eukaryotic transcription Flashcards
messenger RNA (mRNA)
encodes the AA sequence for a protein; primary transcript of a gene undergoes RNA processing to generate a mature mRNA that can be used by the ribosome
transfer RNA (tRNA)
delivers an amino acid to the ribosome
ribosomal RNAs (rRNA)
components of a ribosome
small nuclear RNA (snRNA)
components of the spliceosome, the enzyme that catalyzes removal of introns during RNA processing
microRNA (miRNA) and small interfering (siRNA)
act on mature mRNAs to decrease translation of the mRNA
small nucleolar RNAs (snoRNA)
small RNA molecules that guide posttranscriptional base modifications in tRNAs, rRNAs, and snRNAs
long non-coding RNA (lncRNA)
RNA molecules that do not encode protein; some lncRNAs influence gene expression
eukaryotic genes stand alone in single transcription units. each gene has its own ___________ and __________
promoters and terminators
the genes are organized with ___________ structure
- _____ code for sequence that will be included in a mature mRNA
- ______ sequences will be eliminated during RNA processing
- a _______________ includes both introns and exon sequences
intro-exon; exons; introns; primary transcript
___________ is a light staining material
- the level of staining suggests a more open chromatin structure
- the genes in _______ are available for transcription
euchromatin
___________ is the dark staining matter in a nucleus
- the level of staining reflects a condensed chromatin structure
- the DNA contains silenced genes and many types of repetitive DNA
heterchromatin
constitutive heterchromatin
always in heterochromatin state; telomeres (no genes so nothing to express
facultative heterchromatin
differs between cell types; can revert to euchromatin under certain stimuli
the ___________ is the basic unit of chromatin
nucleosome
DNA-histone core contacts are ___________________
- ______________ and ___________ occur between the positively charged ______________ and the negatively charged ________________ of DNA
sequence independent; electrostatic interactions and H-bonds; histone proteins; sugar-phosphate backbone of DNA
a _______________ contains two copies each of histones ____, _____, ___, and ____
- disordered histone tails interact with other nucleosomes
histone core; H2A, H2B, H3, and H4
_____________ locks DNA to the nucleosome
Histone H1
chromatin structure is a product of the combined actions of _____________, such as _________________ and _____________, and trans-acting _____________________ that bind to epigenetic marks or to DNA
epigenetic marks; histone modifications; DNA methylation; transcription factors
condensed chromatin is “closed” and viewed as transcriptionally silent
- inaccessible to most activators and chromatin remodeling complexes
- accessible only by ___________________________
pioneering transcription factors
____________ means above genetics. the mediators of epigenetics are covalent modifications of the chromatin or DNA that do NOT affect the DNA sequence of bases (just affects access)
epigenetics
the ___________ provide areas for interaction between ______________
histone tails; nucleosomes
hypermethylation
often associated with closed chromatin (heterochromatin)
histone acetylation
is found in areas of open chromatin (euchromatin)
the histone tails include the N termini of histones ___ and ____, plus both the N and C termini of ____ and ____.
H3 and H4; H2A and H2B
histone acetyltransferase (HAT)
acetylates lysine in the histone tails (euchromatin region)
histone deacetylase (HDAC)
removes acetyl groups from the histone tails (not as accessible so transcription turns off; in euchromatin region)
histone methyltransferase (HMT)
methylates lysine and arginine (lot harder to reverse; heterochromatin regions)
the actions of HATs and HDACs oppose each other so acetylation of histone tails is _____________
readily reversible
acetylation…
- reduces the electrostatic attraction between nucleosomes and with DNA
- favors recruitment of a _______________
- highly associated with transcriptional activation
neutralizes the positive charge on lysine in histone tails
chromatin remodeling complex
methylation …
- effect on transcription depends on location of amino acid and # of methyl groups
- H3K4/H3K36/H3K79 (activation)
- H3K9/H3K27/H4K20 (silencing)
retains the positive charge on lysine/arginine in histone tails
hypermethylation (DNA) of a CpG island near a promoter ______________________
silences that promoter
cytosine in the sequence CG is called a “CpG” and can be methylated by ______________________ at many sites within the genome
- some promoter proximal regions of genes have a cluster of CG’s in the sequence called a __________
DNA methyltransferase (DNMT); CpG island
once chromatin structure is open, transcription factors (___________) bind specifically to sites in DNA to facilitate transcription. In eukaryotes, most gene regulation is positive, because activators are required to recruit ___________________ to a _____________
