BI2BMG4 MOLECULAR GENETCS - Eukaryotic Gene Expression Regulation

Flashcards covering key vocabulary and definitions related to eukaryotic gene expression regulation, transcription factors, and DNA-binding domains.

DNase I hypersensitive sites

More open chromatin configuration site, upstream of the transcription start site

Histone modification

Addition of methyl groups to the histone protein tails, or addition of acetyl groups to histone proteins

Histone acetylation

Alters chromatin structure and permits some transcription factors to bind to DNA; disrupts the interaction between histones and DNA by neutralizing the positive charge on lysine residues, leading to a more relaxed chromatin structure and increased accessibility for transcription factors

Flowering locus C (FLC) gene

Encodes a protein that represses flowering

Flowering locus D (FLD) gene

Encodes a deacetylase

Transcriptional activators

Regulate the initiation of transcription

Transcriptional repressors

Regulate the initiation of transcription

Transcriptional coactivators

Regulate the initiation of transcription

Transcription factors

Proteins required by eukaryotic RNA polymerases to first bind to a promoter

Core promoter

Shortest sequence at which an RNA polymerase can initiate transcription

Basal/General transcription factors

Required by all RNA polymerases to form the initiation complex at promoters; initiate minimum level transcription

Basal transcription apparatus

Formed by basal/general transcription factors together with the RNA polymerase

Trans-acting factors

Usually proteins that bind to the cis-acting sequences to control gene expression

Activators

Stimulate transcription

True activators

Directly interact with basal transcriptional machinery

Anti-repressors

Stimulate chromatin remodeling

Architectural proteins

Bend DNA

Repressors

Inhibit transcription

Coactivators

Factors required for transcription that do not bind DNA; connect activators to basal transcriptional machinery

Architectural protein

A protein that, when bound to DNA, can alter its structure (e.g. introduce a bend)

General transcription factors

Required for the transcription of ALL eukaryotic genes

Specific transcription factors

Act on INDIVIDUAL genes or group of genes

Core promoter

The site where the basic machinery for transcription initiation assembles, including RNA polymerase, general transcription factors, and the preinitiation complex; often located immediately upstream of the gene coding sequence and includes essential elements like the TATA box.

Regulatory promoter

Includes sequences that can be far from the core promoter; these sequences interact with enhancers, silencers, and additional transcription factors that either increase or decrease the rate of transcription of the associated gene.

Transcriptional activator proteins

Have two distinct functions: binding of DNA at a specific base sequence, usually a consensus sequence in a regulatory promoter or enhancer, and the ability to interact with other components of the transcriptional apparatus and influence the rate of transcription.

DNA-binding domain

Determines specificity for the target promoter or enhancer; responsible for localizing a transcription-activating domain in the proximity of the basal apparatus.

Transcriptional co-activators

Employ diverse mechanisms, including inducing posttranslational changes, ATP-dependent motor activities, promoting transcription by enabling the recruitment of RNA polymerase II, and serving as scaffolds for the recruitment of other co-regulators.

Mediator complex

A large protein complex associated with eukaryotic RNA polymerase II that contains factors necessary for transcription from many or most promoters; a basic function is to communicate regulatory signals from DNA-binding transcription factors directly to RNA polymerase II.

Zinc finger

A DNA-binding motif that typifies a class of transcription factor.

Steroid receptor

Transcription factors that are activated by binding of a steroid ligand.

Helix-turn-helix

The motif that describes an arrangement of two α-helices that form a site that binds to DNA, one fitting into the major groove of DNA and the other lying across it.

Homeodomain

A DNA-binding motif that typifies a class of transcription factors.

Helix-loop-helix

The motif that is responsible for dimerization of a class of transcription factors called HLH proteins.

bZIP

A bZIP protein has a basic DNA- binding region adjacent to a leucine zipper dimerization motif.

Enhancer

DNA sequence stimulating transcription a distance away from promoter

Insulator

DNA sequence that blocks or insulates the effect of enhancers

Metallothionein genes

Encode cysteine-rich, low-molecular-weight proteins that play a crucial role in metal homeostasis, detoxification, and protection against oxidative stress

Response elements (REs)

Short DNA sequences within a gene's promoter or enhancer region that bind specific transcription factors, influencing gene expression of a group of genes in response to a common stimulus

Promoter

Binding site for the basal transcriptional apparatus - RNA polymerase and its co-factors, the minimum machinery necessary to allow transcription of the gene.

Enhancer regions

Found at a distance from the promoter and are binding sites for a variety of cell- or region-specific transcription factors that interact with the basal transcriptional machinery at the promoter to enhance (or sometimes diminish) the transcription rate of the gene.

Constitutive promoters

Active in all circumstances in the cell.