Human ribosomal RNA intergenic spacer sequence

The human rDNA tandem repeat consists of 13.3 kb of transcribed sequence and about 30 kb of intergenic spacer of unknown function. For descriptive purposes, it is convenient to divide the ribosomal repeat into 4 EcoRI fragments, A D . The C fragment contains only intergenic spacer sequences, and ends some 500 bp upstream of the ribosomal RNA promoter. We had previously described the terminal BamHI—EcoRI segment of the C fragment (CBE) (1) and have now completed our characterization of this spacer fragment by sequencing the remaining 7.4 kb from 5' EcoRI through BamHI no. 6 (CEB6) (Figure 1). Comparison of the CEB6 segment with other parts of the rDNA repeat shows some similarities and some marked differences: (i) Its base composition is A: 23.4%; G, 24%; C: 25.4% and T: 27%, while other parts of the repeat have skewed base compositions, GC-rich and CT-rich (1—3). (ii) It contains relatively few simple sequence repeats, and these are found adjacent to and between Alu (SINE) elements. The simple sequence repeats include: [GTTT], [CAGG], and [TTTA]. This contrasts with large blocks of simple sequence repeats found both in the transcribed regions and in previously reported spacer segments (1—4). (iii) This spacer segment contains no large repeated blocks as are found in the spacer just upstream of the promoter (1) and in the spacer 3' to the transcribed region (3). (iv) A survey covering 1.2 kb each from six individual CEB6 clones showed a low level of sequence variability at 4 sites: 1038 G to C, 1 clone; 4,160 C to T, 1 clone; 4,189 G to A, 2 clones; 6,424 1 additional TTTA repeat, 1 clone, (v) Just like other spacer segments, CEB6 contains Alu elements; these are mostly complete, in contrast with those found in the first 6,500 bp section of the 3' spacer which contains 1 complete and 1 slightly truncated elements (3), plus 12 Alu fragments ranging in size from 32 to 177 bp (as identified by ILG). Three complete (c) and 3 truncated (t) Alu elements are found at positions 1220-1385 (t), 2219-2499 (c), 5779-5928 (t), 6058-6341 (c), 6457-6741 (c), and 6821—6927 (t), as indicated by arrowheads in Figure 1; also indicated in the Figure are the Alu elements previously identified in the adjacent CBE segment (1). Alu elements 6 and 9 are of relatively recent origin: they are flanked by recognizable direct repeats and they belong to the 'younger' families (Alu6 belongs to class Sc and Alu9 to class Sb) (5). However, these Alu elements have had time to become fixed in all copies of the rDNA, as shown in the Southern blot of Figure 2, where Alu 6 and 9 probes hybridize to distinct single bands. REFERENCES