Physiology 3140A Lecture Notes - Lecture 2: Intergenic Region, Transcription Factor, Intron
22 May 2018
School
Department
Course
Professor
Physiology 3140
Dr. Pin
Lecture 2
What are we going to talk about?
Transcription
1. Makeup of the genome
2. Promoters and enhancers
3. General transcription factors
4. Genome organization
5. Transcription factor families
6. Regulation of transcription factors
What are the different regions of the genome?
1. Genes – introns and exons
o There are 3 parts of a gene:
▪ exons,
▪ introns
▪ untranslated regions
• when you make the protein there is a region upstream called the 5’
untranslated region and another region called the 3’ untranslated
region
• these are part of the RNA but is not made into protein
2. Promoters
o Normally located upstream of the gene
o Note: when he says upstream of 5’, he is talking about the promoter
3. Enhancers
o A lot of mutations (most) affect the enhancers
o Promoters are close to the gene, enhancers can be anywhere
o Enhancer involved in saying when the gene is going to be on
o The gene itself doesn’t tell where its going to be expressed
o The promoter ad enhancer is what tells where the gene is going to be expressed
4. Intergenic regions
o Non coding DNA
▪ Don’t do much ppl thought it was garbage
o Regulatory regions that get transcribed
o Transcribed areas
- Promoters and enhancers work in concer
o the promoter is close to the gene (upstream of it)
o The ehancer is all over the gene – it can be anywhere
o Tell you where and when the expression is going to take place for that change to occur
o Ex: if you were to take this gene X
DNA to RNA to mRNA
find more resources at oneclass.com
find more resources at oneclass.com
- Introns in blue; exons in green
- Central dogma: gene →RNA → protein
- Promoter upstream causes the expression of the gene
- Have start and stop codon for the proteins
- Coding region for this gene is green (this is what is coding for the protein)
o All the other things regulate where it is expressed, how it is expressed, the stability of
the RNA and have an effect on transcription
- Mature RNA also have:
o Have the mRNA with 5’ UTR and 3’ UTR
o PolyA tail:
▪ Prevents degradation and involved in stability of mRNA
▪ Without it, RNA is rapidly degraded (RNA with a polyA tail is even rapidly
degraded)
o 5’ cap
▪ helps with translation
▪ increases expression of protein from this region
- it has now been discovered that you can get DNA encoded from RNA
o this happens in viruses
- intergenic region bw genes
- have enhancers
- this is how the DNA is set up to be regulated
Promoters
- tell the gene where and when
- Position is fixed – upstream 5’ of the Transcriptional Start Site TSS
- Generally 150-500 bp in length (not that long)
- contains the consensus DNA sequences TATA/CAAT
o 70% of promoters have this
o to bind proteins that are required for transcription
- there are other recognition sites
o BRE
o INR (22 bp upstream of transcriptional start site)
- Proximal control elements such as TFIIB recognition element (BRE) and initiator sequences
(INR)
- There are other regions of the promoter which will bind General (Basal) Transcription Factors
o There are bout 1200-1400 transcription factors that will give you tissue specificity and
time specificity
- there are sequences within the promoter that recruit polymerases needed to make RNA
o these are general
o it’s the same machinery needed for all the RNA
find more resources at oneclass.com
find more resources at oneclass.com
o but there are also transcription factors that are going to cause expression
o this is where the differences lie
o not every gene is going to be on all the time
o not every gene is going to be expressed everywhere in the body
o so there has to be some specificity and some specificity comes from the promoter and
some specificity comes from the enhancer
- Promoters are tissue dependent and orientation dependent (you cant just flip it around – it has
to be in the right sequence)
Process by which a promoter will bind a transcription factor to generate transcription
- This is the process that works for all genes
- May bind tissue specific transcription factors(TSTF)
o This is one of the proteins that will initiate the whole process
o Its going to open up the DNA so that you can actually bring in these other proteins
- TBP (TATA binding protein) will bind to the TATA box
- This is going to recruit the TFIID
- TBP and TFIID binding together will stabilize that interaction bw the TBP and the TATA box
- TFIID binds the core promoter region and may bind additional sequences near the TSS, such as
the INR (initiator sequence)
- This leads to recruitment of TFIIA and TFIIB
- TFIIA and TFIIB help to stabilize TFIID binding
o These are all now associated to these common elements within the promoter
o This is a really large complex (its bringing in about 12-14 proteins to do this)
- TFIIB helps recruit RNA polymerase II (very large)
o RNA poly II sits at the promoter
o Once you brought the RNA poly )), it doesn’t automatically start transcribing
o There are a lot of genes that have this arrangement but don’t have any transcription
o So the presence of RNA poly )) alone doesn’t cause transcription – it just sits this gene in
an area that now is ready to be transcribed
o So why would you do this?
o So that they have a minute/quick response – bc having these genes primed like this will
allow for a response within seconds
- TFIIF binds RNA PolII and TFIIB which aids in recruitment of RNA polymerase II
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Transcription: makeup of the genome, promoters and enhancers, general transcription factors, genome organization, transcription factor families, regulation of transcription factors. Promoters and enhancers work in concer: tell you where and when the expression is going to take place for that change to occur, ex: if you were to take this gene x. Promoter upstream causes the expression of the gene. Have start and stop codon for the proteins. Coding region for this gene is green (this is what is coding for the protein: all the other things regulate where it is expressed, how it is expressed, the stability of. Have enhancers this is how the dna is set up to be regulated. Position is fixed upstream (cid:523)5"(cid:524) of the transcriptional start site (cid:523)tss(cid:524) Generally 150-500 bp in length (not that long) contains the consensus dna sequences tata/caat: 70% of promoters have this to bind proteins that are required for transcription there are other recognition sites, bre.
