Nontranscribed Spacer Sequences Promote in Vitro Transcription of Drosophila Ribosomal DNA

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1982 Nov 11

PMID 6817304

Citations 48

Authors

B D Kohorn

P M Rae

Affiliations

Soon will be listed here.

Abstract

Tandem repeats of ribosomal RNA transcription units in Drosophila melanogaster are separated by a nontranscribed spacer that is comprised in part of serial repeats of a 0.24 kb sequence. DNA sequence analysis shows that such repeats are imperfect copies of a region that includes the site of in vivo rRNA transcription initiation (ca. -240 to +30). Subclones of the rDNA spacer that are copies of the sequence extending from -34 through the initiation site support detectable in vitro transcription in a mixture involving a Drosophila cell-free extract, but accurate in vitro transcription is considerably enhanced when a nontranscribed spacer template includes a copy of the sequence extending upstream of -34. From a comparison of the sequences and transcription template-effectiveness of various rDNA subclones, we infer that a major promoter of RNA polymerase I activity lies between -150 and -30 in the rDNA nontranscribed spacer. The nontranscribed spacer copies of the initiation region are less effective templates for transcription than is the region of in vivo initiation, and there are differences between spacer repeats and the authentic sequence downstream of -240 that may account for this.

Citing Articles

Variation in the ribosomal RNA genes among individuals of Vicia faba.

Rogers S, Honda S, Bendich A Plant Mol Biol. 2013; 6(5):339-45.

PMID: 24307384 DOI: 10.1007/BF00034941.

Structure and variation in ribosomal RNA genes of pea : Characterization of a cloned rDNA repeat and chromosomal rDNA variants.

Jorgensen R, Cuellar R, Thompson W, Kavanagh T Plant Mol Biol. 2013; 8(1):3-12.

PMID: 24302519 DOI: 10.1007/BF00016429.

Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers.

Ryu S, Do Y, Fitch D, Kim W, Mishra B J Mol Evol. 2008; 66(4):368-83.

PMID: 18363028 DOI: 10.1007/s00239-008-9090-8.

Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum.

Kaufman L, Watson J, Thompson W Proc Natl Acad Sci U S A. 1987; 84(6):1550-4.

PMID: 16578799 PMC: 304473. DOI: 10.1073/pnas.84.6.1550.

Widely differing degrees of sequence conservation of the two types of rDNA insertion within the melanogaster species sub-group of Drosophila.

Roiha H, Read C, Browne M, Glover D EMBO J. 1983; 2(5):721-6.

PMID: 16453453 PMC: 555176. DOI: 10.1002/j.1460-2075.1983.tb01491.x.

References

McKnight S, MILLER Jr O . Ultrastructural patterns of RNA synthesis during early embryogenesis of Drosophila melanogaster. Cell. 1976; 8(2):305-19. DOI: 10.1016/0092-8674(76)90014-3. View

Scheer U, Trendelenburg M, Krohne G, Franke W . Lengths and patterns of transcriptional units in the amplified nucleoli of oocytes of Xenopus laevis. Chromosoma. 1977; 60(2):147-67. DOI: 10.1007/BF00288462. View

Sutcliffe J . pBR322 restriction map derived from the DNA sequence: accurate DNA size markers up to 4361 nucleotide pairs long. Nucleic Acids Res. 1978; 5(8):2721-8. PMC: 342202. DOI: 10.1093/nar/5.8.2721. View

Boseley P, Moss T, Machler M, Portmann R, BIRNSTIEL M . Sequence organization of the spacer DNA in a ribosomal gene unit of Xenopus laevis. Cell. 1979; 17(1):19-31. DOI: 10.1016/0092-8674(79)90291-5. View

Long E, Dawid I . Restriction analysis of spacers in ribosomal DNA of Drosophila melanogaster. Nucleic Acids Res. 1979; 7(1):205-15. PMC: 328006. DOI: 10.1093/nar/7.1.205. View

Reeder R . The nucleotide sequence of the initiation and termination sites for ribosomal RNA transcription in X. laevis. Cell. 1979; 18(2):485-99. DOI: 10.1016/0092-8674(79)90066-7. View

Chooi W . The occurrence of long transcription units among the X and Y ribosomal genes of Drosophila melanogaster: transcription of insertion sequences. Chromosoma. 1979; 74(1):57-74. DOI: 10.1007/BF00344483. View

Maxam A, Gilbert W . Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980; 65(1):499-560. DOI: 10.1016/s0076-6879(80)65059-9. View

Grummt I . Specific transcription of mouse ribosomal DNA in a cell-free system that mimics control in vivo. Proc Natl Acad Sci U S A. 1981; 78(2):727-31. PMC: 319875. DOI: 10.1073/pnas.78.2.727. View

10.

Long E, Rebbert M, Dawid I . Nucleotide sequence of the initiation site for ribosomal RNA transcription in Drosophila melanogaster: comparison of genes with and without insertions. Proc Natl Acad Sci U S A. 1981; 78(3):1513-7. PMC: 319161. DOI: 10.1073/pnas.78.3.1513. View

11.

Bach R, Allet B, Crippa M . Sequence organization of the spacer in the ribosomal genes of Xenopus clivii and Xenopus borealis. Nucleic Acids Res. 1981; 9(20):5311-30. PMC: 327522. DOI: 10.1093/nar/9.20.5311. View

12.

Bakken A, MORGAN G, Roan J, Busby S, Reeder R . Mapping of transcription initiation and termination signals on Xenopus laevis ribosomal DNA. Proc Natl Acad Sci U S A. 1982; 79(1):56-60. PMC: 345660. DOI: 10.1073/pnas.79.1.56. View

13.

Miller K . Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites. Cell. 1981; 27(1 Pt 2):165-74. DOI: 10.1016/0092-8674(81)90370-6. View

14.

Kohorn B, Rae P . Accurate transcription of truncated ribosomal DNA templates in a Drosophila cell-free system. Proc Natl Acad Sci U S A. 1982; 79(5):1501-5. PMC: 346002. DOI: 10.1073/pnas.79.5.1501. View