In mammalian cells RNA polymerase II efficiently transcribes nucleosome-packaged 
DNA. In this regard, a fundamental question concerns the nature and mechanism of 
action of the accessory factors that are necessary and sufficient for, or 
enhance, transcription through nucleosomal arrays by RNA polymerase II. Here we 
describe a highly purified system that allows for efficient activator-dependent 
transcription by RNA polymerase II from the promoter through several contiguous 
nucleosomes on defined chromatin templates. The system contains natural or 
recombinant histones, chromatin assembly factors, the histone-acetyltransferase 
p300, all components of the general transcription machinery, general 
coactivators and the elongation factor SII (TFIIS). As examples of the 
applicability of this system for mechanistic analyses of these and other 
factors, representative experiments show (i) that activated transcription from 
chromatin templates is concomitantly dependent on the activator, p300-mediated 
histone acetylation and elongation factor SII/TFIIS. (ii) that SII/TFIIS acts in 
a highly synergistic manner with p300 (and histone acetylation) at a step 
subsequent to preinitiation complex (PIC) formation and (iii) that SII/TFIIS 
works directly at the elongation step of chromatin transcription. Here we 
describe purification methods for the different factors employed and the 
specific transcriptional assays that led to the above-mentioned conclusions. 
This purified system will be very useful as an assay system for the discovery of 
new factors or the mechanistic analysis of known or candidate factors involved 
in transcription initiation or elongation on chromatin templates, including 
factors that effect specific histone modifications or nucleosomal remodeling.