Tails of Intrigue:

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Tails of Intrigue Phosphorylation of RNA
Polymerase II Mediates Histone Methylation
Michael Hampsey and Danny Reinberg
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• Chromatin structure Histone Modification
• Histone code hypothesis
• The RNA polymerase II elongation factors
• Chromosomal modifications by histone methylation

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Chromatin organization and the tail of Histone H3

• General chromatin organization. Like other
  histone tails, the N terminus of H3(red)
  represents a highly conserved domain that is
  likely to be exposed or extend outwards form the
  chromatin fibre. A number of distinct
  post-translational modifications are known to
  occur at the N terminus of H3 indluding
  acetylation (green flag), phosphorylation(grey
  circle) and methylation(yellow hexagon)

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The histone code hypothesis

• .Distinct histone modifications, on one or more
  tails, act sequentially or in combination to form
  a histone code that is read by other proteins
  to bring about distinct downstream events
• Regulates chromatin function through its ability
  to recruit specific interacting proteins that
  recognize a single or combinatorial set of
  modifications

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Transcriptional Elongation by RNA polymerase II
and Histone Methylation
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The RNA polymerase II elongation factors
The RNA Pol II CTD cycle
The white circle represents Pol II, the black
line represents the gene with the arrow denoting
the promoter, and the smaller shapes represent
capping enzyme and other RNA-processing factors.
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Model representing the composition of
transcriptional machinery during transcription
initiation and elongation in living cell
The transcription initiation complex includes
Mediator and general transcription factors. RNA
polymerase II leaves the initiation accessory
factors at the promoter, and Spt5 and the
Paf1/Cdc73 complex accompany RNA polymerase II
during transcription elongation. Under stress
conditions, TFIIS also associates with elongating
RNA polymerase II complexes.
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Chromosomal modifications by histone methylation
The identification of histone methyltransferase
(HMT)

• SUV39 protein in Drosophila as a suppressor of
  position-effect variegation
• telomeric silencing, transcriptional activation,
  and transcriptional repression
• Trithorax and polycomb group proteins contain a
  130-140 amino acid motif
• called the SET domain,which is found in a
  variety of chromatin-associated
• proteins.
• SETSu(var)3-9, Enhancer of zeste (E(z)), and
  Trithoraxdomain-containing
• protein

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Structural features within the SET-domain
families

• The SUV39 family
• The presence of a PRE-SET domain
• Specificity for the SET domain to methylate
  lysine 9 of histone H3

• The SET1 family
• The capacity to methylate lysine 4 of histone
  H3.
• A SET domain at the very carboxyl terminus of the
  protein is mostly followed by a POST-SET domain.

• The SET2 family
• The capacity to methylate histone H3
• SET-POSTSET-AWS domain

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A role for histone methylation of lysine 4 of
histone H3 in transcription elongation

• Preinitiation complex containing Pol II,
  mediator(Med), TFIIH(H), and other general
  transcription factors at the initiation site.
  TFIIH phosphorylates the CTD at seine 5 (green
  stars). Nucleosomes contain dimethylated H3-K4

• Early stage of elongation in which mediator and
  GTFs have dissociated and the Set1 and Paf/Rtf
  complexes are recruited to the 5portion of the
  coding region. Set1 generates a localized domain
  of H3-K4 trimethylation (red nucleosomes)

• Late stage of elongation in which CTD becomes
  phosphorylated at serine 2 (purple stars) and
  dephosphorylated at serine 5. Set1 dissociates
  from the elongating Pol II machinery, whereas the
  Paf/Rtf complex remains associated

• Localized mark of H3-K4 trimethylation persists
  for considerable time after cessation of
  transcription

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A role for histone methylation of lysine 4 of
histone H3 in transcription elongation

• Set1 targeting to mRNA coding regions is
  mediated by elongating Pol II and requires CTD
  phosphorylation at serine 5
• Rtf1 and Paf1 components of the paf1 complex are
  important for targeting of set1 to mRNA coding
  regions
• Localized marking a active Poll genes by
  targeted recruitment of set1 provides a memory of
  recent transcriptional activity
• A possible role for H3-K4 methylation in
  orchestrating the recruitment of 3-end
  processing factors.

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A role for histone methylation of lysine 36 of
histone H3 in transcription elongation

• RNAP II transcription initiation competent
  competent complex within chromatin DNA, RNAP II,
  the GTFs and the mediator complex.

• Soon after initiation, the PAF complex is
  recruited.

• The CTK1 kinase complex is recruited to the
  transcriptional apparatus resulting in
  phosphorylation of serine-2 of the CTD. Set2
  associates with the serine 2 phosphoryated form
  of Pol II, indicating that it associates with
  both early elongating and processively elongating
  RNA polymerase II.

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A role for histone methylation of lysine 36 of
histone H3 in transcription elongation

• Recruitment of the Set2 complex results in
  methylation of H3-K36
• Set2 associated with the elongating RNAP II to
  catalyze methylation of H3-K36 as the
  elongation complex encounters downstream
  nucleosomes.
• Set2 interactions with elongation factors,
  including chd1, soh1, and PAF subunit

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Further Schedule
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