Genome-wide expression analysis was used to identify genes whose expression depends on the functions of key components of the transcription initiation machinery in yeast (Figure N4). The mRNA levels of 5460 genes were accurately determined using high-density olionucleotide arrays.
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| Complex and Subunit | Features |
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| RNA pol II: Rpb1 | Largest subunit |
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| SRB/MED: Srb4 | Target of Gal4 activator |
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| SRB/MED: Med6 |
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| SRB/MED: Srb10 | CTD kinase, negative reg. |
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| SWI/SNF: Swi2 | ATP-dependent chromatin remodeling |
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| SAGA: TAF17 | Component of SAGA and TFIID |
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| SAGA: Gcn5 | Histone acetylase |
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| GTF: TFIID (TAFII 145) | Histone acetylase |
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| GTF: TFIIH (Kin28) | CTD kinase |
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From: Thomas et al. (1998) Cell 93, 627-637. Factor SII (or TFIIS) stimulates an intinsic RNA cleavage activity of RNA polymerase II. In the presence of SII, pol II quantitatively removes misincorporated nucleotides from the nascent transcript during rapid chain elongation. The basis of discrimination between the correct and incorrect base is the slow addition of the next nucleotide to the mismatched terminus. SII can also rescue arrested complexes and allow the resumption of elongation. Thus, TFIIS plays a role similar to the E. coli GreA and GreB factors.
Modification of the 5'-ends of eukaryotic mRNAs is called capping. The cap consists of a methylated GTP linked to the rest of the mRNA by a 5' to 5' triphosphate "bridge"(Cap Structure). Capping occurs very early during the synthesis of eukaryotic mRNAs, even before mRNA molecules are finished being made by RNA polymerase II. Capped mRNAs are very efficiently translated by ribosomes to make proteins. In fact, some viruses, such as poliovirus, prevent capped cellular mRNAs from being translated into proteins. This enables poliovirus to take over the protein synthesizing machinery in the infected cell to make new viruses.
Modification of the 3'-ends of eukaryotic mRNAs is called polyadenylation (Polyadenylation Pathway). Polyadenylation is the addition of several hundred A nucleotides to the 3' ends of mRNAs. All eukaryotic mRNAs destined to get a poly A tail (note: most, but not all, eukaryotic mRNAs get such a tail) contain the sequence AAUAAA about 11-30 nucleotides upstream to where the tail is added. AAUAAA is recognized by an endonuclease that cuts the RNA, allowing the tail to be added by a specific enzyme: polyA polymerase.