Levels of Regulation and Chromatin Remodeling- Exam 3

prokaryotes vs eukaryotes

prokaryotes are single celled organisms: have to respond to their environment by modifying processes within a single cell: transcriptional control is limited to “on/off” or in some cases levels of transcription

eukaryotes are often multicellular, have specialized compartments where transcription and translation takes place; engage in processing of mRNA transcripts; have different tissue and cell types with different patterns of expression

more complex processing of gene transcripts allows greater and finer control of expression

Structural features of eukaryotic DNA

eukaryotic genes are situated on chromosomes that occupy a distinct location

eukaryotic DNA is combined with histones and nonhistone proteins to form chromatin

compact chromatin structure inhibits transcription, replication and DNA repair

chromosome territory

in interphase nucleus, each chromosome occupies discrete domain and stays separate from other chromosomes

chromosome structure is continuously rearranged; transcriptionally active genes are cycled to edges of chromosome territories

interchromosomal domains

channels between chromosomes that contain little or no DNA

transcription factories

feature within nucleus that may contribute to gene expression

nuclear sites that contain most of the active RNA polymerase and transcription regulatory molecules

dynamic structures that form rapidly and disassemble upon stimulation and repression of transcription

histone modification

covalent bonding of functional groups onto N-terminal tails of histone proteins: most common; acetyl, methyl, phosphate

acetylation decreases positive charge, which reduces affinity of histone to DNA

histone acetylation of nucleosome is catalyzed by histone acetyltransferase enzymes (HATs); associated with increased transcription

they stay intact through transcription and only briefly separates during replication

chromatin remodeling

involves repositioning or removal of nucleosomes on DNA

repositioned nucleosomes make chromosome regions accessible to transcription regulatory proteins, transcription activators and RNAP II (RNA polymerase II)

SWI/SNF (SWItch Sucrose Non-Fermenting)

one of the best studied remodeling complexes

loosens attachment between histone and DNA

loosens DNA strand from nucleosome core

causes reorganization of internal nucleosome components

Levels of Packing

I: DNA as double helix: 2 nm wide

II: DNA molecules are wrapped around protein octamers (histones) combination of DNA and histone is a nucleosome- 10 nm → appear as “beads on a string”

heterochromatin

highly condensed even during interphase

often contains DNA which is inactivated in a cell

gene regulation at a coarse level

euchromatin

less highly condensed except during metaphase

Modification of Histones → Gene regulation

addition of methyl groups (CH3) suppresses transcription

addition of acetyl groups (COCH3) activates transcription

direct methylation of DNA is used by vertebrates to turn genes off

methyl groups attached to cytosines recruit proteins that remove acetyl groups and also block transcription factors from attaching to promoters

Methyl groups + Imprinting

imprinting refers to situations where only one of the two inherited gene copies is expressed; based on sex of the parent

ex: only the allele inherited from the female parent is expressed

this is not affected by the parent that contributed the alleles to the one producing the gametes