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Chromosomes, Chromatin, and the Nucleosome Chromosomes: DNA associated with proteins 1. The chromosome is a compact form of the DNA that readily fits inside the cell. 2. Packaging the DNA into chromosomes serves to protect the DNA from damage. 3. Only DNA packaged into a chromosome can be transmitted efficient to daughter cells. Table I: variation in chromosome makeup in different organisms The traditional view is that prokaryotic cells have a single, circular chromosome, and eukaryotic cells have multiple, linear chromosomes. Table 2. Comparison of the gene density in different organisms’ genomes Comparison of the chromosomal gene density for different organisms 65kb region The organization and content of the human genome Pseudogenes arise from the action of an enzyme called reverse transcriptase The majority of human intergenic sequences are Composed of repetitive DNA (dinucleotide repeats) ( greater 100bp, mostly transposable element) Table 7-3 Contribution of introns and repeated sequences to different genomes introns (p. 135) Chromosome duplication and segregation Eukaryotic chromosomes require Centromeres, Telomeres, and Original of Replication to be maintained during cell division More or less than one centromere leads to chromosome loss or breakage Centromere size and composition varies dramatically Telomeres 1. Telomeres are bound by a number of proteins. These proteins distinguish the natural ends of the chromosome form sites of chromosome breakage and other DNA breaks in the cell. DNA ends are the sites of frequent recombination and DNA degradation. The Proteins at telomeres form a structure that is resistant to both events. 2. Telomeres act as a specialized origin of replication that allows the cell to replicate the ends of the chromosomes. The eukaryotic mitotic cell cycle Each chromosome of the duplicated pair is called a chromatid, the two chromatids of a given pair are called sister chromatids. The events of mitosis Changes in chromatin structure-DNA condensation and decondensation Chromosomes are maximally condensed in M phase • Sister Chromatid cohension and Chromosome condensation are mediated by SMC ((structural maintenance of chromosome) proteins Models for the structure of cohesins and condensins The structural of cohesin is a large ring composed of two SMC proteins and a third non-SMC protein. SMC (structural maintenance of chromosome) proteins Mitosis maintains the parental chromosome Number Meiosis reduces the parental chromosome number cohesion is lost Formation of chiasma Homologous recombination Formation of chromatin structure nucleosome- building blocks of chromosomes Histones are small, positively-charged proteins H2A: red H2B: yellow H3: purple H4: green The assembly of a nucleosome The N-terminal tails are accessible to protease trypsin (specifically cleaves protein positivelycharged amino acids) The nucleosome has an approximate twofold axis of symmetry Interactions of the histones with nucleosomal DNA H3.H4 tertramer central 60bp region and two ends H2A.H2B dimer Each associate with about 30 bp of DNA on either side of the central 60 bp Histones contact the minor groove of the DNA by forming a large number of hydrogen bonds The large number of the hydrogen bonds provide the driving force to bend the DNA Higher-order chromatin structure H binds to linker DNA at one end of The nucleosome and the central DNA helix The addition of H1 leads to more compact nucleosomal DNA Without H1 Histone H1 induces tighter DNA wrapping around the nucleosome 30-nm fiber Superhelix, 6 nucleosome per turn, supported by EM and X-ray studies Based on zigzag pattern upon H1 addition, requires linker DNA to pass through central axis, The core Histone N-terminal tails are required for the formation of the 30-nm fiber The tail of H2A, H3 and H4 interact with adjacent nucleosome Higher compaction of DNA involves large loops of nucleosomal DNA Nuclear scaffold (Topo II, SMC) Histone variants alter nucleosome function 1. H2A.z histone inhibits nucleosome from forming repressive chromatin structures, creating regions of easily accessible chromatin that are more compatible with transcription 2. CENP-A replace H3, is associated with nucleosomes that include centromeric DNA Regulation of chromatin structure The interaction of DNA with histone octamer is dynamic Unwrapping of the DNA from nucleosome is responsible for the accessibility of the DNA Nucleosome movement by nucleosome remodeling complexes restructure ATP-dependent chromatin remodeling complex SWI/SNF 8-11 subunits Bromodomain ISWI 2-4 subunits No Mi2/NuRD 8-10 subunits chromodomain Nucleosome Positioning by DNA-binding proteins exclusion Nucleosome Positioning by DNA-binding proteins Inducing assembly Modifications of the histone N-terminal tails alters the function of chromatin Acetylation: transcription activation Effects of histone tail modification Nucleosome modifying enzymes Chromatin remodeling complex and histone modifying enzymes work together to alter chromatin structure Nucleosome Assembly The inheritance of histones after DNA replication The old histones are present on both of the daughter chromosome H3.H4 tetramers remain bound to one of the two daughter duplexe at random but H2A.H2B dimers are released and enter the local pool for new nucleosome assembly. Inheritance of parental H3.H4 tetramers facilitate the inheritance of chromatin state Nucleosome Assembly The assembly of nucleosomes is not a spontaneous process, it requires high salt condition in-vitro. Proteins required to direct the assembly of histones to DNA are histone chaperones. Name CAF-1 histones bound H3. H4 RCAF H3. H4 NAP-1 H2A.H2B (negatively-charged protein) How histones chaperones facilitate the assembly of nucleosome during DNA replication (sliding clamp)