Transcription in Eukaryotes: RNA Classes, Promoters, and Initiation Complexes

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Transcription in Eukaryotes

Classes of RNA in Eukaryotes

Eukaryotic cells produce a diverse array of RNA molecules, each with distinct structural and functional properties. These RNAs are classified based on their roles in gene expression and cellular function.

Messenger RNA (mRNA): Serves as the intermediary between DNA and protein synthesis; only RNA type translated into protein.
Transfer RNA (tRNA): Delivers amino acids to the ribosome during translation.
Ribosomal RNA (rRNA): Structural and enzymatic component of ribosomes.
Small Nuclear RNA (snRNA): Involved in pre-mRNA splicing within the nucleus.
Small Nucleolar RNA (snoRNA): Modifies rRNA and tRNA, found in nucleoli.
Micro RNA (miRNA): Regulates gene expression post-transcriptionally by repressing translation.
Small Interfering RNA (siRNA): Silences target mRNA by degradation.
Long Noncoding RNA (lncRNA): Regulates transcription, pre-mRNA processing, and protein function.
Piwi-interacting RNA (piRNA): Silences transposons.

Table of RNA species and their functions

RNA Lengths: Functional RNAs vary in length, from short miRNAs (~19–23 nt) to long lncRNAs (>200 nt).

Table of noncoding RNA lengths

Structural Diversity: Each RNA class has a unique structure suited to its function.

Diagram of RNA classes and their structures

Differences Between Transcription in Bacteria and Eukaryotes

Transcription mechanisms differ significantly between prokaryotes and eukaryotes, reflecting their cellular organization and complexity.

Cellular Compartmentalization: In prokaryotes, transcription and translation occur in the same compartment; in eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm.
RNA Polymerase Types: Prokaryotes have a single RNA polymerase; eukaryotes have three (Pol I, II, III).
Gene Organization: Prokaryotic genes are often in operons; eukaryotic genes are usually single transcription units.
Promoter Function: Prokaryotic promoters bind RNA polymerase directly; eukaryotic promoters bind transcription factors that regulate polymerase access.

Comparison of prokaryotic and eukaryotic transcription and translation

Eukaryotic RNA Polymerases

Eukaryotes utilize three distinct RNA polymerases, each responsible for transcribing specific classes of genes.

RNA Polymerase I: Transcribes most rRNA genes.
RNA Polymerase II: Transcribes protein-coding genes (mRNA) and most snRNA genes.
RNA Polymerase III: Transcribes tRNA, 5S rRNA, and some snRNA genes.

Subunit Composition: Eukaryotic RNA polymerases are structurally more complex than their bacterial counterparts, with additional subunits.

Table comparing RNA polymerase composition in bacteria, archaea, and eukarya

Geography of Transcription

Gene Structure and Nomenclature

The structure of a gene includes several key regions that define the transcription process:

Promoter: Located upstream (5') of the transcription start site; controls RNA polymerase access.
Coding Region: Contains the information for the functional product (RNA or protein).
Termination Region: Located downstream (3') of the coding region; regulates transcription cessation.
+1 Nucleotide: The first nucleotide transcribed into RNA.

Diagram of gene structure and transcription geography

Sense and Antisense Strands

During transcription, the DNA template (antisense/non-coding) strand is read by RNA polymerase, while the coding (sense) strand has the same sequence as the resulting RNA (except for uracil replacing thymine).

Template (Antisense) Strand: Used as the template for RNA synthesis.
Coding (Sense) Strand: Matches the RNA sequence.

Diagram showing sense and antisense strands in transcription Overview of the transcription complex

Promoter Elements and Transcription Factors

Promoter Sequence Elements

Promoters for RNA Polymerase II are diverse, but three elements are commonly found:

TATA Box: Consensus sequence 5'-TATAAA-3', located at -25.
CAAT Box: Often found near -80.
GC-rich Box: Consensus sequence 5'-GGGCGG-3', located at -90 or further upstream.

