Proc. Natl. Acad. Sci. USA Vol. 81, pp. 6451-6455, October 1984 Genetics Human genomic library screened with 17-base oligonucleotide probes yields a novel interferon gene (DNA hybridization/synthetic oligonucleotides/DNA sequencing/lac promoter) RICHARD M. TORCZYNSKI, MOTOHIRo FUKE*, AND ARTHUR P. BOLLONt Department of Molecular Genetics, Wadley Institutes of Molecular Medicine, Dallas, TX 75235 Communicated by S. M. McCann, July 2, 1984 ABSTRACT A method is presented that has permitted a mitted us to identify conserved regions common to several of human genomic library to be screened for low-copy genes us- the genes and has served as the basis for constructing probes ing 17-base synthetic oligonucleotides as probes. Parallel for IFN-a genes (2, 7). screening with two different 17-base probes permitted the un- One of the IFN-a genes that we have isolated from the ambiguous identification of clones containing interferon-a human genomic library has not been reported previously, (IFN-a) genes. The isolated human IFN-a genes were se- and another appears to code for IFN-aL (13). A new IFN-a quenced, and one appears to be IFN-aL; the other is one not gene, IFN-aWA, has been sequenced and compared to the previously described, which we have designated IFN-aWA. lFN-a genes A-L previously described (9, 13). It is most ho- The IFN-aWA sequence differs from those of IFN-a genes A- mologous overall with IFN-aC and with the 5' and 3' regions L at -10% of the positions and is most similar to IFN-aC, of IFN-aF and -alH, respectively. The IFN-aWA gene codes -aF, and -alH. IFN-aWA has been found to encode amino ac- for a functional interferon, which has been expressed in E. ids that differ from those conserved at each of five positions in coli using the M13-lacZ fusion as an expression vector. all previously reported IFN-a species. The IFN-aWA gene codes for an active interferon, which has been expressed in MATERIALS AND METHODS Escherichia coli using an M13-lacZ fusion as an expression vector. About 5 x 106 units of IFN-aWA were obtained per Strains and General Methods. M13mp8 bacteriophage and liter of bacterial culture. The described screening procedure E. coli K-12 JM103 (Alac-pro thi strA endA sbcB15 hsdR4 using short probes should permit the isolation of genes for supE F'traD36 proAB lacI ZA mlS) were obtained from Be- which sequence information is available from animal or plant thesda Research Laboratories. M13mpll bacteriophage genomic libraries. DNA was obtained from P-L Biochemicals. Restriction en- donucleases were obtained from Bethesda Research Labora- Although short synthetic oligonucleotides have been used to tories except for Xmn I, which was obtained from New En- screen cDNA libraries and cDNA probes have been used to gland Biolabs. Interferon was assayed at the Interferon screen human genomic libraries (1, 2), synthetic oligonucleo- Production Laboratory at Wadley Institutes using the cyto- tides of less than 20 bases have not been used for isolation of pathic effect-reduction assay (14) on WISH cells (obtained low-copy genes from human genomic libraries. The obvious from Flow Laboratories) challenged with vesicular stomati- advantage of genomic libraries over cDNA libraries is the tis virus. presence of specific genes independent of gene expression. Oligonucleotide Synthesis and Labeling. Probe A (see Re- The synthesis of short oligonucleotides either by the phos- sults) was obtained from BioLogicals (Toronto). Probe B photriester (3) or the phosphoramidite (4) method is a conve- (see Results) was synthesized by the solid-phase phospho- nient technique for generating probes for screening pur- triester method using a Bachem DNA Synthesizer (Bachem poses, especially since the chemistry involved has become Fine Chemicals, Torrance, CA) and purified as described by reliably automated. The improved sensitivity of hybridiza- Itakura and Riggs (3). The two probes were labeled at the 5' tion techniques has resulted in the detection of single-base ends with [y-32P]ATP (New England Nuclear; 5000 Ci/ differences using probes less than 20 nucleotides long (5), mmol, 1 Ci = 37 GBq) using T4-infected E. coli polynucleo- permitting the use of such probes for diagnosis of genetic tide 5'-hydroxyl-kinase (P-L Biochemicals). The end-labeled diseases (6). They have also been used for screening cDNA DNA probes were separated from unincorporated [y- libraries that have been enriched in specific gene sequences 32P]ATP by gel filtration through a Sephadex G-50 column (1). and filtration through a 0.2-gm Acrodisc filter (Gelman) (2, Utilizing 17-base oligonucleotides, we have optimized the 7). Specific activities of the probes were 2-5 x 108 cpm/,ug. plaque-hybridization screening procedure and have been