Gene Transcription and Regulation Quiz

Gene Expression: From DNA to RNA

• Gene expression is the process of producing RNA and proteins from a gene
• DNA stores and transmits genetic information
• Proteins catalyse essential chemical reactions
• RNA has a catalytic function, ribozymes, in cutting/binding sequences and replication
• RNA's role has shifted from catalyst to primarily information storage and transfer, but different types of RNA play diverse roles

Intended Learning Outcomes (ILOs)

• Describe the structure of eukaryotic genes
• List and compare the main RNA classes and RNA polymerases
• Outline the stages of eukaryotic transcription
• Explain the function of promoters and enhancers/silencers
• Define RNA processing and the concept of alternative splicing

The Flow of Information

• DNA synthesis (DNA replication)
• RNA synthesis (transcription)
• Protein synthesis (translation)
• This is the central dogma of molecular biology

The Transcription Unit

• Regions of a gene include a promoter, RNA coding region and a terminator.
• The first transcribed nucleotide is numbered +1.
• Promoter region contains information on frequency/level of transcription.

The Basis of Transcription

• Transcription copies DNA to RNA
• All three major RNA classes (mRNA, tRNA, rRNA) are involved in protein synthesis
• Gene expression in eukaryotes is a multistage and compartmentalised process

Three Main RNA Classes

• Messenger RNA (mRNA)
• Ribosomal RNA (rRNA)
• Transfer RNA (tRNA)

The Toolkit of Transcription

• Starting DNA template
• Transcription unit (promoter, RNA sequences)
• Machinery for transcription (enzymes, proteins)
• Transcription starts in a bubble and occurs in the 5' to 3' direction.
• The template strand is used to produce the RNA transcript.

RNA Polymerase - An Enzyme

• RNA polymerase synthesizes RNA using a DNA template.
• Transcription proceeds from 5' to 3' on the template strand (3' to 5' on the non-template strand).

The Transcription "Christmas Tree"

• The image displays a complex molecular structure in transcription.

Transcription Unit

• Promoter, RNA coding region, and terminator regions make up a transcription unit.
• Transcription starts at +1 nucleotide. The template strand and non-template strand are identified.

Stages of Transcription

• Initiation involves recognizing and binding to the promoter.
• DNA unwinds
• Elongation involves polymerase moving along the template strand synthesizing RNA.
• Termination involves polymerase dissociating at the end of the transcription unit.

Key Players in Transcription

• Chromatin structure modification (by regulatory proteins near the promoter) makes DNA accessible.
• RNA polymerase is an enzyme for transcription
• Transcription factors, mediator complex, and cis DNA elements (promoters, regulatory DNAs) are involved.

Regulation of Transcription Initiation (i and ii)

• Eukaryotic RNA polymerase cannot recognize DNA sequence on its own; regulatory proteins are required.
• Regulatory proteins bind to DNA to change chromatin structure
• RNA polymerase II + general transcription factors + mediator = basal apparatus
• Regulatory promoters (up/down stream) bind transcription factors, allowing enhancers/silencers to regulate transcription.
• Many proteins are involved in the entire transcription machine
• DNA/RNA pol II conformational change exposes single-strand DNA and unwinds a short stretch.

Different Types of RNA Polymerases

• Three main RNA polymerases in eukaryotes: I, II, and III
• Different polymerases bind to different promoters/transcribe different genes.
• RNA polymerase II transcribes genes encoding proteins.

RNA Polymerase II Promoters

• Core promoter and a regulatory promoter.
• Special sequences such as: TATA box, BRE, INR, DPE etc., are recognized by TFs
• Transcription factors bind to these initiation sequences facilitating RNA polymerase positioning to start point/transcription.

The Intervening Sequences: Introns

• Introns are non-coding regions within genes, absent in mature mRNA.
• Introns are typically present in eukaryotes
• Intron size/number correlates with complexity of the organism.

The Structure of mRNA

• 5' cap (modified guanine nucleotide)
• Coding regions / Exons
• Poly(A) tail (adenine nucleotides)
• Modification after transcription, e.g., 5' cap, poly(A) tail, splicing
• mRNA stability / translation regulation

Alternative Splicing

• The same DNA molecule can be spliced in various ways, producing different mRNA products and proteins.

RNA Transport from Nucleus to Cytoplasm

• mRNA processing, maturation, and assembly with export factors occurs.
• Proteins escort mRNA from nucleus for translation in cytoplasm

Nuclear Export of mRNA

• mRNA export is a complex process requiring multiple regulatory proteins.

Splicing

• The process that removes introns before mRNA translation.
• Introns are removed and exons joined.
• Spliceosome (RNA and proteins) facilitates the splicing process.
• Splicing is a two-step process.

The Royal Disease (Haemophilia)

• An intronic mutation in factor IX leading to incorrect splicing can cause haemophilia.

DNA Replication Analogy (with transcription) and differences

• Analogy with DNA replication involves use of DNA template to generate a copy.
• Differences exist in the enzymes, substrates/products.

Colinear or not colinear?

• Colinearity suggests a DNA sequence proportional to a protein's amino acid sequence.
• Evidence from studies contradict this, implying non-colinearity in some cases.

Abortive Initiation

• Likely to be a rate-limiting control on gene activation
• After synthesis of a ~9-12nt long strand, elongation begins.
• When the transcript is around 30 nt long, RNA polymerase II leaves the promoter region.

Termination

• RNA Pol II lacks specific termination sequences and may continue after stopping transcription.
• mRNA is degraded (e.g., by Rat1) once it forms after reaching a sequence.