Ch 10 - Nucleosomes, Chromatin, Chromosome structure

Exam 1

Telomerase

• ribonucleoprotein enzyme (protein + essential RNA) adds telomeres

• promotes T-loop structure (prevents end from being perceived as double stranded break)

• not expressed in somatic cells

TER RNA

acts as template for addition of G rich telomeres added to 3’ end

TERT

reverse transcriptase that copies TER template

stem cell disease

caused by telomeropathies that lead to premature telomere shortening

centromeres

DNA sequence where sister chromatids stick to each other before anaphase

Kinetochore

large protein complex where microtubules of spindle attach to chromosome

Chromosome disjunction

normal separation of sister chromatids

anaphase promoting complex (APC)

• activated by Cdc20 and drives anaphase

• degrades cyclins → reduces CDK activity from M phase

cyclin-dependent kinase (CDK)

• regulate cell cycle by phosphorylating proteins

• needs cyclin to bind to it to be active

Nucleosomes

• part of DNA that is wrapped around histones (~147 bp or 1.65 turns) + histone core octamer

• straight 10 bp segments + bends

• DNA slightly underwound

• GC inhibits nucleosome placement (more H bonds = less bending/flexibility)

• AT positions nucleosome

Histone octamer

2 of each histone H2A, H2B, H3, H4

histone dimers

• H2A/H2B and H3/H4 form dimers first before octamer

negative supercoiling

DNA twisted in opposite direction → underwinding → torsional strain

nucleosome compaction

6x more compact than linear (11 nm)

Histone H1

compacts the nucleosome (“linker”) to 30 nm fiber

N-terminal tail of histones

interact with adjacent nucleosome to compact chromatin more

cell divides every 20 minutes

why bacteria don’t have nucleosomes

chromosomal scaffolds

attached to DNA loops during replication after histones are removed

topologically associating domains (TADs)

regions of DNA that interact more with themselves than with regions outside

molecular condensates

• liquid phase separated region containing active genes in TADs (topologically associating domains)

• has increased concentration of RNA polymerase, transcription factors, etc.

condensins

protein that associates with chromosomes to induce compaction during mitosis and meiosis

cohesion

associates with chromosomes to keep sister chromatids together after S phase until anaphase

H2AZ and H3.3

• replacement for H2 and H3 histones in euchromatin (more transcriptionally active and partially decondensed)

• inhibits nucleosome-nucleosome interaction

• deletion of H2AZ lethal in embryonic mammals

reversible

modification and remodeling of nucleosome assembly work together and are ____

histone chaperones

help with histone assembly

alternative chaperones

help with histone variant assembly

MacroH2A1

histone variant that is concentrated on inactive X-chromosome

H2AX

histone variant that is involved in DNA repair and recombination

CENPA

H3 histone variant associated with centromeres (deletion is lethal)

ATPase

histone remodeling complexes

inherited

epigenetic modifcation of histones are ____

bromodomain proteins

binds to histones that have been acetylated → increase gene expression

chromodomain proteins

binds to histones that have been methylated → decrease gene expression

N-terminal lysine

amino acid that is acetylated in histone (modification)

glutamic acid

amino acid methylated on histone (modification)

histone acetyltransferases (HATs)

histone modifying complex that activates (bromodomain)

histone deacetylases (HDACs)

histone modifying complex that represses

euchromatin

open, less condensed state of chromatin

heterochromatin

closed, more condensed state of chromatin

histone

most actively transcribed DNA lacks ___

histone code

different histone modifications have specific functions

H2A and H2B

after replication, the new daughter duplex lacks which histones

H3 and H4

which histones are retained during replication?

randomly on old and new strand

• how do the old and new H2A, H2B, H3, and H4 histones assemble?

• epigenetic marks are copied onto new histones

Lyonization

one X-chromosome is randomly inactivated

aneuploidy

abnormal number of chromosomes (any number other than 23 in humans)

trisomy 21 (Downs syndrome)

only successful aneuploid in humans

tortoiseshell or calico

random X-chromosome inactivation causes orange and black patches in cats because gene for coat color is on X

XIST

• long non-coding RNA (lncRNA) that coats X-chromosome and inactivates genes

• 17,000 base pairs

• not expressed in males

• permanent in somatic cells

DNA methylation and nucleosome modification

how does XIST inactivate genes on X chromosome?

pseudoautosomal region

• region at the ends of X and Y chromosomes that allow pairing during meiosis

• need two active copies of genes in this region for both sexes (from both X or from X and Y)

• only one copy in Turners syndrome (XO) but two are needed for functional ovaries