Week 4 Notes: Mechanisms of Eukaryotic transcription
Features of eukaryotes
In contrast to prokaryotes and bacteriophage: a nucleus and packaged DNA
Heterchromatin: periphery of nucleus & only in eukaryotes
o Highly compacted chromatin so easily observed when DNA is stained
o No transcription
o Has 2 forms: constitutive & facultative
Euchromatin: inner core of nucleus, present in eukaryotes and prokaryotes
o Lightly packed chromatin so easy access of DNA for transcription
o Most active portion of genome
o Transcription
o Extended structure
Interrupted gene: gene in which the coding sequence is not continuous due to presence of introns
Exon: DNA segment that is transcribed and retained in the mature RNA product
Intron: DNA segment that is transcribed, but later removed by splicing together sequence of exons
Mature transcript: modified RNA transcript. Modification may include removal of intron sequences and
alterations to the 5’ and 3’ ends
Eukaryotic RNA polymerases
3 RNA polymerases, with distinct properties and with one each specifically dedicated to tRNA, mRNA, rRNA
synthesis
Require numerous transcription factors and factors to modify chromatin structure to allow RNA pol access
Enzyme Location RNA products
RNA pol I (14 subunits) Nucleolus Pre-rRNA leading to rRNA
RNA pol II (12 subunits) Nucleoplasm Pre-mRNA and some snRNA
RNA pol III (17 subunits) Nucleoplasm tRNA, 5S rRNA, U6 snRNA
(spliceosome) and 7SL RNA (signal
recognition particle)
RNA pol I, II & III share some subunits (Rpb5, Rpb6, Rpb8, Rpb10 & Rpb12) but not others
o Many RNA pol II subunits have homologs in RNA pol I and/or III
o Bacterial RNA pol subunits has at least one homolog in each eukaryotic polymerase
Schematic of the transcription bubble and mRNA product *W1 page 1*
Transcription has 3 stages *W1 page 1*
Transcription initiation can be focused or dispersed
RNA pol I-III initiate transcription with assistance transcription factors
o Each RNA pol has its own specific set of TF to assist in locating start sites
Around each transcriptional start site is a core promoter
Around 70% of vertebrate core promoters are dispersed promoters (allows
multiple mRNAs to be produced from single gene)
Eukaryotic core Pol II promoter motifs
TATA box: TATAXAX consensus sequence (X is A or T) located 25-30bp upstream of transcription start site
Initiator element (Inr): overlaps transcription initiation site
Downstream promoter element (DPE): extends from about +28 to +34
TFIIB recognition element (BRE)
XCPE1: present in TATA-less human core promoters (1% human genes)
Features of eukaryotes
In contrast to prokaryotes and bacteriophage: a nucleus and packaged DNA
Heterchromatin: periphery of nucleus & only in eukaryotes
o Highly compacted chromatin so easily observed when DNA is stained
o No transcription
o Has 2 forms: constitutive & facultative
Euchromatin: inner core of nucleus, present in eukaryotes and prokaryotes
o Lightly packed chromatin so easy access of DNA for transcription
o Most active portion of genome
o Transcription
o Extended structure
Interrupted gene: gene in which the coding sequence is not continuous due to presence of introns
Exon: DNA segment that is transcribed and retained in the mature RNA product
Intron: DNA segment that is transcribed, but later removed by splicing together sequence of exons
Mature transcript: modified RNA transcript. Modification may include removal of intron sequences and
alterations to the 5’ and 3’ ends
Eukaryotic RNA polymerases
3 RNA polymerases, with distinct properties and with one each specifically dedicated to tRNA, mRNA, rRNA
synthesis
Require numerous transcription factors and factors to modify chromatin structure to allow RNA pol access
Enzyme Location RNA products
RNA pol I (14 subunits) Nucleolus Pre-rRNA leading to rRNA
RNA pol II (12 subunits) Nucleoplasm Pre-mRNA and some snRNA
RNA pol III (17 subunits) Nucleoplasm tRNA, 5S rRNA, U6 snRNA
(spliceosome) and 7SL RNA (signal
recognition particle)
RNA pol I, II & III share some subunits (Rpb5, Rpb6, Rpb8, Rpb10 & Rpb12) but not others
o Many RNA pol II subunits have homologs in RNA pol I and/or III
o Bacterial RNA pol subunits has at least one homolog in each eukaryotic polymerase
Schematic of the transcription bubble and mRNA product *W1 page 1*
Transcription has 3 stages *W1 page 1*
Transcription initiation can be focused or dispersed
RNA pol I-III initiate transcription with assistance transcription factors
o Each RNA pol has its own specific set of TF to assist in locating start sites
Around each transcriptional start site is a core promoter
Around 70% of vertebrate core promoters are dispersed promoters (allows
multiple mRNAs to be produced from single gene)
Eukaryotic core Pol II promoter motifs
TATA box: TATAXAX consensus sequence (X is A or T) located 25-30bp upstream of transcription start site
Initiator element (Inr): overlaps transcription initiation site
Downstream promoter element (DPE): extends from about +28 to +34
TFIIB recognition element (BRE)
XCPE1: present in TATA-less human core promoters (1% human genes)
