Transcription and mRNA processing

know

Basics of transcription to produce mRNA

• core promoter

• enhancer

• mediator

• the bursting nature of transcription

RNA processing

• 5’ capping

• Polyadenylation

• RNA splicing to remove introns

• Alternative splicing to modulate the functions of proteins

Distinct RNA Polymerases produce different classes of RNA

Pol II produces mRNAS, lncRNAs, and miRNAS

Simple model of transcriptional initiation

• enhancer with transcription factors bound (which interact directly with DNA) and COF which activate transcription factors

• GTFs: general transcription factors

• PIC: pre-initiation complex (Pol II and GTFs) on gene

  • produces pre-mRNAs

Histones, Looping, and Mediator complex for transcription

• Histones: modification and remodeling (moving)

• Looping: loops form between enhancers that can be 100,000s bp upstream or downstream of the transcriptional start and the PIC

• Mediator complex: links the enhancer and polymerase complex

The ______ and __________ are the basic unit for initiation of transcription

proximal, core promoter

Cis elements within core promoters

• NFR: nucleosome free region around the start sight (allows space for things to bind)

• Elements are not in all promoters

  • Inr: 46% of promoters

  • TATA: 24% of human promoters

Sequence motifis within promoters and the proteins that bind them ***

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Distinct types of promoters for classes of genes

a. Adult tissue-specific genes or terminally differentiated cell-specific genes

• focused, sharp initiation

b. Housekeeping genes

• expressed in all cells, dispersed, broad initiation

c. Developmental transcription factors

• dispersed, broad initiation

two big (prominent) histones in promotors

Transcriptional initiation and elongation steps (4)

1. transcription factor binding to enhancer region

2. recruitment of co-activators which act on chromatin structure

3. PIC formation (the mediator helped facilitate the PIC assembly by looping the enhancer region to the promoter)

4. promoter escape

Overview of transcription and processing

• there is promoter-proximal pausing that must be released

• additional pausing at the first nucleosome that requires additional factors to proceed through

Transcription speeds

• single cell techniques reveal that tehre are bursts of transcription that vary in the amount of RNA produced and the frequency of the burst

  • measurements of populations show smooth levels of transcriptions even though on the individual level this is not the case

• it is thought that the core promoter regulates the burst size and the enhancer regulates burst frequency

5’ Cap addition pros (5)

• protects from degradation of 5’ → 3’ exonuclease

• facilitates nuclear export

• facilitates splicing

• enhances translation

• helps distinguish between self and non-self RNAs

Polyadenylation

• PolyA stabilizes the mRNA

• Alternative PolyA usage can change stability, localization, translation efficiency, and C-terminus of the protein

The spliceosome complex

• splices RNA to remove introns

• composed of RNA and proteins

  • individual components of RNA and protein are referred to as snRNP - small nuclear ribonucleoprotein

  • the RNA components are essential for the catalystic removal of the intron

• The sequence of the cis elements are relatively degenerate

Alternative splicing

produces proteins with different modules to preform distinct functions

• 90% of human genes are alternatively spliced

alternative splicing is a mechanism for

• genomic evolution

• developmental processes

• modulation of protein function

Regulators of alternative splicing

Cis elements in pre-mRNA regulating splicing

• ESE – exonic splicing enhancer

• ISE – intronic splicing enhancer

• ESS – exonic splicing silencer

• ISS – intronic splicing silencer

Two main families of alternative splicing regulators

• SR – ser / arg rich proteins

• hnRNP–heterogeneous nuclear ribonucleoproteins