Genetics Chapter 15 - Robert J. Brooker

gene regulation

the phenomenon in which the level of gene expression can vary under different conditions.

transcription factors

a broad category of proteins that influence the ability of RNA polymerase to transcribe DNA into RNA.

GTF (general transcription factor)

one of several proteins that are necessary for basal transcription at the core promotor.

regulatory transcription factor

a protein or protein complex that binds to a regulatory element and influences the rate of transcription via RNA polymerase.

regulatory element (control element)

a sequence of DNA (or possibly RNA) that binds a regulatory protein and thereby influences gene expression. Bacterial operator sites and eukaryotic enhancers and silencers are examples.

activator

a transcriptional regulatory protein that increases the rate of transcription.

enhancer

a DNA sequence that functions as a regulatory element. the binding of a regulatory transcription factor to the enhancer increases the level of transcription.

repressor

a regulatory protein that binds to DNA and inhibits transcription.

silencer

a DNA sequence that functions as a regulatory element. the binding of a regulatory transcription factor to the silencer decreases the level of transcription.

combinatorial control

the phenomenon common in eukaryotes in which the combination of many factors determines the expression of any given gene.

domain

a segment of a protein that has a specific function.

motif

the name given to a domain or amino acid sequence that functions in a similar manner in many different proteins.

homodimer

when two polypeptides encoded by the same gene bind to each other to form a dimer.

heterodimer

when two polypeptides encoded by different genes bind to each other to form dimer.

up regulation

genetic regulation that leads to an increase in gene expression.

down regulation

genetic regulation that leads to a decrease in gene expression.

orientation-independent

refers to certain types of genetic regulatory elements that can function in the forward or reverse direction. certain enhancers are orientation independent.

bidirectionally

the phenomenon in which two replication forks move in opposite directions outward from the origin.

TFIID

a type of general transcription factor in eukaryotes that is needed for RNA polymerase II function. It binds to the TATA box and recruits RNA polymerase II to the core promotor.

coactivators

bind to other proteins like basal factors, transactivators, or chromatin remodeling complexes

mediator

a protein complex that interacts with RNA polymerase II and various regulatory transcription factors. Depending on its interactions with regulatory transcription factors, mediator may stimulate or inhibit RNA polymerase II.

steroid receptor

A category of transcription factors that responds to steroid hormones. An example of a glucocorticoid receptor.

glucocorticoid receptors

a type of steroid receptor that functions as a regulatory transcription factor.

CREB protein (cAMP response element-binding protein)

a regulatory transcription factor that becomes activated in response to specific cell-signaling molecules that cause the synthesis of cAMP.

CRE (cAMP response element)

a short DNA sequence found next to certain eukaryotic genes that is recognized by the cAMP response element-binding (CREB) protein.

closed conformation

a tightly packed conformation of chromatin that cannot be transcribed.

open conformation

a loosely packed chromatin structure that is capable of transcription.

ATP-dependent chromatin remodeling

a change in chromatin structure that alters the degree of compaction and/or the spacing and histone composition of the nucleosomes. Requires ATP.

DNA translocases

catalytic ATPase subunit found in all chromatin remodeling complexes, similar to other motor proteins.

histone variants

Histones with a slightly different composition than the standard histone; Exist for all histones except H4; created by an accumulation of mutations in one or several of the 70+ genes that encode for histones

histone acetyltransferases

an enzyme that attaches acetyl groups to the amino terminal tails of histone proteins.

histone code hypothesis

the hypothesis that the pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure.

ChIP-Seq (chromatin immunoprecipitation sequencing)

a method for determining whether proteins bind to a particular region of DNA. this method analyzes DNA-protein interactions as they occur in the chromatin of living cells.

immunoprecipitation

the use of antibodies to cause other molecules, such as proteins, to precipitate, which allows them to be collected by centrifugation.

NFR (nucleosome-free region)

a region within a chromosome where nucleosomes are not found.

DNA methylation

the phenomenon in which an enzyme covalently attaches a methyl group to a base in DNA.

CpG island

a group of CG sequences that may be clustered near a promoter region of a gene. the methylation of the cytosine bases usually inhibits transcription.

housekeeping genes

a gene that encodes a protein required in most cells of a multicellular organism.

tissue-specific genes

a gene that is highly regulated and is expressed in a particular cell type.

methyl-CpG-binding proteins

a protein that binds to a CpG island when it is methylated.

de novo methylation

the methylation of DNA that has not been previously methylated. This is usually a highly regulated event.

maintenance methylation

the methylation of hemimethylated DNA following DNA replication.

insulator

a segment of DNA that insulates a gene from the effects of nearby regulatory elements such as enhancers.

alternative splicing

refers to the phenomenon in which a pre-mRNA can be spliced in more than one way.

constitutive exon

an exon that is always found in mRNA following splicing.

alternative exons

an exon that is not always found in mRNA. it is only found in certain types of alternatively spliced mRNAs.

splicing factor

a protein that regulates the process of RNA splicing.

SR proteins

a type of splicing factor.

exon skipping

when an exon is spliced out of a pre-mRNA.

polyA-binding proteins

a protein that binds to the 3' end polyA tail of mRNAs and protects the mRNA from degradation.

3'-UTR (3'-untranslated region)

the untranslated region of mRNA

ARE (AU-rich element)

a sequence found in many short-lived mRNAs that contains the consensus sequence AUUUA.

miRNAs (microRNAs)

small RNA molecules that can inhibit the expression of specific mRNAs via RNA interference

siRNAs (short-interfering RNAs)

small RNA molecules that silence the expression of specific mRNAs via RNA interference.

Dicer

an endonuclease that makes a cut in double-stranded RNA.

RISC (RNA-induced silencing complex)

the complex that mediates RNA interference.

IRP (iron regulatory protein)

a translational regulatory protein that recognizes iron response elements that are found in specific mRNAs. It may inhibit translation or stabilize the mRNA.

IRE (iron response element)

an RNA sequence that is recognized by the iron regulatory protein