Screening the A Phage Library for IFN Clones. The human able to isolate several interferon-a (IFN-a) genes from the genomic library in Charon 4A (15) was obtained from T. human in 4A Maniatis. Phage were used to infect E. coli DP-50 [supF genomic library contained Charon (2, 7). Previ- supE dapD8 lacY (gal-uvrB) thyA nalAr hsd] at a density of 1 ously, human IFN-a genes have been isolated from cDNA x 104 plaque-forming units (pfu) per 80-cm2 dish. A total of libraries made using mRNA from virus-induced leukocytes 180,000 pfu were screened separately with each probe using (8, 9). Certain IFN-a genes isolated from such a human a modification (7) of the plaque-hybridization method of cDNA library and expressed in Escherichia coli are undergo- Benton and Davis (16). Duplicate nitrocellulose-filter ing extensive analysis in preclinical (10) and clinical trials (Schleicher & Schuell BA85-SD) copies were made from (11) of their utility in producing IFN-as as antiviral and anti- on filter tumor agents. IFN-a genes have also been isolated from a each plate. The DNA was alkali-denatured paper human genomic library using IFN-a cDNAs as probes (12). A detailed comparison of the different IFN-a genes has per- Abbreviations: IFN, interferon; pfu, plaque-forming units; kb, kilo- base pair(s). *Present address: Biotechnology Division, Phillips Research Cen- The publication costs of this article were defrayed in part by page charge ter, Phillips Petroleum Company, Bartlesville, OK 74004. payment. This article must therefore be hereby marked "advertisement" tTo whom correspondence and reprint requests should be ad- in accordance with 18 U.S.C. §1734 solely to indicate this fact. dressed. 6451 Downloaded by guest on October 1, 2021 6452 Genetics: Torczynski et aL Proc. NatL Acad. Sci. USA 81 (1984) saturated with 0.5 M NaOH/1.5 M NaCl, neutralized on pa- 100,000 x g for 1 hr at 40C. The supernatant was assayed for per saturated with 1 M Tris HCl, pH 7.5, and again neutral- IFN activity as described above. ized on paper saturated with 0.5 M Tris HCl, pH 7.5/1.5 M NaCl. The filters were baked in a vacuum oven at 80'C for 2 RESULTS hr. Prehybridization was performed at 37TC in 0.9 M Construction of Synthetic Probes. Part of the strategy em- NaCl/6.0 mM Na2EDTA/19.8 mM Tris-HCl, pH 8.0/0.1% ployed in our isolation of human IFN-a genes from a human Ficoll/0.1% polyvinylpyrrolidone/0.1% bovine serum albu- genomic library involved the construction of short synthetic min/0.1% NaDodSO4/10% dextran sulfate. After overnight probes homologous to well-conserved regions of IFN-a prehybridization, the solution was removed and new hybrid- genes A-H (9). From the published sequences for part of the ization solution (identical to prehybridization solution) con- IFN-a genes A-H (9), two (G + C)-rich regions of homology taining labeled probe at a concentration of 2 ng/ml was add- contained within the gene sequences defined by bases 401- ed. Hybridizations were performed at 370C for 20 hr with 500 were selected as the bases for probe synthesis. constant agitation by rotation. Filters were washed four Probe A (5'-C-A-G-C-C-A-G-G-A-T-G-G-A-G-T-C-C-3') times (20 min per wash) at room temperature in 0.9 M is homologous to IFN-aB, -aC, -aE, -aH, and -aL and con- NaCl/90 mM sodium citrate, pH 7, and twice at 450C (1 hr tains one mismatch with IFN-aA, -aD, -aF, and -aK and two per wash) in the same buffer containing 0.1% NaDodSO4. mismatches with IFN-aG (9, 13). Probe B (5'-C-C-T-C-C-C- Autoradiography was done for 64 hr at -80'C using Kodak A-G-G-C-A-C-A-A-G-G-G-3') is homologous to IFN-aA, XAR film plus two intensifying screens (DuPont Cronex Hi- -aC, -aD, -aH, -aK, and -aL and has one mismatch with Plus). Positive clones were identified and isolated by several IFN-aB, -aE, -aF, and -aG. cycles of plaque purification and phage DNA stocks were -Screening the Human Genomic Library. A human genomic prepared as described (17). library contained in Charon 4A (15) was screened for IFN-a Restriction and Hybridization Analysis of Cloned DNA. genes using the synthetic probes A and B. From -180,000 Phage DNA from isolated recombinants was digested with pfu, the phage DNA of five foci appeared to hybridize to BamHI, Xmn I, EcoRI, or Dde I under the conditions recom- both probe A and probe B. One example is shown in Fig. 1. mended by the supplier. The digested DNA was fractionated When phage from the five foci were replated at lower den- on agarose gels, transferred to nitrocellulose paper as de- sities (500 pfu/dish), three clones were isolated that hybrid- scribed by Southern (18), and hybridized with probes A and ized to both A and B and were designated X-77, X-85, and X- B under the conditions described for the screening proce- 105.