Genome Structure, Chromatin, Nucleosomes PDF

Genome Structure, chromatin, Nucleosomes Half of the molecular mass of eukaryotic chromosome is protein. In eukaryotic cells, a given region of DNA with its associated proteins is called chromatin. The majority of the associated proteins are small, basic proteins called histones (which are...

Genome Structure, chromatin, Nucleosomes Half of the molecular mass of eukaryotic chromosome is protein. In eukaryotic cells, a given region of DNA with its associated proteins is called chromatin. The majority of the associated proteins are small, basic proteins called histones (which are responsible for DNA compacting, packaging). Other proteins, referred to as the non-histone proteins, are also associated with eukaryotic chromosomes. These proteins include the numerous DNA-binding proteins that regulate the replication, repair, recombination, and transcription of cellular DNA. Half of the molecular mass of a eukaryotic chromosome is protein HISTONES ❑Main packaging proteins ❑5 classes: H1, H2A, H2B, H3, H4. ❑Rich in Lysine and Arginine Non-histones ❑DNA binding proteins ❑Regulate the replication ❑DNA repair, recombination, and transcription of cellular DNA.  The Problem The following calculation makes the importance of DNA Compaction Human genome (in diploid cells) = 6 x 109 bp. The average thickness of each base pair is 3.4A.˚ = 0.34nm. 6 x 109 bp X 0.34 nm/bp = 2.04 x 109 nm = 2 m/cell. Diameter of nucleus = 5-10 m. How DNA is backed to fit the size of nucleus? DNA must be packaged to protect it, but must still be accessible to allow gene expression  ❑ Most compaction in human cells (and all other eukaryotic cells) is the result of the regular association of DNA with histones to form structures called nucleosomes. ❑ The formation of nucleosomes is the first step in a process that allows the eukaryotic DNA to be folded into much more compact structures that reduce the linear length by as much as10,000-fold. ❑ Compacting of the DNA does not come without cost. ❑ Association of the DNA with histones and other packaging proteins limits the accessibility of the DNA. Packaging of the DNA into chromosomes serves several important functions ❑ Helping to fit DNA inside the cell. ❑ Packaging the DNA into chromosomes serves to protect the DNA from damage. ❑ Only DNA packaged into a chromosome can be transmitted efficiently to both daughter cells when a cell divides.(gene expression and recombination). ❑ Packaging of DNA in Eukarytic cell (will discus it in details) ❑ Packaging of DNA in prokaryotic cell Packaging of DNA in prokaryotic cell: Although prokaryotic cells typically have smaller genomes, the need to compact their DNA is still substantial. Escherichia coli must pack its ̴1-mm chromosome into a cell that is only 1 µm in length. It is less clear how prokaryotic DNA is compacted. Bacteria have no histones or nucleosomes. They have other small basic proteins that may serve similar functions.  Eukaryotic Chromosomes Require Centromeres, Telomeres, and Origins of Replication to Be Maintained during Cell Division There are several important DNA elements in eukaryotic chromosomes that are not genes and that are not involved in regulating the expression of genes 1- Origin of Replication: are the sites at which the DNA replication machinery assembles, and replication is initiated. 2- Centromeres: are required for the correct segregation of the chromosomes after DNA replication 3- Telomeres: are located at the two ends of a linear chromosome. telomeric proteins distinguish the natural ends of the chromosome from sites of chromosome breakage and other DNA breaks in the cell.  Nucleosome Nucleosomes Are the Building Blocks of Chromosomes What is a nucleosome? How is DNA packaged/organized in Eukaryotes? Where do nucleosomes form? What controls the spacing and structure of nucleosomes on the chromosome? How is DNA inside a nucleosomes accessed?  What is a nucleosome? Electron micrograph of chromatin, Nucleosomes appear as “beads on a string  Nucleosom Histone octomar Core DNA, 146 bp Linker DNA,20-60 bp Nucleosome Structures Histone octamer Crystal Structure of Nucleosome Main body is an octomer formed from two copies each of H2A, H2B, H3, H4. DNA wraps (core DNA) 147 or 146 bp (1.75 turns) around the core Linker DNA H1 attaches to the linker region between nucleosomes. Linker DNA is about 20-60bp.  Properties of histone proteins Histones are Very highly conserved in eukaryotes in both Structure and Function. Histones have similar structural forms. It consists of three histon fold domain but different in the fourth Assembly of core histones octomar Histone H1 Binds to the Linker DNA between Nucleosomes The next step in the packaging of DNA is the binding of histone H1Like the core histones, H1 is a small, positively charged protein and interacts with the linker DNA between nucleosomes, further tightening the association of the DNA with the nucleosome. Histone H1 binds two DNA helices. Upon interacting with a nucleosome, histone H1 binds to the linker DNA at one end of the nucleosome and the central DNA helix of the nucleosome bound DNA (the middle of the 147 bp bound by the core histone octamer). A string of nucleosomes is seen under EM as a 10 nm fiber Chromatin is a thread of nucleosomes. The 10 nm fiber in partially unwound state can be seen to consist of a string of nucleosomes. 30 nm Fiber 30 nm fiber is coil of nucleosomes with 6/turn The 30 nm Fiber (Compacts DNA 7X more)  Fig. 9 Orders of chromatin structure from naked DNA to chromatin to fully condensed chromosomes.  Further Compaction of DNA Involves Large Loops of Nucleosomal DNA The nuclear Scaffold includes two classes of proteins: ❑ Topoisomerase II ❑ The SMC proteins (Structural maintenance of chromosome) Although the true nature of the nuclear scaffold remains mysterious.  REGULATION OF CHROMATIN STRUCTURE ❑ The Interaction of DNA with the Histone Octamer Is Dynamic ❑ Gen expression. Nucleosome-remodeling complexes (NRC). The stability of the histone octamer–DNA interaction is influenced by large protein complexes called Nucleosome-remodeling complexes (NRC). These multi protein complexes facilitate changes in nucleosome location or interaction with the DNA. There are three basic types of nucleosome changes mediated by these enzymes: ❑ Histone Sliding (moving one DNA coiled or turn around the histone core). ❑ Complete transfer (octomar histone transfer into another DNA turn). ❑ Remodeling (this increase Accessibility of DNA).