Lecture 2-2/ Ch.5 Cell Biology Notes

Regulation of Chromatin Structure

Even in Interphase, Chromosomes demonstrate Packing

  • DNA extracted from interphase cells viewed via e-microscopy has rope-like appearance due to packing

  • Chemical loosening of the DNA reveals “beads on a string” structure with bare DNA linking associated w/ proteins

  • DNA + Structural proteins (histones)= nucleosome

  • Complexes of DNA and associated proteins are called Chromatin

Chromatin state varies along length of chromosome

  • loosely packed chromatin (euchromatin) is more accessible to gene expression machinery

  • some regions (like telomeres and centromeres) are constitutively in heterochromatin state

  • coding regions of a chromosome have variable packing according to whether the genes in those regions are expressed

  • Epigenetics: mechanisms controlling gene expression via chromatin packing

Nucleosomes consist of DNA and structural proteins

  • a nucleosome is a repeating chromatin unit consisting of DNA and structural histone proteins

  • histone proteins from 4 families form a core histone octamer

  • a 5th histone (H1) can associate with the nucleosome, but not as part of the core octamer

  • a 147-bp length of DNA wraps around the octamer

  • the balance of the ~200bp DNA serves as a linker between adjacent complexes

  • each octamer subunit belongs to a larger family and composition varies with circumstances

Histone tails project from nucleosomes

DNA-binding “clamps” divide chromosomes into looped domains

Hierarchical packing reduces chromosomes length by 10^4 during mitosis

  • 11nm and 3nm chromatin most common during interphase

  • 11nm “beads on a string” formed from DNA associated with histones/nucleosomes

  • association of adjacent nucleosomes forms 30nm heterochromatin

  • During prophase of mitosis, loops of chromatin wrap into 700nm fibers

Chromatin remodeling complexes alter organization of nucleosomes

  • even in euchromatin, histone-associated DNA cannot be accessed by transcriptional machinery

  • Chromatin remodeling complexes “unspool” DNA from histone octamers

  • This is a non-spontaneous reaction, so it is coupled to ATP hydrolysis

Covalent modifications to histone tails regulate chromatin packing

  • Histone affinity for DNA is relatively constant, but interactions between neighboring histone complexes are variable

  • When adjacent histone complexes bind, the associated chromatin adopts a heterochromatin state

  • Histone affinity is governed by covalent modifications to histone tails: Acetylation, methylation, phosphorylation

  • Some chemical modifications of particular tail residues is the basis of a “histone code” that specifies level of chromatin accessibility

Reader-writer complexes spread covalent histone modifications

  • chromatin states tend to spread

  • Families of proteins (readers) can recognize different chemical modifications on histone tails

  • Readers can recruit other proteins (writers) that are capable of making the same chemical modifications

  • Reader-writer complexes can copy histone modification patterns of one region and spread it to adjacent regions

  • A right, a complex recognizes, and spreads modifications associated with heterochromatin

  • Heterochromatin will spread until it encounters barrier sequences that block it

  • blocking proteins that bind to the barrier sequence physically obstruct the reader-writer complex

  • Complexes can’t hold onto chromatin forever, heterochromatin spread can stop randomly

  • Example: Variegated eyed flies- an inversion that repositions barrier allows for heterochromatin to spread into white gene, but it doesn’t always happen

Mammals with more than one X chromosome produce stable heterochromatin

  • some heterochromatin states are permanent, others reversible

  • Mammals with more than one x will inactivate all but one x

  • Barr Bodies are mostly heterochromatin

  • inactivation process is called lyonization- involves proteins and non-coding RNAs

  • since inactivation is random and permanent, lyonization produces distinct lineages in resultant animal

  • Calico cats!