Lecture 9 Chapter 6 Gene expression and regulation II

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Lecture 9 Chapter 6Gene expression and
regulation II

• Neal Stewart

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Focus questions

• How important are cis-regulatory elements and
  trans-acting factors in gene regulation?
• What are the control points that can regulate
  gene expression?

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Transcription revisited
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Promoter elements not required for transcription
initiation

• CAAT box usually located at -70 to -80 within
  the promoter
• GC box
• Other gene-specific elements (light-responsive,
  nutrient-responsive, etc.)
• Enhancer elements

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What are some biological roles of transcription
factors?

• Basal transcription regulation general
  transcription factors
• Development
• Response to intercellular signals
• Response to environment
• Cell cycle control

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The CRT/DRE response element responds to
dehydration and cold-induced transcription
factors (CBF)
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Figure 6.7
Transcription factors
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Figure 6.8
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Enhancer can work from downstream and upstream
region
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(No Transcript)
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Enhancers

• Their location is not fixed. Location could be
  in the upstream or downstream DNA, in intron,
  exon or in the untranslated region.
• They enhance transcription by acting on promoter
  in cis.
• Each enhancer has its own binding protein. These
  proteins are trans-regulatory activating factors
• Sequence of enhancers is variable.
• Enhancers regulate tissue-specific and temporal
  expression of genes.

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TATA binding protein (TBP) transcription factor
Wikipedia.com
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DNA-binding domains allow transcription factors
to bind directly to a cis-regulatory element
Helix-loop-helix
Zinc finger domain
Leucine zipper domain
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Extreme trans-acting effectors of transcription
TAL effectors

• From plant pathogenic bacteria Xanthomonas
• Secreted by bacteria when they infect
• Transcription activator-like (TAL) effectors bind
  with plant promoters to express genes beneficial
  for the bacteria

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http//www.sciencemag.org/content/333/6051/1843/F2
.large.jpg
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Repression of transcription
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Some trans-acting elements prevent transcription
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Introducing RNAi

• http//www.youtube.com/watch?vH5udFjWDM3Efeature
  related

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What is a microRNA (miRNA)?Controlling gene
expression post-transcriptionally.
microRNA is an abundant class of newly identified
small non-coding regulatory RNAs.

• Major characteristics of miRNAs
• 18-26 nt in length with a majority of 21-23 nt
• non-coding RNA
• derived from a precursor with a long nt
  sequence
• this precursor can form a stem-loop 2nd
  hairpin structure
• the hairpin structure has low minimal free
  folding energy (MFE) and high MFE index

Slide courtesy of Baohong Zhang, East Carolina
Univ
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miRNA regulates plant development
miRNA 156 increasing leaf initation,
decreasing apical dominance, and forming bushier
plant. miRNA 164 stamens are fused
together.
miRNA 172 sepal and petal
disappeared. miRNA 319 Leaf morphology
WT miRNA
Slide courtesy of Baohong Zhang, East Carolina
Univ
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Small interfering RNAs inhibit expression of a
homologous gene
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Biogenesis of miRNAs
Plant
Animal
Bartel, 2004. Cell.
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Mechanisms of miRNA-mediated gene regulation
Post-transcriptional gene regulation Two
major molecular mechanisms

Zhang et al. 2006. Developmental Biology
Slide courtesy of Baohong Zhang, East Carolina
Univ
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Mary-Dell Chilton

• Undergrad and PhD University of Illinois
• Postdoc with Gene Nester and Milt Gorgon Univ
  Washington
• One of the first plant transformation Washington
  University
• Career at Ciba?Novartis?Syngenta

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Pre-transcriptional gene regulation by
methylation of DNA and acetylation of histones
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Special proteins (e.g. chromomethylases) maintain
methylation patterns
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Switching a gene on and off through DNA
methylation and histone modification
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Arabidopsis MET1 Cytosine Methyltransferase
Mutants Kankel et al. 2003. 163 (3)1109 Genetics
Plants mutant for MET1 show late-flowering
phenotypes
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Histone acetyl transferases and chromatin
remodeling allows promoters to be accessible to
RNAPII
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Histone tails are modified and can be studied
easily
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Figure 6.9
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Some post-translational modifications

• Phosphorylation
• Biotinylation
• Glycosylation
• Acetylation
• Alkylation
• Methylation
• Glutamylation
• Glycylation
• Isoprenylation

• Lipoylation
• Phosphopantetheinylation
• Sulfation
• Selenation
• C-terminal amidation

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Phosphorylation is important for intracellular
signalling
http//www.scq.ubc.ca/wp-content/uploads/2006/07/p
hosphocascades.gif
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Protein glycosylation in the ER
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The central dogma revisited

• The order of the DNA template or coding strand is
  3 to 5
• This determines the order of the mRNA strand (5
  to 3) because DNA template is complementary to
  the mRNA strand.

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Eukaryotic gene structure and transcription of
DNA into mRNA
Figure 6.5
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Manipulating gene expression

• Can be done at several levels
• Promoters, enhancers, transcription factors
• Post-transcriptional
• Translational
• Methylation
• Biotechnology typically manipulates promoter
• Post-transcriptional gene silencing (RNAi)
  increasingly important