Gene Control Exam II Cards 2

What is the core idea of epigenetic modification?

Heritable, reversible changes in gene expression without altering the DNA sequence—like “software” running on genetic “hardware.”

Which methods detect DNA methylation and chromatin openness?

DNA methylation: sodium bisulfite or ChIP; Chromatin openness: DNase I sensitivity assay.

What does DNA methylation at CpG islands typically cause?

Gene silencing—methyl groups block transcription factor binding and attract repressors.

Which enzymes perform de novo methylation?

Dnmt3a and Dnmt3b—think “new mark painters.”

Which enzyme maintains methylation during replication?

Dnmt1—“the maintenance worker” that copies methyl marks to daughter strands.

What enzyme initiates demethylation?

TET enzymes convert 5mC to 5OHmC—like “erasers” that oxidize methyl groups.

How does sodium bisulfite sequencing reveal methylation?

Unmethylated cytosines convert to uracil (read as T), while methylated Cs stay C.

What does histone acetylation do to chromatin?

Opens it up—neutralizes histone positive charge, loosening DNA (HATs = “openers”).

What is the function of HATs and HDACs?

HATs (CBP/p300) add acetyl groups → activation; HDACs remove them by phosphorylation → repression.

What recruits HATs and HDACs?

Transcription activators recruit HATs, repressors recruit HDACs.

What histone modification is linked to Polycomb repression?

H3 K9 K27 methylation—creates a landing site for HP1 and chromodomain proteins.

What histone modification activates transcription?

Trithorax proteins demethylate H3 K9 and K27 —> opens chromatin

What does HP1 binding to H3K9me cause?

Heterochromatin formation by recruiting more HMTs—“self-spreading silence.”

What does histone ubiquitination do?

H2A-Ub represses; H2B-Ub activates by promoting H3K4 and H3K79 methylation.

How does histone phosphorylation affect transcription?

Phosphorylation of H3S10 loosens chromatin → promotes acetylation and activation.

What is the histone code hypothesis?

Specific modification combinations recruit specific proteins to regulate transcription outcomes.

What domain recognizes acetylated lysine?

Bromodomain—binds to an acetylated histone better and opens it —> histone activation

What domain recognizes methylated H3 K9?

Chromodomain—binds methylated H3 and inhibits transcription

How do histone and DNA modifications reinforce each other?

H3K9me → recruits HP1 → recruits Dnmt → DNA methylation of H3K3 → stable repression.

What role do lncRNAs play in epigenetic regulation?

They recruit chromatin modifiers (e.g., PRC2) to specific genomic regions—acting as “molecular guides.”

What is the mechanism of X-chromosome inactivation?

XIST Is transcribed which produces → XIST lncRNA which coats one X chromosome, recruiting Polycomb complexes that spread → histone methylation and ubiquitation → heterochromatin (Barr body formation).

What does TSIX do in X-inactivation?

Antisense RNA to XIST—blocks XIST transcription, keeping one X active.

What is genomic imprinting?

Parent-of-origin gene silencing via methylation—one allele (maternal or paternal) is epigenetically silenced.

Which genes are maternally vs. paternally imprinted?

Maternal inactive: IGF2, SMN; Paternal inactive: H19, IGF2R.

What is the imprinting control region (ICR)?

DNA element methylated on one parental allele to control which gene (H19/IGF2) is active.

How does methylation affect CTCF binding in imprinting?

Methylation prevents CTCF binding → activates IGF2 expression on paternal allele.

What is the epigenetic cause of the Agouti mouse color change?

Maternal diet adds methyl groups → methylated Avy gene → black, lean offspring instead of yellow, obese ones.

What principle does the bee caste system illustrate?

Epigenetic regulation drives phenotype differences (queen vs worker) despite identical DNA.

What is the role of MeCP2?

Binds methylated CpG → recruits HDACs → chromatin condensation/repression

What is the relationship between DNA methylation and histone deacetylation?

MeCP2 links the two—methylated DNA recruits HDACs to repress transcription.

What do TET enzymes and OGT do together?

TET oxidates meC → TET+OHMe then recruits OGT → glycosylation of H2B→ ubiquitation of H2B → open chromatin.

Which histone modification is repressive and heritable through division?

H3K9me maintained by HP1-HMT feedback loop.

What is a DNase I hypersensitive site (HS)?

Region of open chromatin accessible to transcription factors—marker of active or regulatory DNA.

What is the function of the SWI/SNF complex?

ATP-dependent nucleosome remodeling → opens chromatin for transcription.

What are pioneer transcription factors?

TFs (like FOXA1) that can bind condensed chromatin to initiate opening for other factors.

What is the hallmark of Polycomb repression?

H3K27me3 and H2A-Ub → compact chromatin, transcriptional silencing.

What is the hallmark of Trithorax activation?

H3K4me3 → recruits chromatin openers (PHD domain proteins like NURF).

Which RNA polymerase transcribes rRNA?

RNA Polymerase I in the nucleolus.

Which polymerase transcribes tRNA and 5S rRNA?

RNA Polymerase III.

Which polymerase transcribes mRNA?

RNA Polymerase II.

What factor binds the TATA box?

TBP (TATA-binding protein), part of TFIID complex.

What are the key steps in RNAP II initiation?

TFIID (TBP+TAFs) → TFIIB → RNA Pol II + TFIIE/F/H → phosphorylation of CTD → elongation.

Which kinase phosphorylates the CTD tail of RNAP II?

TFIIH—its kinase activity triggers elongation.

What is transcriptional pausing and its purpose?

Temporary halt early in elongation (~20–30 nt) to allow RNA capping or factor recruitment.

What signal terminates RNAP II transcription?

