Chromatin Architecture, Epigenetic Modifications, and Transcriptional Regulation

Comprehensive vocabulary flashcards covering eukaryotic genome architecture, nucleosome and histone biochemistry, epigenetic modifications, higher-order chromosome topology, core transcriptional machineries, and molecular profiling technologies.

C-Value Paradox

The observation that total nuclear genome size and chromosome count do not correlate with organismal or phylogenetic complexity across eukaryotes.

Chromosome Territory

A discrete, non-random sub-nuclear spatial domain occupied by an individual chromosome within the interphase eukaryotic nucleus.

B-DNA

The canonical right-handed antiparallel double-helical conformation of DNA with a diameter of $2.0\,\text{nm}$, a helical rise of $0.34\,\text{nm}$ per base pair, and roughly $10.5\,\text{bp}$ per turn ($3.4\,\text{nm}$ pitch).

Major Groove

The wider, deeper groove of the B-DNA double helix that exposes unique patterns of hydrogen bond donors, acceptors, and nonpolar methyl groups, allowing sequence-specific proteins to read base sequences without strand separation.

Nucleosome Core Particle

The fundamental packaging unit of chromatin, consisting of an octamer of core histones (two each of H2A, H2B, H3, and H4) encircled by $146\text{--}147\,\text{bp}$ of DNA in $1.65$ left-handed superhelical turns.

Histone Fold

A conserved tertiary structural motif present in all core histones, consisting of three $\alpha$-helices ($\alpha 1$, $\alpha 2$, $\alpha 3$) separated by two short loops ($L1$, $L2$) that drives dimerization through a reciprocal handshake interaction.

Linker Histone H1

A lysine-rich histone with a molecular weight of approximately $23{,}000\,\text{Da}$ that binds outside the nucleosomal disc at the DNA entry and exit sites to seal the turn and organize linker DNA into higher-order chromatin structures.

Histone Chaperone

A specialized acidic protein (such as CAF1, NAP1, or Nucleoplasmin) that shields the positive charges of histones to prevent aberrant charge-based precipitation with DNA and guide orderly nucleosome assembly or disassembly.

Micrococcal Nuclease (MNase)

An endo- and exonuclease that selectively cleaves unprotected linker DNA while sparing nucleosome-bound DNA, generating a periodic nucleosomal ladder at integer multiples of approximately $200\,\text{bp}$.

Nucleosome Breathing

The spontaneous, transient unwrapping of nucleosomal DNA from the histone core occurring roughly $1/20\text{th}$ of the time, providing sequence-specific DNA-binding factors momentary access to target sites.

SWI/SNF Family

A group of ATP-dependent chromatin remodeling complexes containing catalytic ATPase subunits (such as Swi2/Snf2, BRG1/SMARCA4, or hBRM/SMARCA2) that drive nucleosome sliding, octamer displacement, or nucleosome ejection to expose regulatory DNA elements.

H2AX

A histone H2A variant containing a C-terminal SQEY motif that undergoes phosphorylation at Ser139 by ATM or ATR kinases in response to DNA double-strand breaks to form $\gamma\text{-H2AX}$, which recruits DNA repair machinery.

H2A.Z

A conserved histone H2A variant positioned at nucleosome-depleted regions ($-1$ and $+1$ nucleosomes) flanking active promoters that confers instability to the nucleosome to lower the energetic barrier for RNA Polymerase II elongation.

macroH2A

A specialized histone H2A variant bearing a large C-terminal non-histone globular macrodomain of approximately $30\,\text{kDa}$, enriched on the inactive X chromosome ($\text{Xi}$) in mammalian females to maintain stable epigenetic gene silencing.

CENP-A

A centromere-specific histone H3 variant deposited by the chaperone HJURP in a replication-independent manner that replaces canonical H3 to specify centromere identity and direct kinetochore assembly.

