<P> Crystal structures of RNA polymerases I and II provide an opportunity to understand the interactions among the subunits and the molecular mechanism of eukaryotic transcription in atomic detail . </P> <P> The carboxyl terminal domain (CTD) of RPB1, the largest subunit of RNA polymerase II, plays an important role in bringing together the machinery necessary for the synthesis and processing of Pol II transcripts . Long and structurally disordered, the CTD contains multiple repeats of heptapeptide sequence YSPTSPS that are subject to phosphorylation and other posttranslational modifications during the transcription cycle . These modifications and their regulation constitute the operational code for the CTD to control transcription initiation, elongation and termination and to couple transcription and RNA processing . </P> <P> The initiation of gene transcription in eukaryotes occurs in specific steps . First, an RNA polymerase along with general transcription factors binds to the promoter region of the gene to form a closed complex called the preinitiation complex . The subsequent transition of the complex from the closed state to the open state results in the melting or separation of the two DNA strands and the positioning of the template strand to the active site of the RNA polymerase . Without the need of a primer, RNA polymerase can initiate the synthesis of a new RNA chain using the template DNA strand to guide ribonucleotide selection and polymerization chemistry . However, many of the initiated syntheses are aborted before the transcripts reach a significant length (~ 10 nucleotides). During these abortive cycles, the polymerase keeps making and releasing short transcripts until it is able to produce a transcript that surpasses ten nucleotides in length . Once this threshold is attained, RNA polymerase passes the promoter and transcription proceeds to the elongation phase . </P> <P> Pol II - transcribed genes contain a region in the immediate vicinity of the transcription start site (TSS) that binds and positions the preinitiation complex . This region is called the core promoter because of its essential role in transcription initiation . Different classes of sequence elements are found in the promoters . For example, the TATA box is the highly conserved DNA recognition sequence for the TATA box binding protein, TBP, whose binding initiates transcription complex assembly at many genes . </P>

Where does transcription begin and what are the steps of transition
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