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. 1995 Feb 2;128(4):467–483. doi: 10.1083/jcb.128.4.467

Cell size regulation, a mechanism that controls cellular RNA accumulation: consequences on regulation of the ubiquitous transcription factors Oct1 and NF-Y and the liver-enriched transcription factor DBP

PMCID: PMC2199888  PMID: 7532171

Abstract

Cell sizes can differ vastly between cell types in individual metazoan organisms. In rat liver, spleen, and thymus, differences in average cell size roughly reflect differences in RNA:DNA ratios. For example, hepatocytes were found to have a cytoplasmic:nuclear volume ratio and an RNA:DNA ratio which were 34- and 21-fold higher, respectively, than those in thymocytes. RNA synthesis per DNA-equivalent in the hepatocytes was 25-fold greater than that in thymocytes, suggesting that differences in overall transcriptional activity, not differences in overall RNA stability, were primarily responsible for determining cellular RNA:DNA ratios. The mechanisms determining the capacity of large cells to synthesize and accumulate more ubiquitous cytoplasmic macromolecules, such as ribosomes, than smaller cells is entitled "cell size regulation." Cell size regulation may have important consequences on the tissue distribution of transcription factors. Thus, in liver, lung, kidney, spleen, and brain, cellular levels of the mRNA encoding the leucine zipper protein DBP correlate closely to cellular RNA:DNA ratios. Our results suggest that DBP mRNA levels, like rRNA levels, are transcriptionally determined. Thus the dbp gene, like the ribosomal genes, may be subject to cell size regulation. As a consequence, nuclei from liver, a tissue with a very large average cell size, accumulated higher levels of DBP protein than nuclei from small-celled tissues, such as spleen or lung. In contrast to DBP, the ubiquitous transcription factors Oct1 and NF-Y escaped cell size control. Nuclei from most tissues contained similar amounts of these factors irrespective of cell size. Likewise, tissues with large or small average cell sizes contained similar levels of the mRNAs encoding Oct1 or NF-Ya, one of the subunits of the heteromeric CCAAT-binding factor NF-Y, per DNA-equivalent. Interestingly, mRNA encoding NF-Yb, another subunit of NF-Y, was subject to cell size regulation. Our results suggest that NF-Yb protein escapes cell size regulation at a posttranslational level.

