BIOL 413 - Cell Biology: Chapter 7 Control of Gene Expression

Vocabulary flashcards covering topics on gene expression regulation, transcriptional circuits, epigenetic mechanisms, post-transcriptional control, and noncoding RNAs.

Transcription Regulator

A protein that binds to a specific DNA sequence (cis-regulatory element) to regulate gene expression.

Syncytium

A cellular structure containing multiple nuclei within a common cytoplasm.

Even-skipped (Eve)

A gene critical for embryonic development in Drosophila whose precise stripe expression pattern is determined by combinatorial regulation by multiple transcription regulators.

Induced Pluripotent Stem Cells (iPS cells)

Cells produced by artificially expressing the transcription regulators Oct4, Sox2, and Klf4 in fully differentiated cells, causing them to reprogram and adopt characteristics of pluripotent embryonic cells.

Yamanaka Factors

The set of master transcription regulators—Oct4, Sox2, and Klf4—that are sufficient to trigger a change in cell identity to pluripotency.

Cell Memory

The retained pattern of gene expression within a cell that maintains its specific cell identity and is stably passed on to its daughter cells upon division.

Feed-Forward Loop

A gene expression circuit arrangement where one gene regulates a second gene, and both together regulate a third gene, allowing the cell to measure signal duration and ignore brief input signals.

Maintenance Methyl Transferase

An enzyme that adds a methyl group to cytosine in CG sequences base-paired with methylated CG strands, ensuring the inheritance of DNA methylation patterns during DNA replication.

Heterochromatin

A densely packed region of nuclear DNA in which genes are stably silenced and prevented from being transcribed.

CG Island

A region of the genome rich in unmethylated CG sequences approximately $1000$ nucleotides in length, commonly located near gene promoters.

Genomic Imprinting

An epigenetic process where an allele inherited from one parent is silenced via DNA methylation, resulting in monoallelic gene expression.

Dosage Compensation

A regulatory process that equalizes the expression levels of X-chromosome genes between males and females.

Xist

A long noncoding RNA transcribed from one X chromosome that recruits DNA methylases and histone-modifying enzymes to induce random X-chromosome inactivation in mammalian females.

Epigenetic Inheritance

The transmission of heritable changes in cell phenotype and gene expression patterns that occur without altering the underlying DNA sequence.

Transcription Attenuation

A regulatory mechanism causing premature termination of transcription by RNA polymerase before the full transcript is completed.

Riboswitch

A short RNA sequence located near the $5'$ end of an mRNA that undergoes a conformational change upon binding a regulatory molecule to abort or regulate transcription.

Alternative Splicing

The selective removal or retention of introns and exons during pre-mRNA processing to generate different mRNA and protein variants from a single gene.

RNA Editing

The site-specific covalent modification of bases in an RNA transcript (such as deamination of adenine to inosine or cytosine to uracil) that alters its coding properties.

Internal Ribosome Entry Site (IRES)

A specialized mRNA sequence that allows translation initiation at positions distant from the $5'$ cap.

P-bodies

Membraneless cytoplasmic aggregates of RNA and proteins where mRNAs are stored in an intact form or targeted for degradation.

Stress Granule

A transient, membraneless cytoplasmic organelle formed in response to starvation or stress when translation is blocked, storing mRNAs until stress is alleviated.

MicroRNA (miRNA)

A class of short, genome-encoded noncoding RNAs processed by Dicer and RISC that base-pair with target mRNAs to downregulate translation or promote mRNA degradation.

Small Interfering RNA (siRNA)

A class of double-stranded RNA-derived small noncoding RNAs (~$23$ nucleotides long) processed by Dicer that direct target RNA degradation or transcriptional silencing via RISC and RITS complexes.

Piwi-Interacting RNA (piRNA)

Small noncoding RNAs that associate with Piwi proteins to protect germ line cells by degrading transposon-coded RNA and promoting heterochromatin formation.

CRISPR

Clustered Regularly Interspersed Short Palindromic Repeats; special regions in the bacterial genome where viral DNA is integrated to provide template-based defense against viral infections.

crRNA

Small noncoding RNA transcribed from the bacterial CRISPR locus that complexes with Cas proteins to seek out and destroy complementary foreign viral sequences.

Long Noncoding RNA (lncRNA)

Non-protein-coding RNA molecules longer than $200$ nucleotides that function as protein scaffolds, molecular guides, or antisense regulators.

De Novo DNA Methyltransferase

An enzyme that methylates previously unmethylated CG sequences in early development to establish new patterns of DNA methylation.

Positive Feedback Loop (Gene Control)

A gene circuit motif where a protein stimulates its own transcription, ensuring stable inheritance of gene expression state across cell divisions.

HIV Tat Protein

A viral protein that overcomes host transcription attenuation by binding to newly synthesized viral RNA, allowing RNA polymerase to complete full-length transcription.

HIV Rev Protein

A viral protein that binds to the Rev Response Element (RRE) on unspliced viral transcripts to enable nuclear export past host cell quality control checkpoints.

Shine-Dalgarno Sequence

A conserved sequence in bacterial mRNA upstream of the start codon that binds ribosomal RNA to direct translation initiation.

eIF2

A eukaryotic translation initiation factor that delivers initiator tRNA to the ribosome in a GTP-bound state; its phosphorylation reduces global translation rate.

eIF2B

A guanine nucleotide exchange factor that recycles GDP-bound eIF2 to GTP, whose activity is inhibited when eIF2 is phosphorylated during cell stress.

N6-Methyladenosine ($m^6A$)

A dynamic and reversible covalent modification of adenine in eukaryotic mRNA that regulates mRNA structure, alternative splicing, degradation, and translation.

Alternative Cleavage and Polyadenylation

A post-transcriptional mechanism that selects different $3'$ cleavage sites in mRNA, altering the $C$-terminus of the encoded protein (e.g., membrane-bound vs. secreted antibody).

Dicer

A cytosolic ribonuclease that cleaves double-stranded precursor RNAs into functional $20$ to $30$ nucleotide noncoding RNAs like miRNAs and siRNAs.

RISC (RNA-Induced Silencing Complex)

A ribonucleoprotein complex incorporating Argonaute and small guide RNAs to mediate mRNA degradation or translational repression in the cytoplasm.

RITS (RNA-Induced Transcriptional Silencing)

A complex loaded with siRNAs that targets nascent transcripts to direct heterochromatin formation and transcriptional silencing at specific genomic loci.

Cas Protein

A bacterial endonuclease that complexes with crRNA to recognize and cleave foreign viral DNA sequences during adaptive immune defense.

Monoallelic Gene Expression

The transcription of only one allele of a gene pair in a diploid cell, seen in phenomena such as genomic imprinting and X-chromosome inactivation.