Chapter 15 - Gene regulation in Eukaryotes
zinc finger motif
A protein structural motif involved in DNA recognition by some DNA-binding proteins; characterized by a single atom of zinc coordinated to four Cys residues or to two His and two Cys residues.
general transcription factors
A set of proteins that bind to the promoter of a gene whose combined action is necessary for basal transcription at the core promoter
microRNA
A small, noncoding RNA molecule, typically about 21 bases long, that binds to mRNA to inhibit its translation.
RNA interference (RNAi)
A technique used to silence the expression of selected genes. RNAi uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene's messenger RNA.
leucine zipper motif
Alternating leucine residues in both proteins interact ("zip up"), resulting in protein dimerization
Covalent modification of histone
Amino terminals of histones are modified in various ways such as Acetylation; phosphorylation; methylation. This one of the ways to loosen chromatin structure for transcription
Transcription factors recognized
Cis acting elements that are located in near the promoter which are known as regulatory sequences
CpG islands
Found in plants and vertebrate, it is a group of CG sequences that are clustered near the promoter to inhibit gene expression.
Mechanism of DNA methylation
Prevent or enhance binding of regulatory transcription factors to promoter region: methyl group protrude into major groove of DNA which block binding of activator to enhancer element and inhibit transcription
Two other ways to alter chromatin structure
Remodelers may evict histone octamers from the DNA, thereby creating gaps where nucleosomes are not found. The other way is remodelers may change the composition of nucleosomes by removing standard histones and replacing them with histone variants
Response to steroid hormones
The hormone enters cytosol of the cell through diffusing through plasma membrane which binds to glucocorticoid receptor. This cause the release of HSP 90. This exposes a nuclear localization signal (NLS)—a sequence of amino acids within the protein that directs the protein into the nucleus. Two glucocorticoid receptors form a homodimer and then travel through a nuclear pore into the nucleus. The binding of the glucocorticoid receptor homodimer to a GRE (runs opposite direction) activates the transcription of the nearby gene, eventually leading to the synthesis of the encoded protein.
histone code
The pattern of modifications of the histone tails that affects the chromatin structure and gene 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. Regulate accessibility of DNA to proteins.
Close conformation
a conformation of chromatin that cannot be transcribed because it is tightly packed not allowing RNA Poly II to enter.
tissue-specific genes
a gene that is highly regulated and is expressed in a particular cell type in this case the Cytosine bases in CpG islands are methylated
Domain
a segment of protein with a specific function such as one domain of transcription factors may have DNA binding function.
phosophorylation
addition of phosphoryl group (-PO32-) to a histone primarily to amino terminal tail
constitutive exons
always found in the mature mRNA from all cell types; encode polypeptide segments that are necessary for a protein's structure and function
acetylation of histones
an enzyme (acetyltransferase) that attaches acetyl group (COCHH3) to the amino terminal tail of a histone protein. eliminates the positive charge on the lysine side chain, thereby disrupting the electrostatic attraction between the histone protein and the negatively charged DNA backbone.
alternative exon
an exon that is not always found in mRNA. It is only found in certain types of alternatively spliced mRNAs.
splicing repressors
bind to a 3' splice site inhibits spliceosomes recognizing spliceosomes binds to the next available 3' splice site
fully methylated DNA
both strands are methylated and methylated DNA are inherited during DNA sequences.
chromatin remodeling
dynamic changes in the structure of chromatin that occur during the life of a cell which occur through ATP chromatin remodeling which use ATP hydrolysis to drive changes in the position or composition of nucleosome
splicing enhancers
enhances ability of spliceosomes to recognize particular splice sites which lead inclusion of an exon in the mature mRNA that is otherwise spliced as a part of intron
alternative splicing
g allows different polypeptides to be made from the same structural gene in order regulate which exons occur in an RNA transcript
house keeping genes
genes that encode proteins required in most cells of a multicellular organism which means Cytosine bases in CpG islands are unmethylated
histone variants
histone proteins whose amino acid sequences are slightly different from the standard histones. They often play a specialized role in chromatin structure and function. Change the composition of nucleosomes by replacing histones. H1,H2A,H2B, H3 are examples.
activator
is a regulatory protein that binds to DNA and increase the rate of transcription (up regulation) . The DNA strand it binds to is called the enhancer (regulatory element)
Insulators
is a segment of DNA that functions as a boundary between two genes. An insulator is so named because it protects, or "insulates," a gene from the regulatory effects of a neighboring gene.