Diagram of promoter elements: TATA, CAAT, GC-rich boxes

Promoters display variability in the number, type, and location of these elements.

Comparison of promoter elements in different genes

Transcription Factors

Transcription factors are proteins that bind promoter elements and regulate the accessibility of RNA polymerases:

General Transcription Factors: Required for most genes; present in all cells.
Specific Transcription Factors: Regulate expression of specific genes in a tissue- or time-specific manner.

Assembly of Transcription Initiation Complexes

Class II (RNA Polymerase II) Initiation Complex

The assembly of the transcription initiation complex at RNA Pol II promoters is a stepwise process:

Step 1: TFIID (containing TBP and TAF) binds the TATA box, forming the initial committed complex.

TFIID binding to TATA box

Step 2: TFIIA, TFIIB, TFIIF, and RNA Pol II join to form the minimal initiation complex.

Minimal initiation complex assembly

Step 3: TFIIE and TFIIH join, forming the preinitiation complex (PIC).
Step 4: RNA Pol II is directed to the +1 position to begin RNA synthesis.

Preinitiation complex and transcription start

These factors are collectively known as "general transcription factors."

Enhancer and Silencer Sequences

Enhancers and silencers are regulatory DNA elements that modulate gene expression at a distance:

Enhancers: Increase transcription by binding activator proteins and coactivators, forming a protein bridge to the promoter complex.
Silencers: Repress transcription by binding repressor proteins, inducing DNA bends that reduce gene expression.

Enhancer sequence function Protein bridge between enhancer and promoter Enhancer location relative to gene

Class I and Class III Transcription Initiation Complexes

Class I (RNA Polymerase I) Initiation Complex

RNA Pol I transcribes rRNA genes located in the nucleolus. Promoters recognized by Pol I have two functional elements:

Core Element: Spans -45 to +20; required for initiation; bound by SL1 protein.
Upstream Control Element: Spans -100 to -150; increases transcription; bound by UBF1.

Core and upstream control elements in Pol I promoters Assembly of Pol I initiation complex

Class III (RNA Polymerase III) Initiation Complex

RNA Pol III transcribes tRNA, 5S rRNA, and some snRNA genes. Promoter elements differ by gene type:

snRNA Genes: Have upstream elements (TATA box, PSE, OCT).
5S rRNA and tRNA Genes: Have internal control regions (ICRs) downstream of transcription start, called box A and box B (tRNA) or box A and box C (5S rRNA).

Promoter elements in snRNA genes Internal control regions in 5S rRNA genes Internal control regions in tRNA genes

Transcription factors (TFIIIA, TFIIIC, TFIIIB) bind these elements and recruit RNA Pol III to initiate transcription.

Termination of Transcription

Termination Mechanisms

Each eukaryotic RNA polymerase utilizes a distinct mechanism for transcription termination:

RNA Pol III: Terminates at a sequence creating a string of uracils, similar to E. coli, but without a stem-loop structure.
RNA Pol I: Terminates at a 17-bp consensus sequence that binds transcription-terminating factor 1 (TTF1).

Summary Table: RNA Classes and Functions

RNA Species	Established Function(s)
mRNA	Messenger for protein production
tRNA	Translation of RNA codon to amino acid
rRNA	Enzymatic and structural part of ribosomes
snRNA	Pre-mRNA processing
snoRNA	Modification of rRNA
miRNA	Repression of translation
piRNA	Silencing of transposons
lncRNA	Regulation of transcription, pre-mRNA processing, miRNA abundance, and protein function

ncRNAs	Length
tRNAs	74–95 nt
rRNAs	121–5000 nt
snRNAs	100–300 nt
snoRNAs	100–300 nt
gRNAs	55–70 nt
miRNAs	19–23 nt
piRNAs	24–30 nt
siRNAs	21–25 nt
lncRNAs	>200 nt

Additional info: These notes cover the molecular biology of transcription in eukaryotes, including RNA classes, promoter elements, transcription factors, and the assembly of initiation complexes, directly relevant to genetics college courses (Ch. 8, Ch. 13).