activators; RNA polymerase II; promoter
_____________________ is recruited to a gene locus by a transcription factor and then acetylates surrounding histones.
histone acetyltransferase (HAT) -> favors DNA accessibility
__________________ like _______ manipulate nucleosomes.
chromatin remodeling complexes; SWI/SNF
______ is recruited to local sites in the genome
- ______ either binds to acetylated histone or is recruited to a gene by protein-protein interactions with a _____________________
SWI/SNF; SWI/SNF; pioneering transcription factor
chromatin remodeling complexes alter chromatin structure by:
- chromatin remodeling “spreads” to surrounding area of the genome changing the accessibility of the DNA for activator proteins
unwrapping DNA from nucleosomes
repositioning nucleosomes
evicting nucleosomes
the combined actions of _______ and ______________________ together lead to open chromatin structure
HATs and chromatin remodeling complexes
the transcription start site is devoid of _________________ to make room for assembly of the _____________________________.
- ______ bind near promoters and act to maintain open chromatin structure
nucleosomes; transcription preinitiation complex; HATS
RNA polymerase II
makes mRNA and some small RNAs
RNA polymerase I
synthesizes ribosomal rRNA
RNA polymerase III
generates tRNA and other small RNAs
if there is no _______ subunit, then it cannot locate and bind to promoters
sigma
mammalian genes have ______________ elements, but also ____________ at distant locations along the chromosome. they are binding sites for transcription factors.
promoter proximal; enhancers
______________ are sequence specific DNA binding proteins. These proteins typically have a modular design with a ________________ and _______________
transcription factors; DNA binding domain (DBD); activation domain (AD)
the DBD is designed to position a _____________ into the major groove forming chemical bonds with the base pairs.
recognition helix
recognition helix
amino acids that interact with base pairs
_____________
major structural features: two anti-parallel B strands and an a helix; Zn coordinated by 2 cys and 2 his; a conserved phe/tyr and leu
- _________ can be used to recognize many different DNA sequences
classical zinc-finger motif; Zn fingers
the recognition helix AAs facing the DNA major groove can be different for each of the Zn fingers. therefore…
each Zn finger recognizes a different sequence of bases
nuclear receptor transcription factors bind DNA as _________
- both subunits contribute one recognition helix
- each subunit has two Zn fingers: only the first Zn finger has a recognition helix and the second is a structural feature that supports the recognition helix
dimers
the level of transcription of a gene depends on the occupancy of its ____________ regulatory elements by _______________. Binding of several activators to a gene is required. The coordinate action between factors is referred to as __________________. The same gene may be subject to different regulatory mechanisms in different cell types.
cis-acting; transcription factors; combinatorial control
before initiation of transcription, what must happen?
a very large protein complex must be assembled on the cis-acting regulatory elements of a gene
transcription factor GR is a nuclear receptor that acts as an ____________ for many mammalian genes
- GR binds to _________________ located at promoter-proximal sites or in enhancers
activator; hormone response element
_____________ contain clusters of the recognition sequences for several different transcription factors; together these transcription factors account for ____________ function
- also relies on DNA bending by ____________________ proteins
enhancers; enhancer; high mobility group (HMG)
although some transcription factors directly interact with the preinitiation complex, __________ provides the primary means of communication between ___________ and the ____________________
mediator; activators; preinitiation complex
transcription preinitation complex
- ______ (complex) binds at the promoter
- _______ may join the complex (creates docking site)
- _______ binds to DNA and TBP (creates docking site)
- _____________ joins the complex by binding to TFIIB
- ____ and _____ enter the complex in succession
- ______ is a complex with two distinct functions: _________________________________ & _____________________________________
TFIID; TFIIA; TFIIB; TFIIF/RNA pol II; TFIIE and TFIIH; TFIIH; DNA helicase to generate transcription bubble and protein kinase that phosphorylated the RNA pol II CTD to initiate transcription
________ is a complex made up of _______ and many _____ proteins
TFIID; TBP; TAF
_______________ locates and binds to TATA boxes in eukaryotic promoters
- TATA boxes are present in only about 10% of promoters
- TBP is an example of a minor groove DNA binding protein
TATA binding protein (TBP)
________________ methylates H3K9->H3K9me3
- provides a docking site for _________________
histone methyltransferase (HMT); heterochromatin protein (HP1)
