Transcription initiation summary and pre-mRNA processing

Eukaryotes have three DNA dependent RNA polymerases that each transcribes a specific sets of RNA molecules:
RNA Polymerase I (pol I) ->

ribosomal RNA (components of the ribosome)

RNA polymerase II (pol II)

mRNA, snRNAs, miRNAs, lncRNAs (messenger RNA: protein coding and noncoding RNAs)

RNA polymerase III (pol III)

t-RNA some snRNAs (“adapters” -> RNA-amino-acids -> translation)

Promoters

structures upstream of genes where General transcription factors (GTFs) are assembled that recruit RNA

promotor proximal elements

modular regulatory elements

distant regulatory elements

enhancers, silencers, insulators,

Regulatory elements

regulate assembly of GTFs and recruitment of polymerases to the cognate promoters and regulate
activation of polymerases -> regulate gene expression

Each RNA polymerase has a designated set of GTFs that assemble on corresponding promoter sequences:

TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH -> pol II specific TFIIIB, TFIIIA, TFIIIC -> pol III specific etc

Chromatin regulates gene expression - heterochromatin

Dense compacted chromatin: Heterochromatin-> hinders access of transcription
factors to cognate sequences in promoters and regulatory elements -> Inactive gene regions

Constitutive heterochromatic regions

Telomers, centromeres, satellite DNA

Chromatin compaction is dynamic and can be regulated by post-translational modification of histone N-terminal tails:

Including phosphorylation, methylation, Acetylation. Acetylation is generally associated with active gene regions.

Each RNA polymerase has a designated set of GTFs that assemble on corresponding promoter sequences:

TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH -> pol II specific TFIIIB, TFIIIA, TFIIIC -> pol III specific etc

To create a functional mRNA three modifications are required:

1) capping of the 5’ end
2) removal of non-coding introns and fusion of coding exons
3) modification of the 3’end by cleavage and polyadenylation

The function of the cap

to protect the mRNA from premature degradation and to recruit the ribosome

Capping

is the addition of a methylated guanosine at the 5’end and the methyl G is recognised by the cap binding complex

Pre-mRNA processing reactions

how described and what is essential for space and space

occur co-transcriptionally

dynamic phosphorylation of the C-terminal domain of the largest subunit of RNA polymerase II

critical for the recruitment of processing factors in space and time.

Exon – intron borders

demarcated by specific sequences including the 5’splice site, the branch point, pyrimidine track and
the 3’ splice site

Spliceosome

is large complex assembles consisting of proteins and 5 snRNAs that assemble on the splice sites and catalyses
Excision of introns and fusion of exons

Alternative splicing

a regulated process

expand the cellular protein repertoire

by selecting different
splice sites

produce many different mRNA isoforms from one gene

Cleavage and polyadenylation

matures the mRNAs by adding a poly A tail at the 3’end

The cleavage ad polyadenylation
machinery is recruited by

a sequence motif consisting of a AAUAAA hexamer and a U-rich element

Mutations in sequences that control splicing

C-> T mutation in exon 6 of the MLH1 gene creates a new 5’ splice site and this results in the omission of four
nucleotides at the end of exon 6 resulting in a final mRNA with a changed
reading frame introducing a premature stop codon in exon 7.

lack of functional mismatch repair proteins

develop various cancers - Lynch syndrome

Hexamer for poly A tail formation mutations cause a decrease in protein output

e.g. in Beta globin

Influenza virus - various mechanisms to halt splicing —> removes caps, inhibits spliceosome

triggers host gene cut-off