Jeffrey A. Kramer,1 Mark D. Adams,2 Gautam B. Singh,3 Norman A. Doggett,4 and Stephen A. Krawetz1,5. 1Department of Obstetrics & Gynecology, Center for ...
Somatic Cell and Molecular Genetics, Vol. 24, No. 2, 1998, pp. 131-133
Brief Communication
A Matrix Associated Region Localizes the Human SOCS-1 Gene to Chromosome 16pl3.13 Jeffrey A. Kramer,1 Mark D. Adams,2 Gautam B. Singh,3 Norman A. Doggett,4 and Stephen A. Krawetz1,5 1Department of Obstetrics & Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, Michigan 48101; 2Solaris Genomics; 3Department of Computer Science and Engineering, Oakland University; 4The Center for Human Genome Studies, Los Alamos National Laboratory
Received 3 April 1998—Final 3 April 1998
Abstract—The MarFinder algorithm was applied to a newly sequenced segment of 16p13.13 abutting the 3' end of the human PRM1 —> PRM2 —> TNP2 locus. A candidate region of matrix attached was identified. Subsequent biophysical analysis showed that this region was attached to the somatic nuclear matrix. Nucleotide sequence analysis also revealed the presence of a CpG island. Data base queries showed that this region contained the SOCS-1 gene. Thus, the SOCS-1 gene is bounded by a somatic MAR and is just 3' of the spermatid-expressed PRM1 —> PRM2 —> TNP2 domain at position 16p13.13.
INTRODUCTION The nuclear matrix serves to organize the eukaryotic genome into discrete domains. It has been suggested that the nuclear matrix also acts to increase the effective local concentration of trans-acting factors thereby promoting their interaction with the corresponding gene-specific cis-elements. Accordingly, a number of faculatative nuclear matrix attachment sites (MARs) have been defined. Unlike their constitutive "cousins" that appear to serve a structural function, the facultative MARs are often marked by the presence of well characterized promoter/ enhancer sequences. They have also been localized to introns (1), enhancers (2), origins of replication (3), sites of transcription initiation (4) and regions of locus control (5). We have postulated that content-specific facultative MARs should be indicative of genie domains (6). A 5To
computational method that identifies MARs within large spans of genomic sequence was developed (7). The utility of this strategy to identify MARs in several human domains including the PRM1 — PRM2 –>TNP2 (8) and b-globin (9) domain has been demonstrated. This detection strategy has been encoded into the MAR-FINDER algorithm (9). Access to this program is provided on the World Wide Web at http: //www. ncgr. org/MarFinder/. MarFinder analysis (version 1) of newly determined sequence segment of the 3' boundary region of the human PRM1 —> PRM2 –> TNP2 multigenic domain revealed a region with significant nuclear matrix association potential (Fig. la). As shown in Fig. 1b, the PCR-based MAR detection assay (10) showed that this region was only attached to the somatic nuclear matrix. This is in direct contrast to its neighbor, the PRM1 –> PRM2 — TNP2 locus, which is
whom correspondence should be addressed.
131 0740-7750/98/0300-0131$15.00/0 c 1998 Plenum Publishing Corporation
132
Kramer et al
Fig. 1. Matrix association potential and genomic organization of SOCS-1. a) The nuclear matrix association potential along a region of human chromosome 16p13.13 was assessed using MarFinder (version 1). This revealed a large peak at 38,200 bp. The relative position of the SOCS-1 coding sequence (40,758–41,393 bp) is indicated by an arrow, showing the direction of transcription. The human and mouse SOCS-1 coding sequences both lie within a CpG island (39,335–41,532 bp) indicated by the shaded region. b) The PCR-based MAR detection assay was subsequently utilized to assess the veracity of the MarFinder prediction. As shown, in somatic cells (HeLa), the SOCS-1 gene was localized to the nuclear matrix. In contrast the SOCS-1 gene localized to the loop in human sperm.
