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Analysis of chromatin-associated fiber arrays

Abstract

Electron microscopic examination of chromatin from embryonic nuclei ofOncopeltus fasciatus andDrosophila melanogaster reveals arrays of chromatin associated fibers. The lengths and spacings of these fibers were analyzed to provide a basis for defining and interpreting regions of transcriptionally active chromatin. The results of the analysis are consistent with the interpretation of some fibers as nascent RNA with associated protein (RNP). The chromatin segments underlying these fiber arrays were classified as ribosomal or non-ribosomal transcription units according to definitions and criteria described by Foe et al. (1976). — Nascent fibers on active ribosomal transcription units were analyzed and compared forDrosophila melanogaster, Triturus viridescens, andOncopeltus fasciatus. A common feature of the fiber patterns on ribosomal TUs is that origin-distal fibers exhibit greater length variability and a lower slope relative to proximal fibers. The region of increased variability in fiber lengths is correlated with the expected location of 28S ribosomal RNA sequences in the distal half of each ribosomal transcription unit. Because 28S ribosomal RNA appears to contain more extensive regions of base sequence complementarity, we suggest that the length of ribosomal RNP fibers is influenced under our spreading conditions by the secondary structure of the nascent RNA. — In order to calculate the RNA content of RNP fibers, chromatin morphology was used to estimate lengths of transcribed DNA. The packing ratio of DNA in chromatin, which we express as the length of B-structure DNA ÷ length of chromatin, is 1.1.–1.2. and 1.6 for the DNA in active ribosomal and non-ribosomal chromatins, respectively. These DNA packing ratios are used to determine the extent to which nascent RNP fibers are shorter than the transcribed DNA (expressed as DNA/RNP length ratio). For non-ribosomal transcription units and for proximal fibers of ribosomal transcription units, DNA/RNP length ratios are relatively constant within each array. However, considerable variability in this ratio (4–23) is observed for different arrays of fibers. Possible sources of this variability are considered by comparing ratios derived from the presumably identical ribosomal transcription units. — Further analysis of the morphology of nascent fibers may elucidate the contributions of proteins and successive RNA sequences to RNP structure.

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References

  1. Axel, R., Cedar, H., Felsenfeld, G.: The structure of the globin genes in chromatin. Biochemistry (Wash.)14, 2489–2495 (1975)

  2. Baldwin, J.P., Boseley, P.G., Bradbury, E.M., Ibel, K.: The subunit structure of the eukaryotic chromatin. Nature (Lond.)253, 245–249 (1975)

  3. Bloom, F.E., Aghajanian, G.K.: Cytochemistry of synapses: Selective staining for electron microscopy. Science154, 1575–1577 (1966)

  4. Chooi, W.Y., Laird, C.D.: DNA and polyribosome-like material in lysates of mitochondria of Drosophila melanogaster. J. molec. Biol.100, 493–518 (1976)

  5. Davis, R.W., Davidson, N.: Electron-microscopic visualization of deletion mutations. Proc. nat. Acad. Sci. (Wash.)60, 243–250 (1968)

  6. Davis, R.W., Hyman, R.W.: Physical locations of the in vitro RNA initiation site and termination sites of T7 M DNA. Cold Spr. Harb. Symp. quant. Biol.35, 269–281 (1970)

  7. Finch, J.T., Noll, M., Kornberg, R.: Electron microscopy of defined lengths of chromatin. Proc. nat. Acad. Sci. (Wash.)72, 3320–3322 (1975)

  8. Flanagan, J.R.: Maximum likelihood procedures for evaluating data of chromatin-associated fiber arrays. (Appendix to Laird et al., 1976). Chromosoma (Berl.)58, 191–192 (1976)

  9. Foe, V.E.: Activation of transcriptional units during the embryogenesis of Oncopeltus fasciatus. Ph.D. dissertation, University of Texas, Austin (1975)

  10. Foe, V.E., Wilkinson, L.E., Laird, C.D.: Comparative organization of active transcription units in Oncopeltus fasciatus. Cell9, 131–146 (1976)

  11. Gall, J.G.: Nuclear RNA of the salamander oocyte. Nat. Cancer Inst. Monogr.23, 475–488 (1966)

  12. Georgiev, G.P., Samarina, O.P.: D-RNA containing ribonucleoprotein particles. Advanc. Cell Biol.2, 47–110 (1971)

  13. Glover, D.M., White, R.L., Finnegan, D.J., Hogness, D.S.: Characterization of six cloned DNAs from Drosophila melanogaster, including one that contains the genes for rRNA. Cell5, 149–158 (1975)

  14. Gottesfeld, J.M., Murphy, R.F., Bonner, J.: Structure of transcriptionally active chromatin. Proc. nat. Acad. Sci. (Wash.)72, 4404–4408 (1975)

  15. Griffith, J.D.: Chromatin structure: deduced from a minichromosome. Science187, 1202–1203 (1975)

  16. Hackett, P.B., Sauerbier, W.: The transcriptional organization of the ribosomal RNA genes in mouse L cells. J. molec. Biol.91, 235–256 (1975)

  17. Hamkalo, B.A., Miller, O.L., Jr.: Electron microscopy of genetic activity. Ann. Rev. Biochem.42, 379–396 (1973)

  18. Hewish, D.R., Burgoyne, L.A.: Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem. biophys. Res. Commun.52, 504–510 (1973)

  19. Holde, K.E. van, Sahasrabuddhe, C.G., Shaw, B.R.: Electron microscopy of chromatin subunit particles. Biochem. biophys. Res. Commun.60, 1365 (1974)

  20. Karpel, R.L., Swistel, D.G., Miller, N.S., Geroch, M.E., Lu, C., Fresco, J.R.: Acceleration of RNA renaturation by nucleic acid unwinding proteins. In: Processing of RNA. Brookhaven Symp. Biol.26, 165–174 (1975)