Histone Acetyltransferases (HATs / KATs)

Enzymes (including GNAT, MYST, and p300/CBP families) that transfer an acetyl group from Acetyl-CoA to the $\epsilon$-amino group of lysine residues on histone tails, neutralizing positive charge to open chromatin structure.

Bromodomain

A conserved structural protein reader motif consisting of an antiparallel four-helix bundle ($\alpha Z$, $\alpha A$, $\alpha B$, $\alpha C$) that binds specifically to acetylated lysine residues on histone tails.

Histone Deacetylases (HDACs)

Enzymes that catalyze the hydrolytic removal of acetyl groups from lysine residues on histone tails, restoring positive charge, promoting chromatin compaction, and repressing transcription.

Histone Methyltransferases (HMTs)

Enzymes that transfer methyl groups from S-Adenosylmethionine (SAM) to lysine (KMTs, typically carrying a SET domain) or arginine (PRMTs) residues on histone tails without altering the net positive charge.

LSD1 (KDM1A)

A flavin adenine dinucleotide (FAD)-dependent amine oxidase that demethylates mono- and dimethylated H3K4 and H3K9 residues, but is unable to act on trimethylated lysine residues.

Jumonji C (JmjC) Domain Demethylases

A family of $\text{Fe(II)}$- and $\alpha$-ketoglutarate-dependent dioxygenases that utilize radical hydroxylation to demethylate mono-, di-, and trimethylated histone lysine residues.

Chromodomain

A conserved protein reader domain that recognizes and binds specific methylated lysine residues, such as HP1 recognizing H3K9me2/me3 and Polycomb (Pc/CBX) recognizing H3K27me3.

Trans-Histone Cross-Talk

An epigenetic pathway where an initial histone post-translational modification regulates a downstream modification, such as H2BK120ub1 obligatorily activating SET1-mediated H3K4 methylation and DOT1L-mediated H3K79 methylation.

Methyl-Phospho Switch

A regulatory mechanism where the phosphorylation of a histone residue evicts reader proteins bound to an adjacent methylated residue, such as Aurora B-mediated H3S10ph evicting HP1 from H3K9me3 during mitosis.

Bivalent Promoters

Developmental gene promoters in pluripotent embryonic stem cells that simultaneously carry the active histone mark H3K4me3 and the repressive mark H3K27me3, keeping lineage-specifying genes silent yet poised for rapid transcription.

One-Start Solenoid Model

A model of the $30\text{-nm}$ chromatin fiber in which the nucleosomal chain coils into a continuous, hollow cylindrical helix with approximately $6$ nucleosomes per turn around a central lumen of approximately $11\,\text{nm}$.

Two-Start Zigzag Model

A model of the $30\text{-nm}$ chromatin fiber where nucleosomes alternate along a straight linker configuration crossing through the fiber center, placing alternate nucleosomes ($n$ and $n+2$) closer together than adjacent ones ($n$ and $n+1$).

Heterochromatin Protein 1 (HP1)

An essential heterochromatin adaptor that binds H3K9me3 via its N-terminal chromodomain and homodimerizes through its C-terminal chromoshadow domain to recruit SUV39H1, facilitating linear heterochromatin spreading.

Topologically Associating Domains (TADs)

Genomic regions (spanning $100\,\text{kb}$ to several megabases) whose internal sequences interact with one another at high frequency, insulated from neighboring domains by structural boundary elements.

Loop Extrusion Model

The process by which ring-shaped Cohesin complexes translocate along DNA to extrude chromatin loops bidirectionally until halted by pairs of CTCF proteins bound in a convergent orientation.

CpG Island (CGI)

A genomic stretch of $500\text{--}2{,}000\,\text{bp}$ characterized by a $\text{G+C}$ content $>50\%$ and an observed-to-expected CpG ratio $>0.6$, commonly found unmethylated at approximately $70\%$ of human gene promoters.

DNMT1

The primary maintenance DNA methyltransferase that targets hemimethylated $5'\text{-CpG-}3'$ sites at the replication fork to preserve maternal and paternal methylation patterns in the newly synthesized daughter strand.

