Chromatin Remodeling

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Chapter 11

• Part 3

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Chromatin Remodeling

• Chromatin packed DNA is inaccessible to
  non-histone proteins of replication and gene
  expression
• must induce chromatin to change shape chromatin
  remodeling
• Protein model of DNA interacting with histone
• interesting to chromatin remodeling histone
  tails are not folded into core of nucleosome
• appear to enter minor groove and a potential for
  chemical modification

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Histone Modification

• Acetylation histone acetyltransferase (HAT)
  adds acetyl group to amine groups on Lys R group,
  removing the positive charge
• high level of acetylation opens chromatin in
  areas of active genes
• in Barr body, extra X has under acetylated H4
  proteins
• Methylation methyltransferase add methyl
  group to Arg/Lys residues of histone activation
  of genes
• Phosphorylation kinases add PO4 to OH on Ser
  and His, negative charge on protein
• increase H3 phosphorylation at times in cell cycle

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Hetero- and Eu-chromatin

• Some parts of chromosomes remained condensed and
  heavily stained during interphase
  heterochromatin
• genetically inactive no genes or repressed
• replicates later in the S phase
• composed of area around the centromere and
  telomeres
• X-chromosome and Y-chromosome inactivation
• Uncoiled chromosomal areas euchromatin
• genetically active
• replicates early in S phase

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Position Effect

• Heterochromatic areas from 1 chromosome are
  translocated to new site or another nonhomologous
  chromosome so genetically active areas sometimes
  become genetically inert if located near
  translocated heterochromatin
• position of a gene or group of genes relative to
  all other genetic material may affect their
  expression

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Repetitive DNA

• DNA has areas of unique DNA in single copies that
  make genes
• Most DNA is actually repetitive in mature and at
  various levels of repeats
• various classes and organization within the
  genome
• may be functional genes in more than 1 copy
• much is non-genic

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3 Categories

• Heterochromatin associated with centromere and
  telomeres
• Tandem repeats of both short and long DNA
  sequence
• Transposable sequences that are interspersed
  throughout the genome of eukaryotes

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Repetitive DNA/Satellite DNA

• Usually DNA has same density in sedimentation
  equilibrium centrifugation
• 1 fraction may have different density satellite
  DNA variable portion of total DNA (varies
  between species)
• Profile of main band and satellite DNA (highly
  repetitive DNA sequence
• Tandem repeats clustered in area known to be
  heterochromatic regions flanking centromeres

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Mouse Satellite DNA

• In situ molecular hybridization probe (DNA or
  RNA) of DNA in chromosomes of a cytological
  preparation
• Satellites differs in molecular composition than
  main band DNA
• composed of repetitive sequence
• heterochromatic centromeric regions

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Centromeric/Telomeric DNA Sequence

• CEN region support function of chromosomal
  segregation bind a platform of proteins forming
  centromere includes kinetochore which binds
  spindle fiber during division
• similar in organization
• 3 regions I and III are 9 and 11 bp
  respectively highly conserved region II is
  100 bp rich in A and T, varies in sequence among
  different chromosome
• region III is critical to centromere function,
  important in spindle fiber
• can tolerate mutations in I and II without loss
  of function

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Alphoid Family

• Repeats around centromere vary considerably in
  size
• Most recognized satellite DNA is the alphoid
  family that is mainly in the centromere area
• each is 170 bp, present in tandem repeats up to
  1x106 bp
• not sure the function of repetitive DNA near the
  centromere

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Telomeres

• Adds stability to the end of chromosomes
• Keeps the ends inert so they do not interact with
  other chromosomes and with enzymes that use dsDNA
  ends as substrates
• telomere sequences are repetitive in nature
• use the mechanism of finishing the chromosome to
  make a loop that protects the ends of chromosomes

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Middle Repetitive Sequence VNTRs and STRs

• Highly repetitive - 5 of human genome
• Middle or moderately repetitive DNA most are
  either non-coding tandemly repeated or
  interspersed sequence (few are rRNA as well)
• Variable number tandem repeats (VNTRs)
• 15-100 bp long, found within and between genes
• dispersed throughout genome minisatellites
• of tandem copies localized regions
  1000-20,000 bp
• basis for forensic technique DNA fingerprint
• Microsatellites or short tandem repeats (STRs)
• di-, tri-, tetra- and pentanucleotides tandemly
  repeated
• dispersed in genome most common human (CA)n n5
  to 50
• molecular markers during genome analysis
• sequence of choice in DNA fingerprinting

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Repetitive Transposed Sequences

• 2 types SINEs and LINEs
• Not tandem repeats dispersed thru the genome,
  long or short
• Transposable elements mobile and can
  potentially move to different location within
  genome
• Large portion of human genome

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SINEs

• Short interspersed elements 100-500 bp, present
  1.5 million times in humans
• alu family (named after the enzyme that cuts the
  DNA, AluI)
• 200-300 bp dispersed throughout genome, between
  and within genes, may transcribe into RNA of
  unknown function may help to move around genome
• 13 of genome

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LINEs

• Long interspersed elements transposable
  elements
• 6 kb in length, present 850,000 times
• L1 family 6400 bp and 100,000 repeats
• transcribed into an RNA, serves as template to
  make DNA complement by reverse transcriptase,
  encoded by part of L1 gene
• new cpy inserts (integrates) into DNA at new site
• similar to retroviruses so also called
  retrotransposons
• 21 of genome

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Middle Repetitive Multiple Copy Genes

• Functional genes present in multiple copies
• like rRNA genes, many copies in the p arm of 13,
  14, 15, 21 and 22

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Eukaryote Genome

• Vast majority of eukaryotic genome does not
  encode functional genes
• many single copy DNA sequences appear to be
  non-coding pseudogenes evolutionary vestiges
  of duplicated copies, undergone significant
  mutational alterations
• Only small portion of genome actually codes for
  proteins