| what are basal transcription factors ? | Transcription factors required by RNA polymerase II to form the initiation complex at all RNA polymerase II promoters. theses factors are TFIIX, where X is a letter. |
| what are core promoter ? | The shortest sequence at which an RNA polymerase can initiate transcription (typically at a much lower level than that displayed by a promoter containing additional elements). |
| what are core promoters when considering RNA polymerase ll? | it is the minimal sequence at which the basal transcription apparatus can assemble, and it includes three sequence elements: the Inr, the TATA box, and the DPE.
It is typically ~40 bp long. |
| what are enhancers? | A cis-acting sequence that increases the utilization of (most) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. |
| what's a silencer? | A short sequence of DNA that can inactivate expression of a gene in its vicinity. |
| what are housekeeping genes? | Genes that are (theoretically) expressed in all cells because they provide basic functions needed for sustenance of all cell types. |
| what's a coactivator? | Factors required for transcription that do not bind DNA, but are required for (DNA-binding) activators to interact with the basal transcription factors. |
| what are the roles of RNA polymerase l , RNA polymerase ll ,and RNA polymerase lll ? | -RNA polymerase I synthesizes rRNA in the nucleolus.
-RNA polymerase II synthesizes mRNA in the nucleoplasm.
-RNA polymerase III synthesizes small RNAs in the nucleoplasm. |
| what are heterogeneous nuclear RNA (hnRNA) ? | RNA that comprises transcripts of nuclear genes made primarily by RNA polymerase II; it has a wide size distribution and variable stability. |
| how many subunits do eukaryotic RNA polymerases have, what's the most common and biggest subunit? | have ~12 subunits and are complexes of ~500 kD.some of these subunits are common in all 3 polymerases. The largest subunit in RNA polymerase II has a CTD (carboxy-terminal domain) consisting of multiple repeats of a heptamer. |
| what's a nontranscribed spacer, what's RNA Polymerase I Has a Bipartite Promoter ? | -its the region between transcription units in a tandem gene cluster.
The RNA polymerase I promoter consists of a core promoter and an upstream promoter element (UPE).
The factor UBF1 wraps DNA around a protein structure to bring the core and UPE into proximity. |
| what's factor does SL1 include? what does RNA polymerase l bind to? | SL1 includes the factor TATA-binding protein (TBP) that is involved in initiation by all three RNA polymerases.
RNA polymerase I binds to the UBF1-SL1 complex at the core promoter. |
| what are the 2 types of RNA polymerase promotors? | 1-Internal promoters have short consensus sequences located within the transcription unit and cause initiation to occur at a fixed distance upstream.
2-Upstream promoters contain three short consensus sequences upstream of the start point that are bound by transcription factors. |
| what are RNA polymerase lll assembly factors ? | Proteins that are required for formation of a macromolecular structure but are not themselves part of that structure.
TFIIIA and TFIIIC bind to the consensus sequences and enable TFIIIB to bind at the startpoint , it has TBP as one subunit and enables RNA polymerase to bind. |
| what's the preinitiation complex ? | The assembly of transcription factors at the promoter before RNA polymerase binds in eukaryotic transcription. |
| what are RNA polymerase II 's transcription factors and promoters? what's common component of these promoters? | general transcription factors (called TFIIX) to initiate transcription.the promoters frequently have a short conserved sequence Py2CAPy5 (the initiator Inr) at the start point.
-The TATA box is a common component of RNA polymerase II promoters and consists of an A-T-rich octamer located ~25 bp upstream of the start point. |
| what's the RNA Polymerase II downstream promoter element (DPE)? | a common component of RNA polymerase II promoters that do not contain a TATA box (TATA-less promoters).
A core promoter for RNA polymerase II includes the Inr and, commonly, either a TATA box or a DPE. |
| what is the TBP factor ? | TBP is a component of the positioning factor that is required for each type of RNA polymerase to bind its promoter. it binds to TATA box in the minor groove of DNA، as well as TATA box in the minor groove of DNA.
The factor for RNA polymerase II is TFIID, which consists of TBP and ~14 TAFs, with a total mass ~800 kD. |
| how does the Basal Apparatus Assembles at the Promoter? | The upstream elements and the factors that bind to them increase the frequency of initiation.
Binding of TFIID to the TATA box or Inr is the first step in initiation. |
| what other factors bind to the complex in a defined order to extend the length and protect the DNA region? | -TFIIB, TFIIE, and TFIIH are required to melt DNA to allow polymerase movement.
-Phosphorylation of the CTD is required for promoter clearance and elongation to begin.
-Further phosphorylation of the CTD is required at some promoters to end pausing and abortive initiation.
RNA polymerase II binds to the complex, it may initiate transcription. |
| what is the Promoter Clearance and Elongation that follows initiation to begin ? | FIIB, TFIIE, and TFIIH are required to melt DNA to allow polymerase movement.
Phosphorylation of the CTD is required for promoter clearance and elongation to begin.
Further phosphorylation of the CTD is required at some promoters to end pausing and abortive initiation. |
| what happens to the Promoter Clearance and Elongation? | The histone octamers must be temporarily modified during the transit of the RNA polymerase.
The CTD coordinates processing of RNA with transcription.
Transcribed genes are preferentially repaired when DNA damage occurs.
TFIIH provides the link to a complex of repair enzymes. |
| what Enhancers Contain Bidirectional Elements That Assist Initiation? what the role of a receptor? | -An enhancer activates the promoter nearest to itself and can be any distance either upstream or downstream of the promoter as well as form complexes of activators that interact directly or indirectly with the promoter.
-creating an upstream activating sequence (UAS) in yeast behaves like an enhancer, but works only upstream of the promoter.
the repressor – A protein that inhibits expression of a gene.
It may act to prevent transcription by binding to an enhancer or silencer. |
| how do Enhancers increase concentration of activators near the promoter? | Enhancers usually work only in cis configuration with a target promoter.
The principle is that an enhancer works in any situation in which it is constrained to be in the same proximity as the promoter. |
| how is Gene Expression Is Associated with Demethylation ? | Demethylation at the 5′ end of the gene is necessary for transcription. |
| what are CpG islands ? | they are regulatory targets that surround the promoters of constitutively expressed genes where they are unmethylated.
CpG islands also are found at the promoters of some tissue-regulated genes.
There are ~29,000 CpG islands in the human genome. |
| what does methylation of CpG islands do? | it prevents activation of a promoter within it.
Repression is caused by proteins that bind to methylated CpG doublets. |
