Bioc 406 Lecture 18 DNA Transcription II & Epigenetics

Contrast the spatial location of transcription and translation in eukaryotes.

Transcription occurs in the nucleus, while translation occurs in the cytoplasm.

In which type of organism are transcription and translation described as 'coupled'?

Bacteria (Prokaryotes)

What is the primary function of a promoter DNA sequence?

It directs the transcription machinery to the transcription start site ($TSS$).

Where is the eukaryotic TATA box typically located relative to the transcription start site?

At the -25 position.

Unlike promoters, where can eukaryotic enhancers be located relative to a gene?

They can be upstream, downstream, or even within the gene.

Which proteins bind to enhancers to stimulate transcription by stabilizing bound RNA Polymerase?

Activators

How do repressors bound to enhancers inhibit transcription?

By blocking RNAP binding.

Which specific general transcription factor (GTF) contains the TATA-binding protein (TBP)?

TFIID

What structural change does TBP induce in DNA to facilitate melting?

It bends the DNA sharply.

Which general transcription factor binds directly to TBP during the assembly of the pre-initiation complex?

TFIIB

Which general transcription factor contains helicase subunits (Rad3 and Ssl2) and a kinase subunit (TFIIK)?

TFIIH

What is the specific target of the kinase subunit TFIIK within the transcription machinery?

The RNA Pol II C-terminal domain (CTD).

Approximately how many repeats of the heptapeptide consensus are found in the human RNA Pol II CTD?

52 repeats.

Phosphorylation of which residue on the CTD is specifically associated with promoter escape?

Serine 5 (Ser5-P)

The recruitment of RNA processing factors and elongation is linked to the phosphorylation of which CTD residue?

Serine 2 (Ser2-P)

Which factor is responsible for phosphorylating Ser on the RNA Pol II CTD to promote elongation?

Positive Transcription Elongation factor b ($P-TEFb$)

At what stage of transcription is the 7-methylguanosine cap added to the 5' end of the pre-mRNA?

While elongation is still in progress.

What methyl donor is required by RNA (guanine-N7)-Methyltransferase (N7MTase) to complete the 5' cap?

S-Adenosyl methionine (SAM)

What are the two main biological functions of the 5' cap on mRNA?

Protection from degradation and assistance in ribosome binding for translation.

What specific hexameric sequence serves as the polyadenylation signal in eukaryotic genes?

AAUAAA

Where does Poly(A) polymerase add the poly(A) tail relative to the AAUAAA signal?

5 to 25 nucleotides downstream.

Describe the 'torpedo' mechanism of transcription termination in eukaryotes.

A 5' to 3' exonuclease chases and catches the RNA Polymerase II after the mRNA is cleaved.

How does the poly(A) tail facilitate the mature mRNA's function?

It protects against degradation, aids cytoplasmic export, and assists in translation initiation.

Define 'Epigenetics' as it relates to gene expression.

The study of heritable phenotype changes that do not involve alterations in the DNA sequence.

Which large complex bridges activators at distant enhancers to the transcription initiation factors at the promoter?

The Mediator complex

Which enzymes act as 'Writers' by adding acetyl groups to histone tails to relax chromatin?

Histone acetyltransferases (HATs)

Which class of enzymes acts as 'Erasers' for histone acetylation, leading to transcription being 'Off'?

Histone deacetylases (HDACs)

What energy source is required by chromatin remodeling factors to move nucleosomes?

ATP

Identify two specific histone methylation marks associated with active transcription ('On').

H3K4me and H3K36me

Identify three specific histone acetylation marks associated with active transcription ('On').

H3K27ac, H4K12ac, and H4K8ac

Which histone modification establishes facultative heterochromatin?

H3K27me3

Which histone modification is the hallmark of constitutive heterochromatin?

H3K9me3

What are the three core subunits of the PRC2 complex?

SUZ12, EED, and EZH1/2.

Within PRC2, which subunit acts as the 'Writer' for H3K27 methylation?

EZH2 (or EZH1)

Which PRC2 subunit acts as the 'Reader' by binding to H3K27me3?

EED

What is the biological significance of the 'write-read mechanism' during cell division?

It is critical for re-establishing repressive chromatin domains in daughter cells.

Which enzyme converts Cytosine into 5-methylcytosine in a CpG dinucleotide?

DNA methyltransferase (DNMT

Which family of enzymes acts as 'Erasers' for DNA methylation?

TET methylcytosine dioxygenases (TETs)

Why is DNA methylation typically considered a repressive modification?

It promotes a 'Transcription OFF' state by facilitating chromatin condensation.

Contrast the gene content of constitutive versus facultative heterochromatin.

Constitutive contains repetitive regions and transposable elements, while facultative contains developmental and signaling genes.

Which modification to the DNA itself is described as a 'repressive modification' to transcription?

Cytosine methylation

The formation of the 'Open PIC' from the 'Closed PIC' is triggered by the addition of which molecule?

ATP

Which general transcription factor contains subunits that bend the DNA to facilitate melting?

TFIID (specifically the TBP subunit).

According to the slide on chromatin remodeling, how is a promoter sequence 'hidden' or 'exposed'?

By moving nucleosomes along the DNA fiber.

Which type of RNA polymerase is responsible for transcribing protein-coding genes in eukaryotes?

RNA Polymerase II (RNAP II)

Which general transcription factors remain associated with the promoter as the elongation complex moves forward?

Initiation factors

The 'initially transcribing complex' converts into the 'elongation complex' following the recruitment of which factors?

Elongation factors

Which histone modification establishes heterochromatin in repetitive regions?

H3K9me3

The Mediator complex facilitates 'Transcription initiation' by interacting with which two main entities?

Activators at enhancers and general transcription factors at the promoter.

What is the specific numeric coordinate assigned to the first nucleotide of the transcribed mRNA?

+1 (or Transcription Starting Site (TSS)).

What term describes a gene that is 'On' and actively being transcribed in terms of chromatin state?

Decondensed chromatin (or Euchromatin).