DNMT3A and DNMT3B

De novo DNA methyltransferases stimulated by DNMT3L that establish new genomic DNA methylation marks during early embryonic development and cell fate specification.

TET Dioxygenases

Enzymes (TET1, TET2, TET3) that catalyze active DNA demethylation by sequentially oxidizing $5\text{-methylcytosine (5mC)}$ to $5\text{-hydroxymethylcytosine (5hmC)}$, $5\text{-formylcytosine (5fC)}$, and $5\text{-carboxylcytosine (5caC)}$ in an $\text{Fe(II)}$- and $\alpha$-ketoglutarate-dependent cascade.

Methyl-CpG-Binding Domain (MBD) Proteins

Adaptor proteins (such as MeCP2, MBD1, and MBD2) that selectively recognize methylated DNA and recruit corepressor complexes containing HDACs and HMTs to enforce chromatin compaction and transcriptional repression.

RNA Polymerase I (Pol I)

A $14$-subunit eukaryotic RNA polymerase localized exclusively in the nucleolus that transcribes the $45\text{S}$ pre-rRNA precursor and is completely insensitive to $\alpha$-amanitin.

RNA Polymerase II (Pol II)

A $12$-subunit eukaryotic RNA polymerase localized in the nucleoplasm that synthesizes all protein-coding mRNAs, most snRNAs, miRNAs, and lncRNAs; highly sensitive to $\alpha$-amanitin ($\text{IC}_{50} \approx 0.02\,\mu\text{g/mL}$).

RNA Polymerase III (Pol III)

A $17$-subunit nucleoplasmic RNA polymerase that transcribes small functional non-coding RNAs ($5\text{S}$ rRNA, tRNAs, U6 snRNA) and exhibits moderate sensitivity to $\alpha$-amanitin ($\text{IC}_{50} \approx 10\text{--}20\,\mu\text{g/mL}$ in mammals).

C-Terminal Domain (CTD) of RPB1

The unstructured tail of the largest Pol II subunit, composed of tandem repeats ($26$ in yeast, $52$ in mammals) of the consensus heptapeptide $\text{Y}_1\text{S}_2\text{P}_3\text{T}_4\text{S}_5\text{P}_6\text{S}_7$, whose phosphorylation cycle orchestrates initiation, elongation, and RNA processing.

TATA-Binding Protein (TBP)

The universal DNA-binding subunit of TFIID that inserts into the minor groove of the core promoter TATA box ($\text{TATAWAAR}$), inducing a sharp bend of approximately $80^\circ$ in the double helix.

TFIIH

A $10$-subunit general transcription factor possessing ATP-dependent helicases/translocases (XPB and XPD) that unwind DNA to form the transcription bubble, and a CAK module (CDK7, Cyclin H, MAT1) that phosphorylates Ser5 of the Pol II CTD.

Mediator Complex

A multi-protein coactivator complex of approximately $30$ subunits ($\sim 1.4\,\text{MDa}$) organized into Head, Middle, Tail, and CDK8 Kinase modules that bridges distal enhancer-bound activators with the basal transcription machinery at the core promoter.

Promoter-Proximal Pausing

A widespread transcription elongation checkpoint occurring $30\text{--}50\,\text{nt}$ downstream of initiation where Pol II arrests due to the actions of NELF and DSIF until released by P-TEFb.

P-TEFb (Positive Transcription Elongation Factor b)

A cyclin-dependent kinase complex (CDK9/Cyclin T1) that triggers pause release by phosphorylating Ser2 of the Pol II CTD, SPT5 within DSIF, and NELF, converting the elongation complex into a fully processive state.

FACT (Facilitates Chromatin Transcription)

A conserved heterodimeric histone chaperone (composed of Spt16 and SSRP1) that temporarily displaces an $\text{H2A}\cdot\text{H2B}$ dimer ahead of advancing Pol II, redepositing the dimer immediately after the polymerase transcribes past the core.

