Biol 3130 Session 12: Gene Regulation in Eukaryotic Cells

Flashcards covering gene regulation in eukaryotic cells, focusing on chromatin structure, transcription, alternative splicing, and RNA interference.

Gene Regulation in Eukaryotic Cells

Occurs at many levels, including chromatin structure, transcription, co- and post-transcriptional processing, and translational/post-translational control.

Epigenetics

A field of study related to heritable changes in gene expression that do not involve changes to the underlying DNA sequence.

Chromatin Remodeling

The process of opening up chromatin to make DNA accessible for RNA polymerase to initiate transcription, often involving chromatin remodeling complexes.

Histone Modifications

Chemical changes, such as methylation or acetylation, to the histone tails that impact gene expression by altering chromatin structure.

DNA Methylation

The addition of methyl groups to DNA, typically at cytosine bases (5-methyl-cytosine), which generally leads to transcriptional repression.

Histone Tails

Positively charged domains of histones that associate with DNA; chemical modifications to these tails affect chromatin structure.

Methylation (Histones)

Addition of methyl (CH3) groups to histone tails, catalyzed by histone methyltransferases, which can either activate or repress transcription.

Acetylation (Histones)

Addition of acetyl groups (CH3COO) to histone tails, catalyzed by histone acetyltransferases, which generally promotes open chromatin and increased transcription.

Acetyltransferases

Enzymes that add acetyl groups to histone tails, promoting a relaxed (open) chromatin structure and increased transcription.

Deacetylases

Enzymes that remove acetyl groups from histone tails, promoting a condensed (closed) chromatin structure and repressed transcription.

Open Chromatin

A state of chromatin where DNA is less tightly packed and accessible for transcription, often promoted by histone acetylation.

Closed Chromatin

A state of chromatin where DNA is tightly packed and inaccessible for transcription, often promoted by histone deacetylation and methylation.

FLC Gene

In Arabidopsis, encodes a transcription factor that represses genes promoting flowering. Its repression by FLD leads to flowering.

FLD Gene

In Arabidopsis, encodes a histone deacetylase that deacetylates histones bound to the FLC gene, leading to lower FLC expression and promotion of flowering.

Core Promoter (Eukaryotic)

A DNA sequence containing several consensus sequences, including the TATA box, where the basal transcription apparatus binds to initiate transcription.

Basal Transcription Apparatus

A complex of proteins including RNA polymerase II, general transcription factors, and mediator, that binds to the core promoter to initiate transcription.

Transcriptional Activators

Regulatory proteins that bind to enhancer or regulatory promoter sequences and stimulate the assembly and stability of the basal transcription apparatus, thereby increasing transcription.

Coactivators

Proteins that do not bind DNA directly but interact with transcriptional activators to enhance their ability to stimulate transcription.

Regulatory Promoter

DNA sequences located upstream from the core promoter where transcriptional activators can bind.

Enhancer

DNA sequences located far from the promoter that bind transcriptional activator proteins and stimulate transcription, often functioning in either orientation and affecting multiple genes.

Insulator

A DNA sequence that limits the effects of enhancers, blocking enhancer action if positioned between the enhancer and the promoter.

Repressors

Proteins that bind to silencer sequences or regulatory promoter sequences to inhibit transcription initiation, often by competing with activators or interfering with basal transcription apparatus assembly.

Silencers

DNA sequences located far from the promoter that bind repressor proteins to inhibit transcription.

Transcriptome

The complete set of messenger RNA (mRNA) transcripts expressed from the genes of an organism, a tissue, or a cell type under specific conditions.

Alternative Splicing

A co-transcriptional regulatory process by which a single pre-mRNA can be spliced in different manners to generate multiple unique RNA transcripts and, by extension, multiple peptide products.

mRNA Degradation

A post-transcriptional control mechanism where the stability of mRNA influences gene expression by affecting the amount of mRNA available for translation.

Ribonucleases (RNAses)

Enzymes that degrade mRNA, such as 5' to 3' exonucleases, which start degradation from the 5' end.

PABP (Poly(A)-Binding Protein)

A protein that protects the poly(A) tail and the 5' cap of mRNA from degradation by exonucleases.

RNA Interference (RNAi)

A post-transcriptional mechanism where small RNAs target homologous transcripts for degradation or translational repression.

Short Interfering RNAs (siRNAs)

21-23 nucleotide small RNAs derived from double-stranded RNAs (e.g., viruses, repetitive transcripts) that trigger RNA interference.

MicroRNAs (miRNAs)

22-nucleotide small RNAs that are encoded by genes, processed into smaller RNAs, and play a key role in regulating gene expression by targeting specific mRNAs.

RNA-Induced Silencing Complex (RISC)

A complex that acts on both siRNAs and microRNAs to dock at target sequences and induce gene silencing, often by cleaving the mRNA or blocking translation.

Dicer

An enzyme that processes double-stranded RNAs into single-stranded miRNAs or siRNAs, each typically 21-25 nucleotides long, for RNA interference pathways.

Slicer (Argonaute)

A component of the RISC complex that is responsible for cleaving target mRNA during RNA interference.