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Nucleic Acids Res. 1991 October 25; 19(20): 5695–5702.
PMCID: PMC328977

The subset of mouse B1 (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts.


B1 (Alu-equivalent) is a murine short interspersed element whose amplification probably involved an RNA intermediate. B1-homologous RNA comprise a population of heterogenous transcripts of questionable function. A cloned B1 is expressed in the injected frog oocyte by RNA polymerase III transcription, ribonucleoprotein formation, post-transcriptional 3'-processing, and nucleocytoplasmic transport. The present study characterizes small cytoplasmic B1 transcripts of mouse cells. Analyses of ten cDNA clones revealed a subset of a high degree of sequence identity (98%) from which a novel consensus was developed. Structural analyses of these RNAs demonstrated a conserved Alu domain originally identified as part of the 7SL RNA within the translational control domain of the signal recognition particle, while this structure was not conserved in the majority of B1s in the sequence database. Furthermore, it was demonstrated that 3'-processing occurred in only a subset of B1 transcripts in-vitro using homologous nuclear extracts, and in the injected oocyte. The data demonstrate that a limited set of B1 sequences are expressed as processed RNA polymerase III-transcripts of a high degree of structural conservation. Although this subset is transcriptionally active, the selective expression may be due to regulation at the levels of processing and cytoplasmic accumulation. Their lack of Poly-(A) or 3'-oligo-(U) tracts argue that these RNAs are unlikely to represent transposition intermediates. Rather, their cytosolic compartmentalization and conservation of a biologically recognized structure, suggests potential involvement in other aspects of cellular metabolism.

