BCH3031 Lecture Notes - Lecture 4: Rna Polymerase Ii, Tata Box, Non-Coding Rna
25 May 2018
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Lecture 4 – Transcription through Chromatin
• Cellular differentiation and function depend on accurate and regulated
transcription of genome
• 2-3% of genome encodes proteins
o ~90% transcribed into noncoding RNA
• Integral to this regulated expression is ability to initiate transcription at precise
genomic sites
Three RNA Polymerases in Eukaryotic Cells
1. RNA polymerase I
• Drive ribosomal DNA/RNA transcription → protein synthesis
2. RNA polymerase II
• Most protein encoding genes are driven by II
• Promotes gene transcription coding for proteins
3. RNA polymerase III
• Drive tRNA transcription
RNA Polymerase II
• Largest subunit – that requires general transcription factors (GTFs)
o Needs to start at right location
o Need to stabilise binding and unwind DNA (e.g. TFIH)
• Requires RNA Pol to drive transcription from start signs after promoter region
• (A): Promoter of gene contains DNA sequence TATA box located at start site
– where transcription is initiated
• (B-C): TFIID that contains TBP domain recognises and binds TATA box
o Enables adjacent binding of TFIIB with tata box
o Binding of TFIID causes distortion of DNA of TATA box → serves as
landmark for location of active promoter
o TFIIB helps to position the RNA pol at start site of transcription
o TFIID – helps create structure on DNA by bending DNA – allows
RNA pol to enter
• (D): Rest of GTFs and RNA POLII itself assemble at promoter
• (E): TFIIH then uses ATP to unwind DNA helix at transcription start point →
expositing template strand
o TFIIH phosphorylates RNA PollII – changing its conformation →
allowing the beginning of transcription initiation
▪ Phosphorylation (add negative charge to histones → weaken
interactions with DNA) occurs on C terminal domain (CTD)
that extends from molecules
find more resources at oneclass.com
find more resources at oneclass.com
Eukaryotic Gene Transcription Control Elements
• Mammalian gene: more complex
o Start site (where transcription occurs) encodes the first 5 nucleotide of
first exon of mRNA
o TATA box located 25-35 base pairs upstream of start site
▪ Directs the binding of RNA pol II to begin transcription
o Instead of TATA box, some genes will have promoter proximal
elements
▪ Can be found 10-30 base pairs within 200 base pair upstream of
start site
o Enhancers: found far away from gene either upstream/down stream
▪ Works together with promoter
o Promoter proximal elements and enhancers: cell type specific
▪ Function only in specific differentiated cell types
o Mediator
▪ Helps bridge between RNA polymerase and transcription
factors
• Alternative promoter elements – initiator element
o Have cytosine C at -1 position and adenine (A) residue at transcription
start site (+1)
o Transcription state site can have multiple start sites
o Genes of lower in transcription rate do not have TATA box or initiator
element
o Transcription of many protein coding genes has been shown to begin at
any one multiple possible sties over an extended region
• CpG Islands
o Lots of promoter regions of genes have CpG islands
▪ Promoter function by destabilizing nucleosomes and attracting
proteins that create a transcriptionally permissive chromatin
state
o Play important role in transcription and gene regulation
▪ CGI in genome contain transcription initiation regions
o Silencing of CGI promoters can be methylated – dense CpG
methylation or polycomb recruitment
▪ Those regions can become heterochromatin
▪ DNA methylation of promoter regions can work with histone
methylation to switch off transcription off particular region in
genome (e.g. centromere, telomere)
o Genes that are actively transcribed – C of CG nucleotides are not
methylated
o CGIs equipped to influence local chromatin structure and simplify
regulation of gene activity
find more resources at oneclass.com
find more resources at oneclass.com
