Eukaryotic Pre-mRNA Processing and Regulation

Pre-mRNA

Initial RNA transcript processed before translation.

Capping

Addition of 7-methylguanylate to 5' end.

Polyadenylation

Addition of ~250 A residues at 3' end.

Splicing

Removal of introns and joining of exons.

Spliceosome

Complex that catalyzes pre-mRNA splicing.

Transesterification

Chemical reaction during mRNA splicing.

Exons

Coding regions of pre-mRNA retained after splicing.

Introns

Non-coding regions removed during splicing.

SR proteins

Proteins that assist in splicing regulation.

snRNPs

Small nuclear ribonucleoproteins involved in splicing.

Cross-exon recognition complex

Complex that specifies correct splice sites.

Alternative splicing

Use of different exons to produce varied mRNAs.

mRNA degradation

Process controlling mRNA stability and translation.

Exosome complex

Degrades improperly processed mRNAs in the nucleus.

Translation initiation factors

Proteins that begin mRNA translation at 5' cap.

P bodies

Cytoplasmic structures where mRNA is degraded.

miRNA

Regulatory RNAs that inhibit mRNA translation.

tRNAs

Transfer RNAs transcribed by RNA polymerase III.

rRNAs

Ribosomal RNAs transcribed by RNA polymerase I.

Poly(A) tail

String of adenine nucleotides at mRNA 3' end.

Cleavage enzyme

Enzyme that cuts primary transcript at poly(A) site.

Branch-point adenosine

Adenosine crucial for lariat formation during splicing.

Polypyrimidine tract

Sequence aiding splicing near intron 3' end.

5' GU and 3' AG

Consensus sequences at intron splice sites.

Translation regulation

Control of protein synthesis from mRNA.

Nuclear exosomes

Degrade RNA precursors in the nucleus.

Cytoplasmic poly(A) polymerase

Enzyme controlling poly(A) tail synthesis.

5' cap

Modified guanine nucleotide protecting mRNA from degradation.

RNA polymerase II

Enzyme responsible for transcribing mRNA from DNA.

snRNA

Small nuclear RNA involved in pre-mRNA splicing.

U1 snRNA

Base-pairs with 5' splice site in splicing.

U2 snRNA

Base-pairs with branch-point A during splicing.

snRNPs

Small nuclear ribonucleoprotein particles formed by snRNAs.

5' splice site

Location where U1 snRNA binds pre-mRNA.

Branch-point A

Key nucleotide for U2 snRNA binding.

Transesterification reaction

Chemical reaction during splicing involving RNA.

Spliceosome

Complex of snRNPs and proteins for splicing.

SF1

Splicing factor 1 that binds branch-point A.

U2AF

U2 snRNP associated factor binding polypyrimidine tract.

First transesterification

Forms 2′,5′-phosphodiester bond in splicing.

Second transesterification

Joins exons with a 3′,5′-phosphodiester bond.

Lariat structure

Formed from excised intron during splicing.

Debranching enzyme

Converts lariat intron into linear RNA.

Exon definition

Process of identifying exons in long pre-mRNAs.

SR proteins

Proteins that enhance exon recognition in splicing.

ESEs

Exonic enhancer sequences recognized by SR proteins.

RS domains

Protein interaction domains rich in arginine and serine.

GU-AG rule

Splicing sites recognized by proximity to exons.

Cooperative binding

SR proteins enhance binding of snRNPs to splice sites.

SMN1 gene

Gene encoding protein crucial for motor neuron function.

SMN2 gene

Gene with silent mutation affecting splicing.

Exon skipping

Inhibition of exon inclusion in mRNA due to mutations.

Poly(A) tail

3' end modification of eukaryotic mRNAs.

Cleavage and polyadenylation

Coupled process for mRNA maturation in eukaryotes.

Intron

Non-coding sequence removed during mRNA splicing.

Exon

Coding sequence retained in mature mRNA.

Mutations in splicing

Alterations that can block or restore splicing.

Average exon length

Approximately 150 bases in human pre-mRNAs.

Average intron length

Approximately 3500 bases in human pre-mRNAs.

CPSF

Binds upstream AAUAAA polyadenylation signal.

CStF

Interacts with downstream GU/U-rich sequences.

CFI and CFII

Stabilize RNA complex during processing.

PAP

Stimulates cleavage at poly(A) cleavage site.

Cleavage factors

Released after RNA cleavage occurs.

Downstream RNA cleavage product

Rapidly degraded post-cleavage.

PABPN1

Binds initial poly(A) tail, signals PAP.

Poly(A) tail

Short A residues added to RNA's 3' end.

Exosome

Digests RNAs, including introns.

Exosome core

Nine-subunit complex, catalytically inactive.

Rrp44

Subunit with processive 3'→5' exonuclease activity.

Nuclear exosome

14 subunits, processes RNA in nucleus.

Mtr4

RNA helicase that associates with exosome.

Alternative promoters

Generate different mRNAs from the same gene.

Alternative splicing

Produces various mRNA forms from primary transcript.

RNA-binding proteins

Regulate splicing by binding near splice sites.

RNA editing

Alters amino acids encoded by mRNA codons.

Sex-lethal (Sxl) protein

Intronic splicing silencer in female Drosophila.

Tra protein

Promotes specific Dax splicing in females.

Dsx transcription factor

Regulates sex-specific gene expression.

Female Dsx isoform

Activates genes for female characteristics.

Male Dsx protein

Represses genes for female characteristics.

Premature stop codon

Results from exon 3 inclusion in males.

Cooperative binding

Tra and SR proteins activate female splicing.

Cleavage/polyadenylation

Occurs at 3' end of exon 4.

Developmental stages

Different mRNA forms arise during organism development.

Single-stranded RNA path

Path through the exosome for RNA processing.

Rrp6 and Rrp47

Heterodimer associates with exosome core.

Catalytically active exosome

10-subunit complex with active RNA processing.

Chicken cochlea

5-mm tube with auditory hair cells for sound frequency.

Auditory hair cells

Neurons responding to specific sound frequencies.

Ca2+-activated K+ channel

Channel opening regulated by intracellular Ca2+ levels.

Transmembrane α helices

Seven helices forming the structure of K+ channels.

Cytosolic domain

Part of the channel that regulates its opening.

Channel isoforms

Different versions of channels from alternative splicing.

mRNP exporter

Facilitates mRNA transport across nuclear pore complex.

Nuclear pore complex (NPC)

Structure allowing mRNA transport from nucleus.

Exonic splicing enhancers (ESEs)

Sequences aiding in exon recognition during splicing.

SR proteins

Proteins that bind to ESEs for splicing.

Pre-mRNA

Mature mRNA precursor before splicing.

Exons

Coding regions of pre-mRNA, average 150 bases.