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Selected References

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  • Jelinek WR, Schmid CW. Repetitive sequences in eukaryotic DNA and their expression. Annu Rev Biochem. 1982;51:813–844. [PubMed]
  • Singer MF. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982 Mar;28(3):433–434. [PubMed]
  • Georgiev GP, Kramerov DA, Ryskov AP, Skryabin KG, Lukanidin EM. Dispersed repetitive sequences in eukaryotic genomes and their possible biological significance. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1109–1121. [PubMed]
  • Howard BH, Sakamoto K. Alu interspersed repeats: selfish DNA or a functional gene family? New Biol. 1990 Sep;2(9):759–770. [PubMed]
  • Jagadeeswaran P, Forget BG, Weissman SM. Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell. 1981 Oct;26(2 Pt 2):141–142. [PubMed]
  • Van Arsdell SW, Denison RA, Bernstein LB, Weiner AM, Manser T, Gesteland RF. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell. 1981 Oct;26(1 Pt 1):11–17. [PubMed]
  • Mitchell GA, Labuda D, Fontaine G, Saudubray JM, Bonnefont JP, Lyonnet S, Brody LC, Steel G, Obie C, Valle D. Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation. Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):815–819. [PubMed]
  • Daniels GR, Deininger PL. Characterization of a third major SINE family of repetitive sequences in the galago genome. Nucleic Acids Res. 1991 Apr 11;19(7):1649–1656. [PMC free article] [PubMed]
  • Weiner AM. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell. 1980 Nov;22(1 Pt 1):209–218. [PubMed]
  • Ullu E, Murphy S, Melli M. Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence. Cell. 1982 May;29(1):195–202. [PubMed]
  • Walter P, Blobel G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature. 1982 Oct 21;299(5885):691–698. [PubMed]
  • Walter P, Gilmore R, Blobel G. Protein translocation across the endoplasmic reticulum. Cell. 1984 Aug;38(1):5–8. [PubMed]
  • Strub K, Walter P. Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. Mol Cell Biol. 1990 Feb;10(2):777–784. [PMC free article] [PubMed]
  • Siegel V, Walter P. Each of the activities of signal recognition particle (SRP) is contained within a distinct domain: analysis of biochemical mutants of SRP. Cell. 1988 Jan 15;52(1):39–49. [PubMed]
  • Haas B, Klanner A, Ramm K, Sänger HL. The 7S RNA from tomato leaf tissue resembles a signal recognition particle RNA and exhibits a remarkable sequence complementarity to viroids. EMBO J. 1988 Dec 20;7(13):4063–4074. [PubMed]
  • Larsen N, Zwieb C. SRP-RNA sequence alignment and secondary structure. Nucleic Acids Res. 1991 Jan 25;19(2):209–215. [PMC free article] [PubMed]
  • Strub K, Moss J, Walter P. Binding sites of the 9- and 14-kilodalton heterodimeric protein subunit of the signal recognition particle (SRP) are contained exclusively in the Alu domain of SRP RNA and contain a sequence motif that is conserved in evolution. Mol Cell Biol. 1991 Aug;11(8):3949–3959. [PMC free article] [PubMed]
  • Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP. The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res. 1980 Mar 25;8(6):1201–1215. [PMC free article] [PubMed]
  • Bennett KL, Hill RE, Pietras DF, Woodworth-Gutai M, Kane-Haas C, Houston JM, Heath JK, Hastie ND. Most highly repeated dispersed DNA families in the mouse genome. Mol Cell Biol. 1984 Aug;4(8):1561–1571. [PMC free article] [PubMed]
  • Quentin Y. Successive waves of fixation of B1 variants in rodent lineage history. J Mol Evol. 1989 Apr;28(4):299–305. [PubMed]
  • Gundelfinger ED, Krause E, Melli M, Dobberstein B. The organization of the 7SL RNA in the signal recognition particle. Nucleic Acids Res. 1983 Nov 11;11(21):7363–7374. [PMC free article] [PubMed]
  • Ullu E, Tschudi C. Alu sequences are processed 7SL RNA genes. Nature. 1984 Nov 8;312(5990):171–172. [PubMed]
  • Labuda D, Sinnett D, Richer C, Deragon JM, Striker G. Evolution of mouse B1 repeats: 7SL RNA folding pattern conserved. J Mol Evol. 1991 May;32(5):405–414. [PubMed]
  • Kramerov DA, Grigoryan AA, Ryskov AP, Georgiev GP. Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res. 1979 Feb;6(2):697–713. [PMC free article] [PubMed]
  • Kramerov DA, Lekakh IV, Samarina OP, Ryskov AP. The sequences homologous to major interspersed repeats B1 and B2 of mouse genome are present in mRNA and small cytoplasmic poly(A) + RNA. Nucleic Acids Res. 1982 Dec 11;10(23):7477–7491. [PMC free article] [PubMed]
  • White RJ, Stott D, Rigby PW. Regulation of RNA polymerase III transcription in response to F9 embryonal carcinoma stem cell differentiation. Cell. 1989 Dec 22;59(6):1081–1092. [PubMed]