AAUAAA polyadenylation signal → cleavage and poly-A tail addition.

What enzyme degrades RNA downstream of termination?

Rat1 exonuclease “chews” the leftover RNA → dislodges RNAP II.

Why does DNA form loops between initiation and termination?

To recycle RNAP II efficiently back to promoters for rapid re-initiation.

What is a transcription factory?

Clustered nuclear sites enriched in RNAP II where active genes congregate.

What is a reporter gene assay used for?

To test promoter/enhancer activity by linking them to measurable genes (e.g., luciferase, β-galactosidase).

What is an EMSA used for?

To detect protein–DNA interactions—shifts in electrophoretic mobility indicate binding.

What is a DNase I footprint assay?

Identifies specific DNA regions bound by proteins (protected from DNase digestion).

What is ChIP-seq used for?

To identify DNA regions bound by specific proteins or histone marks genome-wide.

What is a promoter?

Core DNA region (+ regulatory sequences) that initiates transcription.

What is dyad symmetry in promoters?

Palindromic sequences that allow dimeric TF binding (like mirrored docking sites).

What are enhancers?

Distal regulatory elements that increase transcription—function in either orientation or location.

What is an enhanceosome?

Multi-protein complex assembled on enhancers to recruit HATs and Pol II.

How do enhancers and promoters communicate?

Through DNA looping mediated by architectural proteins.

What are silencers?

DNA regions that recruit repressors and promote heterochromatin formation.

Which complex mediates silencer repression?

Polycomb complex → H3K27 methylation and H2A ubiquitination.

What’s the difference between Polycomb and Trithorax?

Polycomb = repression (compact chromatin); Trithorax = activation (open chromatin).

What type of transcription factors use helix-turn-helix motifs?

Homeotic proteins—recognition helix fits into major groove for sequence-specific binding.

What are homeotic genes?

Developmental regulators that determine segment identity; mutations cause body structure swaps (e.g., Antennapedia).

What is the POU domain?

A bipartite DNA-binding domain with two helix-turn-helix motifs—found in Oct4 and Pit1.

What is a C2H2 zinc finger?

Zinc-coordinated domain (2 Cys + 2 His) recognizing 3–4 bp of DNA—“finger grip” on DNA.

What is a C4 zinc finger?

Four cysteine-coordinated Zn domain in nuclear receptors—binds DNA as dimers.

What is a leucine zipper?

Repeating leucines every 7 aa create a coiled-coil dimerization domain—positions basic region for DNA binding.

What is a helix-loop-helix domain?

Two α-helices linked by a loop—forms dimers for DNA binding or repression (e.g., MyoD vs Id).

What is the role of the activation domain in TFs?

Interacts with coactivators (Mediator, TAFs, CBP/p300) to recruit Pol II or remodel chromatin.

What is the function of the mediator complex?

Bridges activators and RNAP II → integrates signals and controls transcription rate.

What are coactivators?

Non-DNA-binding proteins (like CBP/p300) that connect activators to the transcription machinery.

How do repressors work?

They block activator binding, recruit HDACs, or compete for BTC components (e.g., Dr1 binds TBP to block TFIIB).

What happens when thyroid hormone binds its receptor?

Conformational change releases corepressor → recruits coactivator → transcription activation.

What is transcriptional repression by MDM2?

Targets activators like p53 for ubiquitination and degradation.

What is transcriptional pausing used for in regulation?

Fine-tunes timing, prevents premature elongation, and synchronizes gene activation.

What does HIV Tat protein do?

Recruits pTEFb kinase to phosphorylate RNAP II CTD → overcomes pausing → elongation proceeds.

What does pTEFb do?

Phosphorylates Ser2 on RNAP II CTD during elongation—marks productive transcription.

What domain of TAFII250 aids transcription?

HAT activity—adds acetyl groups to histones to open chromatin.

Which histone modification marks active enhancers?

H3K27ac—recruits coactivators and signals open chromatin.

Which factor displaces nucleosomes at the hsp70 promoter?

GAGA factor—creates DNase I hypersensitivity before heat-shock induction.

What happens to nucleosome structure during elongation?

HATs and FACT displace and reassemble nucleosomes as RNAP II passes.

What is the main polyadenylation signal sequence?

AAUAAA (not AUAAAAA)—recognized for transcript cleavage and polyadenylation.

Which transcription factor binds closed chromatin and opens it?

Pioneer TFs like FOXA1—bind DNA and histones simultaneously to open chromatin.

Which domain recognizes acetylated histones in remodelers?

Bromodomain—recruits proteins like SWI/SNF.

What is the main feature of euchromatin?

Open, transcriptionally active chromatin with acetylated histones and low methylation.

What is the main feature of heterochromatin?

Compact, transcriptionally silent chromatin enriched in H3K9me and DNA methylation.

What is the function of FACT?

Facilitates chromatin transcription by removing H2A-H2B dimers ahead of RNAP II and redepositing them afterward.

What modification links Polycomb repression to DNA methylation?

H3K9me → HP1 → recruits Dnmt → DNA methylation.

What does sodium butyrate do?

Inhibits HDACs → increases histone acetylation → reactivates silent genes.

How does 5-azacytidine affect gene expression?

Inhibits DNA methylation → can reactivate silenced genes (e.g., fibroblast → muscle conversion).

What type of RNA mediates transcriptional silencing in plants?

siRNA via RITS complex—recruits HP1 → histone and DNA methylation.

What does histone glycosylation generally cause?

Chromatin opening and activation, often linked to 5hmC recognition.

Which histone variant affects transcription regulation?

H3.3 variant—associated with active chromatin and dynamic nucleosome turnover.