Gene Transcription and RNA Modification Overview

Transcription

Process of copying DNA into RNA.

Gene

Segment of DNA encoding functional products.

Central Dogma

Flow of genetic information: DNA to RNA to protein.

Template Strand

DNA strand used for RNA synthesis.

Coding Strand

DNA strand identical to RNA transcript, except thymine.

Transcription Factors

Proteins that regulate transcription initiation.

Promoter

DNA sequence that initiates transcription.

Open Complex

Denatured DNA bubble during transcription initiation.

RNA Polymerase

Enzyme synthesizing RNA from DNA template.

Elongation

Synthesis phase of RNA transcript formation.

Termination

Process where RNA synthesis ends and dissociates.

Transcription Start Site (TSS)

Location where transcription begins on DNA.

Consensus Sequence

Most common promoter sequence for high expression.

-35 and -10 Sequences

Specific promoter regions important for transcription.

E. coli

Bacterium used for studying transcription mechanisms.

RNA Transcript

Complementary RNA copy of the DNA template.

Denaturation

Separation of DNA strands during transcription initiation.

Functional Product

Result of gene expression, either RNA or polypeptide.

Gene Expression

Process of using gene information to produce products.

Regulatory Sequences

DNA elements controlling transcription levels.

Bacteriophage

Virus that infects bacteria, used in transcription studies.

RNA Synthesis

Formation of RNA from a DNA template.

RNA polymerase holoenzyme

Complex of core enzyme and sigma factor.

Core enzyme

Composed of five subunits: α2ββ'ω.

Sigma factor

Single subunit that aids in promoter recognition.

Promoter

DNA sequence where RNA polymerase binds to initiate transcription.

Closed complex

Formed when RNA polymerase binds to the promoter.

Open complex

Created when TATAAT box unwinds during transcription.

TATAAT box

Part of the -10 sequence crucial for unwinding.

Antisense strand

Template DNA strand for RNA synthesis.

Coding strand

Non-template DNA strand with same sequence as RNA.

RNA transcript

Newly synthesized RNA molecule during transcription.

Elongation phase

Stage where RNA strand lengthens during transcription.

3' to 5' direction

Direction RNA polymerase reads the template strand.

5' to 3' direction

Direction RNA is synthesized using nucleotides.

Nucleoside triphosphates

Building blocks used for RNA synthesis.

Pyrophosphate release

Byproduct of RNA synthesis during elongation.

RNA-DNA hybrid

Temporary structure formed during RNA synthesis.

Termination

End of RNA synthesis, releasing RNA and polymerase.

Rate of RNA synthesis

Approximately 43 nucleotides per second.

Helix-turn-helix structure

Region in sigma factor for tighter DNA binding.

Direction of transcription

Specified by promoter, varies for adjacent genes.

Open complex length

About 17 bases long during transcription.

Rho-dependent termination

Requires rho protein for transcription termination.

Rho-independent termination

Does not require rho protein for termination.

Uracil-rich sequence

Located at the 3' end of RNA.

Stem-loop structure

Forms upstream of uracil-rich sequence.

Eukaryotic transcription complexity

More complex due to larger cells and multicellularity.

RNA polymerase I

Transcribes all rRNA genes except 5S rRNA.

RNA polymerase II

Transcribes protein-encoding genes and some snRNA.

RNA polymerase III

Transcribes tRNA, 5S rRNA, and microRNA genes.

Core promoter

Short DNA sequence influencing transcription start.

TATA box

Common element in core promoters for transcription.

Basal transcription

Low level of transcription from core promoter alone.

Regulatory elements

Short DNA sequences affecting RNA polymerase binding.

Transcription factors

Proteins that influence transcription rate by binding elements.

Enhancers

Regulatory elements that stimulate transcription.

Silencers

Regulatory elements that inhibit transcription.

Cis-acting elements

DNA sequences affecting only specific genes.

Trans-acting factors

Regulatory proteins binding to DNA sequences.

General transcription factors (GTFs)

Proteins required for basal transcription at promoters.

Mediator complex

Mediates interactions between RNA pol II and factors.

Basal transcription apparatus

RNA pol II plus five GTFs for transcription.

Open complex formation

Initial step in transcription involving RNA polymerase.

Transcriptional start site

Location where transcription begins in the core promoter.

Rho-dependent termination

Termination requiring the rho protein for RNA synthesis.

Rho-independent termination

Termination without rho, using RNA sequences.

Uracil-rich sequence

A sequence at RNA's 3' end aiding termination.

Stem-loop structure

RNA structure upstream of uracil-rich sequence.

Core promoter

Short DNA sequence essential for transcription initiation.

TATA box

Common core promoter element for transcription start.

Basal transcription

Low-level transcription from the core promoter alone.

Regulatory elements

DNA sequences influencing RNA polymerase binding.

Transcription factors

Proteins that bind regulatory elements to modulate transcription.

Enhancers

Regulatory elements that stimulate gene transcription.

Silencers

Regulatory elements that inhibit gene transcription.

Cis-acting elements

DNA sequences affecting only nearby genes.

Trans-acting factors

Proteins that bind to cis-acting elements.

General transcription factors (GTFs)

Proteins required for RNA polymerase II transcription.

Mediator complex

Protein complex mediating interactions for transcription regulation.

Open complex formation

Initial step in transcription where DNA unwinds.

Basal transcription apparatus

RNA pol II and GTFs required for transcription.

RNA polymerase II subunits

Composed of 12 subunits for transcription activity.

TFIID

Complex of TBP and TAFs; binds TATA box.

TBP

TATA-binding protein; essential for transcription initiation.

TAFs

TBP-associated factors; assist TBP in promoter recognition.

TFIIB

Binds TFIID; enables RNA polymerase II binding.

TFIIF

Facilitates RNA polymerase II binding to TFIIB.

TFIIE

Maintains open complex; aids TFIIH binding.

TFIIH

Multisubunit protein; helicase and kinase activities.

CTD

Carboxyl terminal domain; phosphorylated during transcription.

Mediator

Multisubunit complex; links regulatory factors to RNA polymerase II.

Open Complex

Formation of unwound DNA for transcription initiation.

Phosphorylation

Addition of phosphate group; regulates protein activity.

Helicases

Enzymes that unwind DNA during transcription.

Core Promoter

Region where transcription factors bind to initiate transcription.

Regulatory Transcription Factors

Proteins that influence gene expression via mediator.

Elongation Phase

Stage where RNA polymerase synthesizes RNA strand.

Subunits

Individual protein components of larger protein complexes.

Cell Type Variability

Different mediator subunits depending on cell conditions.