  21. Keyl, H.G.: Lampbrush chromosomes in spermatocytes of Chironomus. Chromosoma (Berl.)51, 75–92 (1975)

  22. Kornberg, R.: Chromatin structure: A repeating unit of histones and DNA. Science184, 868–871 (1974)

  23. Kornberg, R.D., Thomas, J.O.: Chromatin structure: Oligomers of the histones. Science184, 865–868 (1974)

  24. Lagowski, J., Yu, M.-Y.W., Forrest, H.S., Laird, C.D.: Dispersity of repeat DNA sequences in Oncopeltus fasciatus, an organism with diffuse centromeres. Chromosoma (Berl.)43, 349–373 (1973)

  25. Laird, C.D.: Chromatid structure: relationship between DNA content and nucleotide sequence diversity. Chromosoma (Berl.)32, 378–406 (1971)

  26. Laird, C.D., Chooi, W.Y.: Morphology of transcription units in Drosophila melanogaster. Chromosoma (Berl.)58, 193–218 (1976)

  27. Langmore, J.P., Wooley, J.C.: Chromatin architecture: Investigation of a subunit of chromatin by dark field electron microscopy. Proc. nat. Acad. Sci. (Wash.)72, 2691–2695 (1975)

  28. Lian, M., Hurlebert, R.B.: The topological order of 18S and 28S ribosomal nucleic acids within the 45S precursor molecule. J. molec. Biol.98, 321–332 (1975)

  29. Lindsley, D.L., Grell, E.H.: Genetic variations of Drosophila melanogaster. Carnegie Inst. Wash. Publ.527 (1968)

  30. Loening, U.E., Jones, K.W., Birnstiel, M.L.: Properties of the ribosomal RNA precursor in Xenopus laevis; comparison to the precursor in mammals and plants. J. molec. Biol.45, 353–366 (1969)

  31. McKnight, S.L., Miller, O.L., Jr.: Ultrastructural patterns of RNA synthesis during early embryogenesis of Drosophila melanogaster. Cell8, 305–319 (1976)

  32. Martin, T., Billings, P., Levey, A., Ozarslzn, S., Quinlan, T., Swift, H., Uurbas, L.: Some properties of RNA: protein complexes from the nucleus of eukaryotic cells. Cold Spr. Harb. Symp. quant. Biol.38, 921–931 (1974)

  33. Miller, O.L., Jr.: Visualization of genes in action. Sci. Amer.228, 34–12 (1973)

  34. Miller, O.L., Jr., Bakken, A.H.: Morphological studies of transcription. Acta endocr. (Kbh.), Suppl.,168, 155–157 (1972)

  35. Miller, O.L., Jr., Beatty, B.R.: Visualization of nucleolar genes. Science164, 955 (1969)

  36. Olins, A.L., Olins, D.E.: Spheroid chromatin unit (nu bodies). Science183, 330–332 (1974)

  37. Oudet, P.M., Gross-Bellard, M., Chambon, P.: Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell4, 281–300 (1975)

  38. Perry, R.P., Cheng, T.Y., Freed, J.J., Greenberg, J.R., Kelley, D.E., Tartof, K.D.: Evolution of the transcriptional unit of ribosomal RNA. Proc. nat. Acad. Sci. (Wash.)65, 609–614 (1970)

  39. Scherrer, K., Latham, H., Darnell, J.E.: Demonstration of an unstable RNA and or a precursor to ribosomal RNA in HeLa cells. Proc. nat. Acad. Sci. (Wash.)49, 240–248 (1963)

  40. Shaw, B.R., Herman, T.W., Kovacic, R.T., Beaudreau, G.S., Holde, K.E. van: Analysis of subunit organization in chicken erythrocyte chromatin. Proc. nat. Acad. Sci. (Wash.)73, 505–509 (1976)

  41. Watson, J.D., Crick, F.H.C.: The structure of DNA. Cold Spr. Harb. Symp. quant. Biol.18, 123–131 (1953)

  42. Weintraub, H., Groudine, M.: Transcriptionally active and inactive conformations of chromosomal subunits. Science (in press, 1976)

  43. Wellauer, P.K., Dawid, I.B.: Secondary structure maps of ribosomal RNA and DNA. I. Processing of Xenopus laevis ribosomal RNA and structure of single-stranded ribosomal DNA. J molec. Biol.89, 379–395 (1974)

  44. Wellauer, P.K., Dawid, I.B., Kelley, I.B., Perry, R.P.: Secondary structure maps of ribosomal RNA. II. Processing of mouse L-cell ribosomal RNA and variations in the processing pathway. J. molec. Biol.89, 397–407 (1974)

  45. Woodcock, C.L.F.: Ultrastructure of inactive chromatin. J. Cell Biol.59, 368a (1973)

  46. Woodcock, C.L.F., Safer, J.P., Stanchfield, J.E.: Structural repeating units in chromatin. Evidence for their general occurrence. Exp. Cell Res.97, 107–110 (1976)

References

  1. Hogg, R.V., Craig, A.T.: Introduction to Mathematical Statistics. New York: Macmillan 1976

  2. Laird, C.D., Wilkinson, L.E., Foe, V.E., Chooi, W.Y.: Analyses of chromatin-associated fiber arrays. Chromosoma (Berl.)58, 169–190 (1976)

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Laird, C.D., Wilkinson, L.E., Foe, V.E. et al. Analysis of chromatin-associated fiber arrays. Chromosoma 58, 169–190 (1976). https://doi.org/10.1007/BF00701357

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Keywords

  • Transcription Unit
  • Fiber Array
  • Nascent Fiber
  • Fiber Pattern
  • Chromatin Segment