Exam III Review control of transcription initiation chapter 16 Flashcards
Promoters
Regulatory regions for genes transcribed in a cell type specific manner, always very close to the genes protein coding region. Upstream.
Tata box
Part of the promoter upstream of the transcription initiation site binding of RNA polymerase occurs here, An initiation box consisting of roughly 7 nucleotide sequence T a T a (a or T) a (A or T), Allows basal level of transcription
Enhancer
A regulatory site that can be quite distant – up to 10,000’s nucleotides away from the promoter, can augment or repress Basal levels of transcription. A single _______ may have multiple binding sites for different transcription factors. Maybe located either five prime or three prime to the transcription start site
Sequence specific DNA binding proteins that influence transcription (basal factors, activators, or repressors)
Transcription factor
Tata box binding protein, assists in the binding of RNA polymerase II to the promoter
Basal transcription factor TBP
Tata box binding protein associated factor recruited by TBP, assists in the binding of RNA polymerase two
Basil transcription factor TAF (Tbp – associated factors)
Transcription factors that bind to enhancers to increase transcriptional activity by interacting directly or indirectly with Basal factors at the promoter. Responsible for much of the variation in levels of transcription of different genes.
Activators
The structural domain with in an activator protein which mediates binding to enhancer DNA, which interact with other proteins to activate transcription
DNA – binding domain
DNA-binding motifs found in activators
DNA binding domain helix loop helix
DNA-binding structure found mainly in eukaryotic activator proteins
Zinc fingers
DNA-binding structure found mainly in prokaryotes Activator proteins for example the lack repressor
Helix turn helix
Part of an activator that binds to DNA, binds to either identical (homodimer) or non-identical heterodimer subunits
Dimerization domain
A helix with Leucines at regular intervals, June – June homodimers May interact, June – fos heterodimers may interact. Both are motifs found in activator proteins
Leucine zipper dimerization domain
Eukaryotic transcription factors that bind specific DNA sites near a gene and prevent the initiation of transcription of the gene by recruiting call repressor proteins that either prevent the RNA polymerase II complex from finding the promoter or modify histones to close chromatin structure
Repressor
Indirect repression. A protein can bind the activation domain of an activator bound to an enhancer and thereby prevent the activator from functioning
Quenching
Part of the activator protein that binds to other proteins
Activation domain
Competition due to overlaping binding sites, quenching, (repressor blocks activation domain) cytoplasmic sequestration, heterodimerization
Ways and indirect repressor can interfere with the function of an activator
DNA sequences located between a promoter and an enhancer that block the enhancer from activating transcription from that promoter
Insulators
Binds insulators and facilitates the formation of DNA loops
Ccctc binding factor CTCF
One chromatin is isolated from the cell nuclei. Two DNA and proteins are chemically cross-linked wig formaldehyde. Three DNA is fragmented by sonication. Four antibody specific to the protein of interest is used. Five DNA to which protein was bound is purified and sequenced.
Chromatin immunoprecipitation-sequencing Chip-seq)
Beyond genetics specifically beyond the nucleotide sequence of DNA (modifications)
Epigenetics
A methyl group is added to a cytosine base that is followed by a guanine by DNA methyl transferases. Control of transcription.
DNA methylation
Regions with a high concentration of CPG dinucleotides
CPG islands
When a cpg island near a promoter is unmethylated, the gene is transcriptionally active. In the absence of a transcriptional activator, the CPG Island becomes methylated. Methyl CPG binding proteins bind and close the chromatin structure.
DNA methylation at cpg islands silences gene expression
Caused by a loss of function mutations in meCPg (methyl CPG binding protein) gene on the X chromosome.
Rhett syndrome
Long term repression through DNA methylation
Silencing
Expression of an allele depends on the parent that transmits it. Methylation at imprinting control regions ICRs silences Jean expression.
Genomic imprinting
Paternal allele is silence, maternal allele is expressed
Paternally imprinted
Maternal allele is silenced, paternal allele is expressed
Maternally imprinted
Deletion on a chromosome 15 passed from mother
Angelman syndrome
Deletion on chromosome 15 passed from father, never feel full
Prater – Willi syndrome
In IGF-II transcriptional repressor binds to unmethylated DNA and prevents transcription
CTCF
Imprinting only occurs in placental mammals. Maternally imprinted paternally express genes like IGfr II promote prenatal growth while paternally imprinted maternally express genes like IGFr2 restrict prenatal growth
Parental conflict hypothesis
At the level of RNA, splicing, stability, and localization (where it gets to). At the level of protein, synthesis, stability, localization, and modifications.
Post transcriptional regulation can occur at many steps
a class of small, RNAs They play an important regulatory role by targeting specific mRNAs for degradation or translation repression. Negative regulators of target mRNAs resulting in the destruction of these mRNAs or preventing them from being translated
Micro RNA’s
Ribonuclease enzyme in the nucleus that processes/crops pre-miRNAs (double-stranded stem loops)
Drosha
Ribonuclease enzyme that cuts loop in the cytoplasm
Dicer
MiRNAs become incorporated into ribonucleoprotein complexes that contain particular member of the Argonaut protein family. Becomes functional and highly specific by eliminating the MiRNA strand that is partially complementary to the MiRNA that will serve as the guide.
MiRISC’s
After transcription pri-mirna are recognized by Drosha in the nucleus which crops out pre-MiRNA stem loop structures. When transported into the cytoplasm pre MiRNA is diced by dicer. MiRNA MiRNA duplex is degraded and picked up by risc. Risc degrades the strand that is complementary to the MiRNA that will serve as the guide to RIsC (RNA induced silencing complex).
MiRNA processing
Rna induced silencing complex. Binding to messenger RNA results in cleavage.
RISC
RNA polymerases one, two, and three.
One, transcribes genes that encode the major RNA components of ribosomes (rRNAs). Two, transcribes genes that encode all proteins. Three, transcribes Genes that encode the transfer RNAs as well as certain other small RNA molecules
Post transcriptional processing
Splicing, polyadenylation, 5’ cap addition
Sqcchd
Sequestration, quenching, competition, chromatin, direct
Indirect repression. Repressor vs activator
Three ways eukaryotes regulate their genes
Three are in a polymerases. Post transcriptional regulation. Imprinting.
Post transcriptional regulation. RNA. SLs.
Splicing, localization, stability.
Post transcriptional regulation. Protein. SSLM.
Synthesis, stability, localization, modifications.
Post transcriptional regulation. RNA. SLs.
Splicing, localization, stability.
Post transcriptional regulation. Protein. SSLM.
Synthesis, stability, localization, modifications.
Transcription factors that bind to enhancers to increase transcriptional activity by interacting directly or indirectly with Basal factors at the promoter. Responsible for much of the variation in levels of transcription of different genes.
Activator
