Flashcards in 18.01.04 Gene structure Deck (19):
What is a gene?
Region of coding DNA either for:
mRNA encoding for a functional polypeptide chain or
a functional RNA molecule (ncRNa)
What is the sequence of the start codon?
What is the sequence of the stop codon.
Give three examples of cis-acting transcriptional regulatory DNA element.
All contains recognition sites for trans-acting DNA-binding TFs
What is the structure of the promoter?
Core promoter and nearby regulatory elements
Where is the core promoter located? Describe some of its features
Located at 5' end of the gene
Docking site for transcriptional machinery
Defines transcription start site
Defines direction of transcription (sense/antisense)
Contains the TATA box
Describe the TATA box.
Conserved 8bp sequence - TATA(T/A)A(T/A)N
Binding site for TATA-box-binding protein subunit of RNA polymerase II transcription factor
Reversal of sequence (seen in some mutations) will remove its ability to promote transcription
Name three other regulatory elements associated with the promoter.
1) Initiator element
2) Downstream promoter element (DPE)
3) Downstream core element (DCE)
4) RNA polymerase II transcription factor-recognition element
5) Motif ten element
Describe proximal promoter elements
Immediately upstream of core promoter
Contains multiple binding sites for activators
Describe the role of enhancers.
Typically long-distance transcriptional control elements that can be situated distally from the promoter.
Regulates transcription in spatial or temporal way
Functions independently of the distance and orientation of the promoter
Functionally similar to PPEs
Often associated with genes that are abundantly expressed e.g. IG
Describe the role of silencers.
1) Sequence-specific elements that confer a negative effect on transcription of target gene.
2) Functions independently of the distance and orientation of the promoter
3) Can be situated as part of the proximal promoter,distal enhancer or further away.
4) Can be located in and intron or 3'UTR
5) Can act synergistically with negative TFs
Describe the role of insulators.
Can block genes from being affected by the transcriptional activity of neighbouring genes. Two main properties:
1) Block enhancer-promoter communication
2) Prevents the spread of repressive chromatin
Usually 0.5-3kb in length. Functions independently of the distance and orientation of the promoter.
Describe some features of the 5'UTR.
1) Binds ribosome for translation
2) Usually ~100-200nt
3) High GC content
4) 10-18% express alternative 5'UTRs by using multiple promoters for regulation of gene expression
e.g. BRCA1 has two different transcripts relating to two different promoters and therefore have 5'UTR differences. Longer transcript predominantly expressed in breast cancer.
Describe some features of the 3'UTR.
1) Contains a terminator sequence for RNA polymerase release
2) Regulatory elements in this region can influence mRNA polyadenylation, translation efficiency, localiation and stability.
3) Contains primary signal for the polyadenylation signal (AATAAA/AAUAAA)
4) PolyA tail added to mRNA transcript to control nuclear export, translation and stability of mRNA.
Name a disease associated with mutations in the core promoter?
B-Thalassemia - mutation in TATA box
Name two diseases associated with mutations in the proximal promoter.
FH - promoter variants reported in LDLR
CMT - mutation in connexin 32 promoter
Name a disease associated with mutations to an enhancer.
X-linked deafness. 900kb deletion upstream of POU3F4 gene.
Name a disease associated with mutations to a silencer.
FSHD - deletion of D4Z4 repeats