Transcription can be easier explained by breaking the entire process into three steps: initiation, elongation, and termination. The entire transcription process takes place within the nucleus of the cell, in which RNA polymerase II is the key component. RNA polymerase II combines with five transcription factors (TFIIB, TFIID, TFIIE, TFIIF, TFIIH), and Mediator at a promoter sequence on the DNA strand. Together, this complex contains at least 50 polypeptide strands, or 62 subunits.

TFIIB, along with TFIID, is responsible for determining the start site on the DNA strand. Together, these three components make up the main initiation complex. TFIID binds to the TATA box on the DNA strand through TBP (TATA binding protein). The TATA box is otherwise known as the initiation binding site, which is a DNA sequence of 5'-TATAA-3'.

TFIID, once bound to the TATA box, is able to bend the DNA strand around the TFIIB. The requirement for TFIIB interaction with the polymerase II protein through the DNA strand has been shown through various research studies involving yeast systems to be necessary for transcription because it is directly bound to the polymerase. This connection is done through a zinc ribbon domain that contact with the docking domain of the polymerase. [4]

Until this point, the DNA strand is still in a closed complex or the double helix is still intact.

As mentioned before there are five total transcription factors and Mediator that play important roles in the initiation step.  TFIIF interacts with the non-template side of the DNA strand in order to block this side from re-binding to the template strand.  TFIIE couples polymerase II with TFIIH, which promotes the opening of the double helix and weakens the bonds between the paired nucleotides.

The site at which DNA replication takes place has recently been researched by Roger D. Kornberg, resulting in specific and detailed information regarding this process.  At the activation site within the polymerase, the entire DNA double helix enters the protein, begins to split, and the template side of the strand forms a hybrid helix with individual nucleotides found free-floating within the nucleus.  The hybrid helix is a stable molecule that is usually only a few nucleotides long, usually eight or nine residues, and forms at a 90° angle to the incoming DNA strand.  The nucleotides enter through an opening in the bottom part of the polymerase II active center.  As the hybrid helix moves through the active site, the complementary DNA strand is split from the template strand, forming a single strand known as mRNA that exits through the top of the enzyme, while the template strand reforms as the DNA double helix.

 At the active site, new nucleotides are added to the RNA strand by matching them with the template strand of the DNA. The active site of the transcription process is composed of two metal ions. Metal A is responsible for the binding of the incoming nucleoside triphosphate by coordinating with the alpha-phosphate, while the other, Metal E, coordinates with the beta and gamma-phosphates.

Within the polymerase, three protein loops interact with RNA, DNA and one another to assist with the transcription process. [5]  Residues 256-264 (subunit Rpb1) are known as “the lid” and serves as a wedge to drive RNA/DNA hybrid helix apart, forming a separation of the strands and acting to guide the RNA strand along an exit path.  Residue Phe 252 is located at the tip of the wedge and uses its aromatic side chain to connect with the DNA base at a perpendicular angle.  The rudder, which resides on residues Rpb1 310-324, acts to stabilize the unwound DNA strand just beyond the separation with the hybrid helix, before it reconnects with the non-template strand.    In bacterial, or prokaryotic transcription, the rudder also connects with the RNA, allowing for protein-RNA cross-linking.  The third protein loop, or fork loop 1, interacts with RNA at the hybrid region.  Residues Lys 471 and Arg 476 bind with RNA phosphates, preventing the unwinding of the hybrid helix. 

Like previously noted, these three protein loops interact with one another as well as with the RNA and DNA strands, in that the lid interacts with the rudder, and the rudder with fork loop 1. 

This process of elongation continues until the enzyme reaches a stop codon located within the DNA helix, and the extruded RNA is cleaved off at the active site.  Another transcription factor, labeled TFIIS is responsible for this cleave.  The polymerase complex, along with the transcription factors, then disintegrates from the DNA double-helix.