Transcription Regulation in RNA Polymerase II

Molecular Mechanisms of Disease

• This course, HSS2305, covers molecular mechanisms of disease.
• The diagrams and lecture content refer to cell structure and processes.
• The course material moves through eukaryotic gene transcription and translation.
• A central dogma is described: DNA, transcription, RNA, translation, and protein.

Eukaryotic Gene Transcription and Translation

• Eukaryotic gene transcription and translation are key topics.
• Transcription is the process of creating mRNA from DNA.
• Translation converts mRNA into proteins.
• A detailed process of transcription and translation was presented.
• Post-transcriptional modifications to mRNA were noted.

From Genes to Proteins overview

• The Central Dogma of molecular biology (DNA --> RNA--> Protein) is described through a diagram.
• The process of mRNA synthesis from DNA template is emphasized.
• RNA polymerase is a key enzyme in transcription.
• The process of translation, converting mRNA to protein, is discussed with a diagram.

From Genes to Proteins (Complex) Overview

• A more complex depiction of the process is shown.
• mRNA, post-transcriptional modification, translation, ribosomal proteins, cytosol and others are visible.
• A diagram shows the nucleus and cytosol with the movement of mRNA during translation, as well as other elements like tRNA and ribosomes.

Protein Synthesis (Video)

• A video presentation discussing protein synthesis (DNA, transcription, translation) and folding was referenced.
• The video is identified with a URL.

Transcription (Summary)

• Transcription is the synthesis of RNA from a DNA template within the nucleus.
• Starting material includes DNA, RNA polymerase II, and transcription factors.
• The end product is messenger RNA.

Translation (Summary)

• Translation is the synthesis of proteins from mRNA in the cytoplasm.
• Starting material includes mRNA, ribosomal RNA, transfer RNA, and ribosomal proteins.
• The end product is a polypeptide.

Sense vs Antisense DNA Strands

• The coding strand's sequence is identical to the mRNA sequence, except for uracils replacing thymines.
• The template strand is the opposite strand.

Transcription (General)

• Both DNA strands encode genes.
• The DNA strand of a gene has ~3.6 x 10^4 base pairs.
• Several other important elements or factors for transcription are referred to.

Transcription - RNA Polymerase

• RNA polymerase binds to DNA and initiates transcription at promoter regions.
• It incorporates nucleotides into an RNA strand complementary to the DNA template strand.

Eukaryotic RNA Polymerases

• Prokaryotes use single RNA polymerase for transcription of all types of RNA.
• Eukaryotes use three different RNA polymerases (I, II, and III) in transcription.
• Specific RNA polymerases have unique roles.
• Enzymes and molecules required for initiation and more are discussed.

Eukaryotic Transcription - RNA Polymerase

• RNA polymerase is DNA-dependent, RNA polymerase, and synthesizes RNA from DNA in the 5' to 3' direction.
• A diagram shows elements like Enhancer sites (-50,000 to + 50,000), proximal elements, and core promoters.
• other important elements like BRE, TATA box, Inr, and DPE are named.

Eukaryotic Transcription

• Transcription factors, general and specific factors,
• TFII (A,B,D,E,F,H)
• TBP (TATA binding protein) and TAFs (TBP-associated factors) are presented as important elements.
• The need for the initiation complex (PIC) is noted.

Gene Promoter Overview

• The promoter region is a site on DNA where RNA polymerase binds for transcription initiation.
• It dictates which strand acts as the template (anti-sense) for mRNA creation.
• Specific sequences (sometimes referred to as elements) within the promoter region are highlighted. (ex. core and proximal)

Eukaryotic Transcription Core Promoter

• Core promoters contain elements like the TATA box or initiator sequence (INR) and others.
• Consensus sequences within the promoter motifs, (e.g., BRE, TATA, Inr, and DPE) are shown.
• Their locations, relative to the start site, and function in eukaryotic transcription.

Eukaryotic Transcription - Core Promoter Elements

• The initiator elements (INR) overlap with transcription start sites.
• Consensus sequences for the elements like (e.g., YYANWYY,
• Downstream promoters, for instance, RGWYV(T)
• Elements and factors for promoter regions are detailed.

Eukaryotic Transcription - Proximal Promoter Elements

• Proximal promoter elements contain specific binding sites (e.g., CAAT box, GC box) for transcription factors.

Eukaryotic Transcription - Enhancer Regions

• Enhancer regions can be located far from the promoter and can increase transcriptional activity.

Eukaryotic Transcription - Pre-Initiation Complex (PIC)

• A large, multi-protein complex that forms at the promoter prior to transcription initiation.
• Various components like TBP, TAFs, TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH are identified.

Eukaryotic Transcription - Formation of PIC

• Stages in PIC formation are presented with diagrams, showing the roles of TFII(Bs, etc.) factors to initiate the formation of the PIC and position RNA polymerase at gene start sites.

Eukaryotic Transcription - Initiation

• Transcription initiation involves the formation of a phosphodiester bond between the first two nucleotides of the RNA transcript.
• RNA polymerase continues moving along the DNA template.

Eukaryotic Transcription- Elongation

• Extension of the RNA molecule using a DNA template is shown.
• RNA polymerase incorporating new nucleotides.
• The DNA-RNA hybrid and supercoils are described.
• Topoisomerases play a role here.

Eukaryotic Transcription - Elongation Factors

• Various elongation factors (like P-TEFb and others) influence the elongation process.
• They regulate the rate and accuracy of transcription.

Eukaryotic Transcription - Termination

• Termination is described including sequences in prokaryotic and eukaryotic cells.
• Processing steps and the addition of adenines (polyadenylation) to form the 3' tail of mRNA are described.