Elsevier

Genomics

Volume 82, Issue 6, December 2003, Pages 637-643
Genomics

Regular article
Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer☆

https://doi.org/10.1016/S0888-7543(03)00199-XGet rights and content

Abstract

DNA from a single bacterial artificial chromosome clone was used to sequence the mouse ribosomal DNA intergenic spacer from the 3′ end of the 45S pre-RNA to the spacer promoter (Accession No. AF441733). This made possible the assembly of a complete mouse ribosomal DNA repeat unit (45,309 bp long, TPA Accession No. BK000964). Analysis of the intergenic spacer (IGS) showed a high density of simple sequence repeats and transposable elements. The IGS contains two long sequence blocks, which are repeated tandemly. Some of the sequences in these blocks are also present in other parts of the IGS. A difference in the mutation rate along the mouse IGS was observed. The significance of sequence motifs in the IGS for transcription enhancement, transcription termination, origin of replication, and nucleolar organization is discussed.

Section snippets

Sequencing of the intergenic spacer and assembly of a complete rDNA repeating unit

We identified a BAC clone (RP23-225M6) that contained one complete rDNA unit and subcloned and sequenced a substantial part of it (see Materials and methods). Sequences from the EcoRI site in the 28S rRNA gene to the SalI site downstream of the spacer promoter were deposited with DDBJ/EMBL/GenBank (31,129 bp; Accession No. AF441733).

The sequences of the enhancer and the 45S pre-rRNA gene are known, which allowed us to assemble one complete mouse rDNA repeating unit (45,309 bp) by combining the

Identification of the RPCI23 library BAC clone

In the database Genome Survey Sequences (dbGSS) we identified a BAC clone that contained rDNA sequences starting and finishing at the same EcoRI site in the 18S rRNA gene (Accession No. AZ700886—the SP6 end; Accession No. AZ700888—the T7 end). The identified clone (RP23-225M6) was from a library of partially EcoRI-digested female C57BL/6J genomic DNA and was obtained through the Internet (http://www.chori.org/bacpac). The clone DNA was Qiagen purified, digested with restriction enzymes,

Acknowledgements

We thank Ingrid Grummt (German Cancer Research Center, Heidelberg, Germany), Barbara Sollner-Webb (The Johns Hopkins University School of Medicine, Baltimore, MD, USA), and Milko Kermekchiev (Washington University, St. Louis, MO, USA) for mouse rDNA clones pSalA 1.0 and pSalA 1.2, p5′-1800, and pMr100, respectively. We thank Bojana Dimitrova (Institute of Molecular Biology, Sofia, Bulgaria) for her excellent technical assistance.

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    Sequence data from this article have been deposited with the DDJB/EMBL/GenBank Data Libraries under Accession Nos. AF441733, AF441734AF441739, AF452414, and AF452415 and in the Third Party Annotation Section of the DDBJ/EMBL/GenBank databases under Accession No. TPA: BK000964.

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