Functional organization of the mammalian genome

A considerable proportion, one third or more by weight, of the nuclear transcripts of the mammalian cell, rat ascites tumor, consists of molecules 15 to 30 kilobases in length. These transcripts contain both middle repetitive and single copy sequences. Analysis of the sequence structure of rat DNA indicates that it is organized into interspersed units of middle and single copy sequences. The middle repetitive DNA consists of sequences about 300 base pairs in length, and, in 60% of the instances, is followed immediately by another repetitive sequence. The single copy spacers range in size from 500 to 16,000 base pairs. The giant transcripts are possibly products of several such DNA structural units of the genome, in which case, it is predicted that they should contain interspersed middle repetitive and single copy sequences, reflecting the organization of the DNA from which they were transcribed. The nucleus also contains smaller RNA molecules which become labeled during a 30 min pulse labeling period. Whether these are true primary transcripts or whether they represent breakdown products of the giant transcripts is a matter for further investigation. The authors further considered the problem of separation of the template active portions of chromatin from the template inactive ones. They enriched the template active portions approximately 4 to 5 fold over the original chromatin. The template active portions of chromatin are characterized by a high content of nonhistone chromosomal protein and a low content of histones. The histone complement of the template active portion, such as it is, is also remarkable in that it lacks histone I and is impoverished in histone IV. The proportion of the template active chromatin isolated from whole chromatin by the methods used is in close agreement with the proportion of chromatin which is template active as transcribed by either homologous or heterologous RNA polymerase.