, • which in yeast contains 146 bp of DNA wrapped around the histone octamer that consists of two molecules of each core histones H2A, H2B, H3, and H4 . • As in higher eukaryotes, nucleosomal arrays fold into a 30- nm fiber.
- 4. • A singlelinker histone H1 gene, HHO1, has been found in yeast that are structurally related to the normal histones but are functionally distinct. • The distances between nucleosomes are not constant and may vary.(20–90 bp) • There are heterochromatic regions that suppress transcription from resident genes. • In such regions, additional proteins bind to the nucleosomes, which leads to gene silencing. • Chromosome compaction is changed at mitosis (or meiosis), when cohesin and condensin proteins bind to chromatin, thereby inducing a more condensed form of DNA called chromosomes during cell division.
- 5. Modification of Chromatin Structure •Two main principles are involve in the modification of chromatin structure. 1. Modification of the histones by various enzymatic activities (chromatin modifying complexes). 2. Temporary reorganization of the local nucleosome structure by chromatin-remodeling complexes.
- 6. Histone Acetylation • Histonemodifications can occur post-translationally at many sites along with basic proteins. • Preferred targets for acetylation are the NH3 groups of lysine residues. • Acetylation were among the first modifications that became recognized, because these modifications reduce the number of positive charges in histones
- 7. Histone Deacetylation • Theremoval of acetyl residues is achieved by histone deacetylases (HDACs). • Several HDACs have been isolated from yeast that catalyze the deacetylation reaction. • HDAC families include the HDAC I class and
- 8. Histone Methylation • Histonemethylation is chemically more stable. The modification adds methyl groups either to a lysine NH3 group, which (according to its structure) can be mono-, di-, or trimethylated • Or to an arginine residue, which can accommodate two methyl groups. • Histone methylation is carried out by histone methyltransferases (HMTs) that use S-adenosylmethionine (SAM) as coenzyme • Unlike acetylation, the charge of the methylated histones will not change. • However, similar to acetylation, methylated residues will recruit additional factors binding to them through a number of protein domains. • As a consequence, these factors lead to remodeling of chromatin structure, thus inducing complex patterns of gene expression.
- 10. Centromeres • The centromericDNA sequences in all yeast chromosomes share a common substructure which extends from 200 bp to 200 kb. • The centromere sequences from S. cerevisiae can be subdivided into three distinct regions, which differ in base composition. • The central part containing the consensus sequence AAWTWARTCACRTGATAWAWWT (centromere DNA element I (CDEI)) represents the binding site for a basic helix–loop– helix (bHLH) DNA binding protein, the centromere-binding factor (Cbf1p).
- 12. Origins of Replication •As early as in 1979, the laboratory of Ron Davis isolated and characterized a yeast chromosomal replicator that turned out to be a comparably short segment of DNA. • Such sequences functioning as autonomous replication origins (autonomous replication sequences (ARSs)) – also suitable for autonomously replicating yeast plasmid vectors. • These sites were found not only to be present within the centromeric regions, but also to occur in similar copies along all yeast chromosomes at about 30 kb intervals.
- 13. • Chromosomal ARSand centromere (CEN) elements were observed to bind specifically to the yeast nuclear scaffold (Amati and Gasser, 1988). • In contrast to the complex and highly conserved replicators present in prokaryotes and viruses, under study in Bruce Stillman’s laboratory no conserved sequences have been detected in the sequences that autonomously replicate in yeast with the exception of a single 11-bp element called the ARS consensus sequence (ACS). • This element was found to be essential, but not sufficient, for replicator function.
- 14. Telomeres • Telomeres arespecialized DNA sequences that enable complete replication of chromosome ends and prevent their degradation in the cell. • Later, analysis of telomeric sequences by Louis and coworkers in conjunction with the yeast genome sequencing project revealed that all yeast chromosomes share characteristic telomeric and subtelomeric structures. • Telomeric (TG1–3/C1–3A) repeats, some 300 nucleotides in length, are found at all telomere ends. • Thirty-one of 32 of the yeast chromosome ends contain the X core sub telomeric elements (400 bp) and 21 of 32 of the chromosome ends carry an additional Y dash element.
- 15. • There aretwo Y dash classes, 5.2 and 6.7 kb in length, both of which include an open reading frame (ORF) for an RNA helicase, • which is a catalytic inhibitor of telomerase in yeast. • Y dash elements show a high degree of conservation, but vary among different strains.