Motif
is the domain or portion of the domain of transcription factor has similar structure and function in different proteins
ferritin and transferrin regulator protein
key proteins that are measured to check for iron deficiency
open conformation
loosely packed chromatin that can be transcribed by allowing RNA Poly II to bind to promoter.
trans-acting factors
orientation independent (bidirectional) and consist of a few bp upstream of the promoter or distant or downstream or in introns
coactivators
proteins that increase the rate of transcription but do not directly bind to the DNA itself. So they bind to activator to exert their effect
recognition helix
recognizes and makes contact with a base sequence along the major groove of DNAHydrogen bonding between an a-helix and nucleotide bases is one way a transcription factor can bind to DNA. Found in helix loop helix motif & helix turn helix motif.
steroid receptors
regulatory transcription factors that respond to steroid hormones such as glucocorticoid receptor
Silencers
repressor protein bind to this DNA strand to decrease the rate of transcription (down regulation)
3'untranslated region
sequence between stop codon and polyA tail. 3'-UTP can contain sequences that act as destabilizing elements, such as adenylate-uridylate-rich elemenT. ARE contains consensus sequence AUUUA→recognized and bound by proteins→regulate degradation of mRNA
siRNAs
small interfering RNAs, turn off gene expression by directing degradation of selective mRNAs and the establishment of compact chromatin structures
de novo methylation
the methylation of DNA that has not been previously methylated.
maintenance methylation
the methylation of hemimethylated DNA following DNA replication
combinatorial control
the phenomenon observed in eukaryotes in which the combination of many factors determines the expression of any gene. ( One or more activators may simulate RNA Polymerase to initiate transcription, one or more repressor inhibit transcription) and the function of activators and repressor may be effected by small effector proteins, protein protein interaction, and covalent modification, DNA methylation, and nucleosome structure)
poly-A binding protein
this protein binds to the 3' end of mature RNA, preventing premature degradation and provides stability. As mRNA ages, polyA tail is shortened by cellular exonucleases → when shorter than 10 to 30 A in length → polyA-binding protein can no longer bind→ degrades the MRNA
heterodimer
when two polypeptides encoded by different genes bind to each other to form a dimer
homodimer
when two polypeptides encoded by the same gene bind to each other to form a dimer.
Mediator
a large complex of proteins that interacts with RNA POLY II and various transcription factors. Depending on it interaction with transcription factors it can inhibit or stimulate transcription
Nucleosome-free region (NFR)
a region within a eukaryotic chromosome where nucleosomes are not found. A site that is missing histones and is Typically 150bp long. Although the NFR may be required for transcription, it is not, by itself, sufficient for gene activation
DNA methylation
a regulatory mechanism in which an enzyme attaches covalently attaches a methyl group (-CH3) to a base in DNA. This occurs through DNA methyltransferase that attaches a methyl group to each cytosine in 5'. This silences gene expression
CREB protein
a regulatory transcription factor that becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentration of the molecule cyclic adenosine monophosphate
iron regulatory element (IRE)
a sequence in MRNA recognized by the iron regulatory protein
regulatory sequence
a sequence of DNA that binds a regulatory protein thereby influences gene expression. Operator sites in bacteria and silencers are examples
cAMP response element
a short DNA sequence found next to certain eukaryotic genes that is recognized by the cAMP response element-binding (CREB) protein. sequence: 5'-TGACGTCA-3'
iron regulatory protein (IRP)
a translational regulatory protein that recognizes iron response elements that are found in specific mRNAs. It may inhibit translation or stabilize the mRNA.
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 promoter.
Glucocorticoids receptor
a type of steroid receptor that functions as regulatory transcription factor. promote glucose utilization, fat mobilization and protein breakdown