Three organizations of human DNA.

Abstract

Human DNA was denatured, annealed to low Cot, and fractionated by centrifugation to equilibrium on gradients of NaL. Three well-defined zones resulted. The topmost, least dense zone contained satellite DNA. The bottom zone contained molecules bearing infrequent sequences and short repeated DNA. The middle zone contained molecules bearing infrequent sequences, short repeated DNA, and long repeated DNA. The Nal pattern was independent of single-strand DNA chain length from 5 to 30 kdlobases. Structural genes were found in the organization bearing long repeats.About 30%o of the human genome consists of repeated sequences (1), of which over half are repeated more than 1() times per genome. Some of these repeated sequences are organized in long, tandem arrays, while others are interspersed among less frequently represented sequences including structural genes. Some of the major families of human interspersed repeated DNA sequences have been identified. The largest family consists of 3 X 105 copies of related sequences, each about 300 nucleotides long, with most members having a site that can be cleaved by the restriction endonuclease Alu I (2). This group of sequences is collectively called the Alu family and is represented by a cloned DNA named "Blur 8" (3). Other, less frequently represented, short, interspersed repeated sequences (SINES) have been reported more recently by Deininger et al (4) and Miesfeld et al. (5).Adams et at (6) reported a longer interspersed repeated DNA sequence (LINES) that was 6,400 nucleotides long on the average and was represented some 4 X 103 times per genome. In six cloned representatives of the 6.4-kilobase (kb) repeat, the region of apparent repetition ranged from 5 to 9 kb, some 20 times longer than members of the Alu family. Maio et al (7) and Gillespie et al (8) reported families of human LINES characterized by two Kpn I sites spaced 1,200, 1,500, 1,800, and 1,900 nucleotides apart, respectively. Each of the four families of Kpn LINES consists of about 5 x 103 members. The 6.4-kb repeat contains Kpn 1,200-nucleotide LINES within it but carries no sequences closely related to Kpn 1,800-nucleotide LINES (9).Though each of the interspersed repeated DNA families is assigned a length, the designation is a matter of convenience and is not meant to define each member. Alu family members, for example, average 300 nucleotides, but lengths of individual members vary from <100 nucleotides to >350 nucleotides. As mentioned above, the 6.4-kb repeat also varies in length.Thus, the length of individual interspersed repeated DNA elements varies both among and within the different repeated DNA families described above. Similarly, infrequent DNA sequences vary in length. For these reasons we were surprised to discover apparent severe limitations on the length ratio of repeated sequences to adjacent infrequent sequences in human DNA elements. Human DNA was denatured, annealed to low Cot so that only repeated DNA formed duplexes, then the hybridized complexes were fractionated according to t...

A series of repetitive DNA sequences are associated with human core and H1 histone genes

“…Although Kpn repetitive sequences were not found elsewhere in any of our 12 recombinant clones, the signal produced by hybridization to the 3.2 kb fragment containing the H3 histone gene was strong and reproducible (data not shown). These results are in agreement with previous work showing Kpn sequences to be located near human structural genes (30).…”

Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA

“…Isochore (chromosome band) organization in mammals. One of the most telling findings in molecular cytogenetics is the observation that mammalian genomes are highly structured entities (Strayer et al, 1983;Holmquist, 1989). The chromosomes of higher vertebrates can be separated into several isochore classes by isopycnic density gradients using special ligands (Bemardi, 1989).…”

Recent amplification of an alpha satellite DNA in humans

“…Alu repeats may be found in the vicinity of known genes or even within a transcription unit (9,10). The Kpn family of primate LINES (11,12) is present in approximately 50,000 copies and members are also located near structural genes (13). Other less abundant species of SINES and LINES exist in primate DNA (14).…”