  • White RJ, Stott D, Rigby PW. Regulation of RNA polymerase III transcription in response to Simian virus 40 transformation. EMBO J. 1990 Nov;9(11):3713–3721. [PubMed]
  • Adeniyi-Jones S, Zasloff M. Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene. Nature. 1985 Sep 5;317(6032):81–84. [PubMed]
  • Kalb VF, Glasser S, King D, Lingrel JB. A cluster of repetitive elements within a 700 base pair region in the mouse genome. Nucleic Acids Res. 1983 Apr 11;11(7):2177–2184. [PMC free article] [PubMed]
  • Maraia R, Zasloff M, Plotz P, Adeniyi-Jones S. Pathway of B1-Alu expression in microinjected oocytes: Xenopus laevis proteins associated with nuclear precursor and processed cytoplasmic RNAs. Mol Cell Biol. 1988 Oct;8(10):4433–4440. [PMC free article] [PubMed]
  • Carey MF, Singh K, Botchan M, Cozzarelli NR. Induction of specific transcription by RNA polymerase III in transformed cells. Mol Cell Biol. 1986 Sep;6(9):3068–3076. [PMC free article] [PubMed]
  • Darlington GJ, Papaconstantinou J, Sammons DW, Brown PC, Wong EY, Esterman AL, Kang J. Generation and chracterization of variants of mouse hepatoma cells with defects in hepato-specific gene expression. I. Albumin synthesis variants. Somatic Cell Genet. 1982 Jul;8(4):451–464. [PubMed]
  • Gross DS, Collins KW, Hernandez EM, Garrard WT. Vacuum blotting: a simple method for transferring DNA from sequencing gels to nylon membranes. Gene. 1988 Dec 30;74(2):347–356. [PubMed]
  • Frohman MA, Dush MK, Martin GR. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998–9002. [PubMed]
  • Zuker M. Computer prediction of RNA structure. Methods Enzymol. 1989;180:262–288. [PubMed]
  • Knapp G. Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol. 1989;180:192–212. [PubMed]
  • D'Amore MA, Gallagher PM, Korfhagen TR, Ganschow RE. Complete sequence and organization of the murine beta-glucuronidase gene. Biochemistry. 1988 Sep 6;27(18):7131–7140. [PubMed]
  • Young PR, Scott RW, Hamer DH, Tilghman SM. Construction and expression in vivo of an internally deleted mouse alpha-fetoprotein gene: presence of a transcribed Alu-like repeat within the first intervening sequence. Nucleic Acids Res. 1982 May 25;10(10):3099–3116. [PMC free article] [PubMed]
  • Blake MC, Jambou RC, Swick AG, Kahn JW, Azizkhan JC. Transcriptional initiation is controlled by upstream GC-box interactions in a TATAA-less promoter. Mol Cell Biol. 1990 Dec;10(12):6632–6641. [PMC free article] [PubMed]
  • Perez-Stable C, Shen CK. Competitive and cooperative functioning of the anterior and posterior promoter elements of an Alu family repeat. Mol Cell Biol. 1986 Jun;6(6):2041–2052. [PMC free article] [PubMed]
  • Balmain A, Krumlauf R, Vass JK, Birnie GD. Cloning and characterisation of the abundant cytoplasmic 7S RNA from mouse cells. Nucleic Acids Res. 1982 Jul 24;10(14):4259–4277. [PMC free article] [PubMed]
  • Gundelfinger ED, Di Carlo M, Zopf D, Melli M. Structure and evolution of the 7SL RNA component of the signal recognition particle. EMBO J. 1984 Oct;3(10):2325–2332. [PubMed]
  • Zwieb C. The secondary structure of the 7SL RNA in the signal recognition particle: functional implications. Nucleic Acids Res. 1985 Sep 11;13(17):6105–6124. [PMC free article] [PubMed]
  • Willard C, Nguyen HT, Schmid CW. Existence of at least three distinct Alu subfamilies. J Mol Evol. 1987;26(3):180–186. [PubMed]
  • Quentin Y. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol. 1988;27(3):194–202. [PubMed]
  • Britten RJ, Baron WF, Stout DB, Davidson EH. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4770–4774. [PubMed]
  • Matera AG, Hellmann U, Hintz MF, Schmid CW. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 1990 Oct 25;18(20):6019–6023. [PMC free article] [PubMed]
  • Matera AG, Hellmann U, Schmid CW. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 1990 Oct;10(10):5424–5432. [PMC free article] [PubMed]
  • Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppens CL, Deininger PL. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11;18(23):6793–6798. [PMC free article] [PubMed]
  • Ribes V, Römisch K, Giner A, Dobberstein B, Tollervey D. E. coli 4.5S RNA is part of a ribonucleoprotein particle that has properties related to signal recognition particle. Cell. 1990 Nov 2;63(3):591–600. [PubMed]
  • Poritz MA, Bernstein HD, Strub K, Zopf D, Wilhelm H, Walter P. An E. coli ribonucleoprotein containing 4.5S RNA resembles mammalian signal recognition particle. Science. 1990 Nov 23;250(4984):1111–1117. [PubMed]

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