Torpedo Model

A mechanism of Pol II transcription termination wherein endonucleolytic cleavage at the poly(A) site allows the processive $5'\text{-to-}3'$ exonuclease XRN2 (Rat1 in yeast) to degrade the remaining uncapped nascent RNA until it collides with and evicts the polymerase.

Biomolecular Condensates

Membraneless sub-nuclear compartments assembled via liquid-liquid phase separation (LLPS), driven by multivalent, weak interactions among intrinsically disordered regions (IDRs) of transcription factors, coactivators, and Pol II.

Super-Enhancers

Expansive clusters of enhancers spanning large genomic intervals ($>12.5\,\text{kb}$) characterized by extraordinarily high densities of master transcription factors, Mediator (MED1), BRD4, and H3K27ac that drive expression of genes determining cell identity.

Locus Control Region (LCR)

A distal cis-regulatory element containing multiple DNase I hypersensitive sites that confers high-level, copy-number-dependent, and tissue-specific expression upon an entire linked gene cluster through long-range looping interactions.

Helix-Turn-Helix (HTH) Motif

A DNA-binding protein motif composed of two $\alpha$-helices separated by a short non-helical turn, in which the C-terminal recognition helix docks directly into the major groove of B-DNA.

Homeodomain

A conserved $60$-amino acid DNA-binding domain encoded by homeobox genes that folds into three $\alpha$-helices, utilizing Helix 3 ($17$ residues) as a major-groove recognition helix and an unstructured N-terminal arm to contact the minor groove.

Basic Leucine Zipper (bZIP) Motif

A protein motif featuring an amphipathic $\alpha$-helix containing a heptad repeat of hydrophobic leucine residues that mediates coiled-coil dimerization, flanked by N-terminal basic regions that contact adjacent major grooves.

Pioneer Transcription Factors

Transcription factors (such as FOXA1, SOX2, and GATA) capable of binding target sequences within compact nucleosomal DNA, displacing linker histone H1 and recruiting remodelers to open chromatin for other factors.

Long Non-Coding RNAs (lncRNAs)

Non-coding RNA transcripts greater than $200\,\text{bp}$ in length, typically transcribed by Pol II, that regulate transcription through signal, decoy (e.g., PANDA), guide, or scaffold (e.g., HOTAIR) mechanisms.

HOTAIR

A $2.2\text{-kb}$ lncRNA transcribed from the HOXC locus that acts as an epigenetic scaffold, binding PRC2 at its $5'$ domain and LSD1 at its $3'$ domain to repress the distant HOXD locus in trans.

ATAC-seq

An epigenomic profiling method that uses hyperactive Tn5 transposase to simultaneously fragment open chromatin regions and insert sequencing adapters (tagmentation) in a single step using as few as $500\text{--}50{,}000$ cells.

CUT&RUN

An in situ chromatin profiling technique where permeabilized nuclei are targeted with a specific antibody and a Protein A-micrococcal nuclease (pA-MNase) fusion, selectively cleaving and releasing target-bound DNA fragments upon addition of $\text{Ca}^{2+}$.

Chromosome Conformation Capture (3C)

A molecular method that quantifies spatial proximity between distal genomic loci via in situ formaldehyde crosslinking, restriction enzyme digestion, dilute proximity ligation, and quantification of crosslinked ligation junctions.

Bisulfite Genomic Sequencing

A high-resolution DNA methylation profiling assay in which sodium bisulfite deaminates unmodified cytosine into uracil while leaving $5\text{mC}$ and $5\text{hmC}$ unaffected, allowing methylation mapping at single-nucleotide resolution.

Electrophoretic Mobility Shift Assay (EMSA)

An in vitro assay that detects sequence-specific protein-DNA interactions by comparing the migration of free labeled DNA probes versus slower-migrating protein-DNA complexes on a native, non-denaturing polyacrylamide gel.