133
MAR Identification, Linked Genes, SOCS-1
only attached to the sperm-nuclear matrix (6). The question thus arose was this MAR indicative of the presence of an unidentified nearby gene? Sequence comparison has now shown that this region contains the human SOCS-1 gene encoding the recently identified SOCS-1/JAB/ SSI-1 protein (11-13). This is one of a family of proteins that act to negatively regulate cytokine mediated signal transduction. Thus, the human SOCS-1 gene maps to human chromosome 16pl3.13. Extended analysis has shown that the human SOCS-1 is an intronless gene located ~7 kb 3' of the PRM1 –> PRM2 –> TNP2 domain. It is in the same orientation as the members of this gene cluster. In contrast to its neighbor, the SOCS-1 gene coding segment lies at positions 40,758–41,393 bp within a CpG island (39,33541,532 bp) that is just 3' of the PRM1 —> PRM2 –> TNP2 gene cluster. As expected, several DNase I-hypersensitive sites are associated with this CpG island in somatic cells yet absent in cells of the spermatogenic lineage (14). This contrasts its PRM1 —> PRM2 –> TNP2 multigenie neighbor, which is only potentiated, i.e., in a DNase I-sensitive conformation in cells of the spermatogenic lineage (15). The close proximity of these independent chromatin domains suggests the presence of an intricate mechanism mediating the differential expression of these closely linked genes. ACKNOWLEDGMENTS This work was supported in part by a grant to S.A.K. from the Wayne State University
School of Medicine F.M.R.E. J.A.K. was supported by a Lalor Foundation postdoctoral fellowship. N.A.D. is supported by the U.S. D.O.E. under contract W-7405-ENG-36. LITERATURE CITED 1. Jarraan, A.P., and Higgs, D.R. (1988). EMBO J. 7:3337-3344. 2. Gasser, S.M., and Laemmli, U.K. (1986). Cell 46:521-530. 3. Kalandadze, A.G., Bushara, S.A., Vassetzky, Y.S., and Razin, S.V. (1990). Biochem. Biophys. Res. Commun. 168:9-15. 4. Dijkwel, P.A., and Hamlin, J.L. (1988). Mol. Cell. Biol 8:5398-5409. 5. Forrester, W.C., can Genderen, C., Jenuwein, T., and Grosschedl, R. (1994). Science 265:1221-1225. 6. Kramer, J.A., and Krawetz, S.A. (1996). J. Biol. Chem. 271:11619-11622. 7. Kramer, J.A., and Krawetz, S.A. (1995). Mammalian Genome 6:677-679. 8. Kramer, J.A., Singh, G.B., and Krawetz, S.A. (1996). Genomics 33:305-308. 9. Singh, G.B., Kramer, J.A., and Krawetz, S.A. (1997). Nucl. Acids Res. 25:1419-1425. 10. Kramer, J.A., and Krawetz, S.A. (1997). BioTechniques 22(5):880-882. 11. Starr, R., Willson, T.A., Viney, E.M., Murray, L.J.L., Rayner, J.R., Jenkins, B.J., Gonda, T.J., Alexander, W.S., Metcalf, D., Nicola, N.A., and Hilton, D.J. (1997). Nature 387:917-921. 12. Naka, T., Narazaki, M, Hirata, M., Matsumoto, T., Minamoto, S., Aono, A., Nishimoto, N., Kajita, T., Taga, T., Yoshizaki, K., Akira, S., and Kishimoto, T. (1997). Nature 387:924–928. 13. Endo, T.A., Mashuhara, M., Yokouchi, M., Suzuki, R., Sakamoto, H., Mitsui, K., Matsumoto, A., Tanimura, S., Ohtsubo, M., Misawa, H., Miyazaki, T., Leonor, N., Taniguchi, T., Fujita, T., Kanakura, Y., Komiya, S., and Yoshimura, A. (1997). Nature 387:921-924. 14. Choi, Y.-C., Aizawa, A., and Hecht, N.B. (1997). Mam. Gen. 8:317-323. 15. Kramer, J.A., McCarrey, J.R., Djakiew, D., and Krawetz, S.A. (1998). Development in press.
