Analysis of the Sea‐Urchin Genome by Homologous RNA Polymerase II Binding

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Abstract
We observe that Paracentrotus lividus RNA polymerase II can form stable complexes with homologous DNA at sites from which it can start RNA synthesis in vitro. The sea‐urchin genome can therefore be described in terms of the distribution of the DNA sites that form such stable complexes with the homologous RNA polymerase II [class A sites as defined in a prokaryotic homologous system by D. Hinkle and M. J. Chamberlin (1972) J. Mol. Biol. 70, 157‐185].We describe the properties of the complexes that P. lividus RNA polymerase II forms with P. lividus DNA: resistance to heparin, dissociation kinetics, temperature and time dependence of their formation, range of RNA polymerase/DNA weight/weight ratios that give rise to the stable binding events.The amount and the distibution of the sites that form stable complexes with P. lividus RNA polymerase II were determined by the analysis of the dissociation of the complexes formed by the enzyme on DNA fragments of various lengths. P. lividus appears to form 4.5 × 104 stable (t1/2≥ 30 min) complexes/haploid genome. A part of these complexes has a distribution corresponding to values between 2000 and 4500 base pairs; the rest of the complexes is more widely spaced (up to a measured interval of 30000 base pairs).