Gene Control Exam II

What does sodium bisulfite treatment reveal about DNA methylation?

Unmethylated cytosines are converted to uracil (read as thymine in sequencing), while methylated cytosines remain cytosine. Think: "Bisulfite burns the unmethylated Cs."

Which enzyme maintains DNA methylation after replication?

Dnmt1 — it “remembers” methylation patterns like a photocopier maintaining old marks.

Which enzymes perform de novo methylation?

Dnmt3α and Dnmt3β — these “start from scratch,” establishing new methylation

CpG methylation in promoter regions typically results in:

Gene silencing or transcriptional repression — think: “CpG = Cages Promoter Genes.”

Which enzymes demethylate DNA?

TET enzymes and DNA repair systems — they “scrub” methyl marks to reactivate genes.

What is the relationship between H3K9 methylation and DNA methylation?

H3K9me recruits HP1 → recruits Dnmt → leads to DNA methylation — histone and DNA silencing reinforce each other.

What does histone acetylation generally do?

It activates gene expression by loosening chromatin; acetyl groups remove positive charge → less DNA-histone grip → open chromatin.

Which enzymes add acetyl groups to histones?

HATs (Histone Acetyltransferases) like CBP and p300 — think “HATs turn genes ON (like caps-lock).”

Which enzymes remove acetyl groups and repress transcription?

HDACs (Histone Deacetylases) — think “HDAC = Hide DNA Access.”

Which histone modification is a hallmark of Polycomb-mediated repression?

H3K9 or H3K27 methylation — both condense chromatin for long-term silencing.

Which modification is linked to Trithorax activation?

H3K4 methylation — think “4ward = activate.”

What does H2B ubiquitination at lysine 120 lead to?

It promotes methylation of H3K4 and H3K79 → gene activation.

What does H2A ubiquitination usually do?

Represses transcription.

What does glycosylation of H2B at S112 do?

Opens chromatin and enhances transcription by recruiting ubiquitin ligase for H2B K120 — think: “Sugar opens the door.”

What is the “histone code hypothesis”?

Specific histone modifications form a combinatorial code recognized by proteins that control gene expression.

Match histone modification with the domain that recognizes it.

Methylated lysine → Chromodomain; Acetylated lysine → Bromodomain; Phosphorylated serine → SH2 domain.

What is the key idea of histone cross-talk?

One modification influences another (e.g., phosphorylation can trigger acetylation) — think “histones gossip.”

Define genomic imprinting.

Expression of only one parental allele due to epigenetic silencing of the other; e.g., Prader–Willi and Angelman syndromes.

Which enzymes or RNAs mediate X-chromosome inactivation (XCI)?

XIST RNA coats one X → recruits Polycomb complexes (PRC1/2) → silences that X.

What does TSIX RNA do in XCI?

It blocks XIST expression, keeping that X chromosome active.

After XIST coats the X chromosome, what happens next?

Recruitment of Polycomb repressive complexes (PRC1/2) to silence gene expression.

What principle does the bee caste system exemplify?

Epigenetic regulation can create phenotypic diversity without genetic variation — same DNA, different “epigenetic software.”

What is the polyadenylation signal sequence for transcription termination?

AAUAAAA — think “AAA = polyA tail start signal.”

Which DNA elements are part of the core promoter?

TATA box, TFIIB recognition element (BRE), and downstream promoter element (DPE).

Which DNA element is not part of the core promoter?

Homeodomain — that’s a protein motif, not DNA.

What does TFIID do?

Recognizes TATA box via TBP and TAFs; essential for preinitiation complex assembly.

True or False”” “TFIID cannot adjust to various promoter architectures”

false, it is highly flexible.

What is transcriptional pausing and why is it useful?

A temporary halt of RNA polymerase II to allow recruitment of factors and proofreading of nascent RNA — like pausing to check your work mid-sentence.

What structural DNA feature links initiation and termination sites?

A looped DNA configuration — brings start and end close to recycle RNA Pol II efficiently.

What are enhancers?

Distal regulatory DNA sequences that bind activators to boost transcription; they can be upstream, downstream, or in introns.

What are silencers?

Regions that bind repressors, often via Polycomb complexes, to reduce transcription.

When pioneer transcription factors bind to closed chromatin, what happens?

They recruit chromatin remodelers and histone modifiers — “pioneers crack open the door for others.”

What are transcription factories?

Nuclear hubs where multiple active genes (even from different chromosomes) are transcribed together by shared RNA Pol II — like coworking spaces for genes.

How are enhancers detected experimentally?

By ChIP-seq or reporter gene assays showing increased expression when enhancer DNA is present.

Which statement about the helix-turn-helix (HTH) motif is correct?

The recognition helix fits into the major groove and makes sequence-specific contacts — classic in bacterial repressors and homeodomain proteins.

What is a POU domain?

A bipartite DNA-binding domain found in transcription factors like Oct4; helps recognize specific enhancer motifs.

What are C2H2 and C4 zinc-finger motifs?

Protein motifs stabilized by zinc ions that bind DNA; C2H2 is common in eukaryotic TFs (like Zif268).

What is a leucine zipper?

A dimeric coiled-coil domain where leucines align every 7th position; binds DNA as a “zipper” (e.g., AP-1).

What is a helix-loop-helix (HLH) motif?

Domain that allows dimerization and DNA binding; regulates tissue-specific genes (e.g., MyoD in muscle).

What is a homeodomain?

A type of HTH domain found in developmental TFs that determine body patterning — “homeotic genes = body home plan.”

What does a reporter gene assay measure?

Promoter or enhancer activity by linking it to a measurable reporter (like luciferase or GFP).

What does EMSA (Electrophoretic Mobility Shift Assay) show?

Protein–DNA binding; bound complexes migrate slower in gel.

What does DNase I sensitivity assay test?

Chromatin accessibility — open chromatin is DNase-sensitive and therefore active

, closed chromatin is resistant to DNase and therefore inactive

What does ChIP (Chromatin Immunoprecipitation) detect?

Protein–DNA interactions or specific histone modifications in chromatin.

How do histone modifications and DNA methylation coordinate gene silencing?

H3K9 methylation → recruits HP1 → recruits Dnmt → methylates nearby DNA → reinforces heterochromatin.

How can epigenetic states be reversed?

Through TET-mediated demethylation or HAT-mediated acetylation — “erasers” of epigenetic marks.

Why are epigenetic changes inheritable yet reversible?

They pass through cell division (via maintenance enzymes) but can be reset by environmental or developmental cues — think of them as “software updates” to DNA’s “hardware.”

What’s the difference between transcriptional activators and repressors in terms of chromatin?

Activators recruit HATs and remodelers → open chromatin; repressors recruit HDACs and Polycomb → compact chromatin.

What do enhancers and silencers have in common?

Both are bound by regulatory proteins that influence transcription rate, regardless of distance or orientation.