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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?
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
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
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 (typically)
• 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.
TATA binding protein (TBP) transcription factor
Wikipedia.com
DNA-binding domains allow transcription factors to bind directly to a cis-regulatory element
Helix-loop-helix
Zinc finger domain
Leucine zipper domain
Extreme trans-acting effectors of transcription: TAL effectors
• From plant pathogenic bacteria Xanthomonas
• Secreted by bacteria when they infect
• Transcriptional activator-like (TAL) effectors bind with plant promoters to express genes beneficial for the bacteria
http://www.sciencemag.org/content/333/6051/1843/F2.large.jpg
Introducing RNAi
http://www.youtube.com/watch?v=H5udFjWDM3E&feature=related
What is a microRNA (miRNA)?What is a microRNA (miRNA)?Controlling gene expression post-transcriptionally.Controlling gene expression post-transcriptionally.
microRNA is an abundant class of newly identified small microRNA is an abundant class of newly identified small non-coding regulatory RNAs.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
miRNA regulates plant development
WT miRNA
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
Slide courtesy of Baohong Zhang, East Carolina Univ
Post-transcriptional gene regulation
Two major molecular mechanisms
Mechanisms of miRNA-mediated gene regulationMechanisms of miRNA-mediated gene regulation
Zhang et al. 2006. Developmental BiologySlide courtesy of Baohong Zhang, East Carolina Univ
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 CibaNovartisSyngenta
Arabidopsis MET1 Cytosine Methyltransferase
Mutants Kankel et al. 2003. 163 (3):1109 Genetics
Plants mutant for MET1 show late-flowering phenotypes
Some post-translational modifications
• Phosphorylation• Biotinylation• Glycosylation• Acetylation• Alkylation• Methylation• Glutamylation• Glycylation• Isoprenylation
• Lipoylation• Phosphopantetheinyl
ation• Sulfation• Selenation• C-terminal amidation
Phosphorylation is important for intracellular signalling
http://www.scq.ubc.ca/wp-content/uploads/2006/07/phosphocascades.gif
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.
Figure 6.5
Eukaryotic gene structure and transcription of DNA into mRNA
TF
TF
AAAAARNA
polymerase II
TFTF
TF