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Selected References

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  1. Barberis A., Superti-Furga G., Busslinger M. Mutually exclusive interaction of the CCAAT-binding factor and of a displacement protein with overlapping sequences of a histone gene promoter. Cell. 1987 Jul 31;50(3):347–359. doi: 10.1016/0092-8674(87)90489-2. [DOI] [PubMed] [Google Scholar]
  2. Baserga R. Growth in size and cell DNA replication. Exp Cell Res. 1984 Mar;151(1):1–5. doi: 10.1007/978-3-642-67986-5_1. [DOI] [PubMed] [Google Scholar]
  3. Boulikas T. Nuclear localization signals (NLS). Crit Rev Eukaryot Gene Expr. 1993;3(3):193–227. [PubMed] [Google Scholar]
  4. Brown K., Park S., Kanno T., Franzoso G., Siebenlist U. Mutual regulation of the transcriptional activator NF-kappa B and its inhibitor, I kappa B-alpha. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2532–2536. doi: 10.1073/pnas.90.6.2532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. CERIOTTI G. Determination of nucleic acids in animal tissues. J Biol Chem. 1955 May;214(1):59–70. [PubMed] [Google Scholar]
  6. Cereghini S., Yaniv M., Cortese R. Hepatocyte dedifferentiation and extinction is accompanied by a block in the synthesis of mRNA coding for the transcription factor HNF1/LFB1. EMBO J. 1990 Jul;9(7):2257–2263. doi: 10.1002/j.1460-2075.1990.tb07396.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chodosh L. A., Baldwin A. S., Carthew R. W., Sharp P. A. Human CCAAT-binding proteins have heterologous subunits. Cell. 1988 Apr 8;53(1):11–24. doi: 10.1016/0092-8674(88)90483-7. [DOI] [PubMed] [Google Scholar]
  8. Chodosh L. A., Olesen J., Hahn S., Baldwin A. S., Guarente L., Sharp P. A. A yeast and a human CCAAT-binding protein have heterologous subunits that are functionally interchangeable. Cell. 1988 Apr 8;53(1):25–35. doi: 10.1016/0092-8674(88)90484-9. [DOI] [PubMed] [Google Scholar]
  9. Corden J. L. RNA polymerase II transcription cycles. Curr Opin Genet Dev. 1993 Apr;3(2):213–218. doi: 10.1016/0959-437x(93)90025-k. [DOI] [PubMed] [Google Scholar]
  10. Courtois G., Baumhueter S., Crabtree G. R. Purified hepatocyte nuclear factor 1 interacts with a family of hepatocyte-specific promoters. Proc Natl Acad Sci U S A. 1988 Nov;85(21):7937–7941. doi: 10.1073/pnas.85.21.7937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Deschatrette J., Moore E. E., Dubois M., Weiss M. C. Dedifferentiated variants of a rat hepatoma:reversion analysis. Cell. 1980 Apr;19(4):1043–1051. doi: 10.1016/0092-8674(80)90095-1. [DOI] [PubMed] [Google Scholar]
  12. Deschatrette J., Weiss M. C. Characterization of differentiated and dedifferentiated clones from a rat hepatoma. Biochimie. 1974;56(11-12):1603–1611. doi: 10.1016/s0300-9084(75)80286-0. [DOI] [PubMed] [Google Scholar]
  13. Descombes P., Chojkier M., Lichtsteiner S., Falvey E., Schibler U. LAP, a novel member of the C/EBP gene family, encodes a liver-enriched transcriptional activator protein. Genes Dev. 1990 Sep;4(9):1541–1551. doi: 10.1101/gad.4.9.1541. [DOI] [PubMed] [Google Scholar]
  14. Edgar B. A., Kiehle C. P., Schubiger G. Cell cycle control by the nucleo-cytoplasmic ratio in early Drosophila development. Cell. 1986 Jan 31;44(2):365–372. doi: 10.1016/0092-8674(86)90771-3. [DOI] [PubMed] [Google Scholar]
  15. Fantes P. A. Control of cell size and cycle time in Schizosaccharomyces pombe. J Cell Sci. 1977 Apr;24:51–67. doi: 10.1242/jcs.24.1.51. [DOI] [PubMed] [Google Scholar]
  16. Fantes P., Nurse P. Control of cell size at division in fission yeast by a growth-modulated size control over nuclear division. Exp Cell Res. 1977 Jul;107(2):377–386. doi: 10.1016/0014-4827(77)90359-7. [DOI] [PubMed] [Google Scholar]
  17. Forsburg S. L., Guarente L. Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev. 1989 Aug;3(8):1166–1178. doi: 10.1101/gad.3.8.1166. [DOI] [PubMed] [Google Scholar]
  18. Fort P., Marty L., Piechaczyk M., el Sabrouty S., Dani C., Jeanteur P., Blanchard J. M. Various rat adult tissues express only one major mRNA species from the glyceraldehyde-3-phosphate-dehydrogenase multigenic family. Nucleic Acids Res. 1985 Mar 11;13(5):1431–1442. doi: 10.1093/nar/13.5.1431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gariglio P., Bellard M., Chambon P. Clustering of RNA polymerase B molecules in the 5' moiety of the adult beta-globin gene of hen erythrocytes. Nucleic Acids Res. 1981 Jun 11;9(11):2589–2598. doi: 10.1093/nar/9.11.2589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Glisin V., Crkvenjakov R., Byus C. Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry. 1974 Jun 4;13(12):2633–2637. doi: 10.1021/bi00709a025. [DOI] [PubMed] [Google Scholar]
  21. Gribnau A. A., Schoenmakers J. G., Bloemendal H. Purification of rat liver RNase inhibitor and its effect on polyribosome integrity. Arch Biochem Biophys. 1969 Mar;130(1):48–52. doi: 10.1016/0003-9861(69)90007-1. [DOI] [PubMed] [Google Scholar]
  22. Hatamochi A., Golumbek P. T., Van Schaftingen E., de Crombrugghe B. A CCAAT DNA binding factor consisting of two different components that are both required for DNA binding. J Biol Chem. 1988 Apr 25;263(12):5940–5947. [PubMed] [Google Scholar]
  23. Henery C. C., Kaufman M. H. Relationship between cell size and nuclear volume in nucleated red blood cells of developmentally matched diploid and tetraploid mouse embryos. J Exp Zool. 1992 Apr 1;261(4):472–478. doi: 10.1002/jez.1402610414. [DOI] [PubMed] [Google Scholar]
  24. Heywood S. M., Dowben R. M., Rich A. The identification of polyribosomes synthesizing myosin. Proc Natl Acad Sci U S A. 1967 Apr;57(4):1002–1009. doi: 10.1073/pnas.57.4.1002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Hooft van Huijsduijnen R., Li X. Y., Black D., Matthes H., Benoist C., Mathis D. Co-evolution from yeast to mouse: cDNA cloning of the two NF-Y (CP-1/CBF) subunits. EMBO J. 1990 Oct;9(10):3119–3127. doi: 10.1002/j.1460-2075.1990.tb07509.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Horvitz H. R., Herskowitz I. Mechanisms of asymmetric cell division: two Bs or not two Bs, that is the question. Cell. 1992 Jan 24;68(2):237–255. doi: 10.1016/0092-8674(92)90468-r. [DOI] [PubMed] [Google Scholar]
  27. Kirk M. M., Ransick A., McRae S. E., Kirk D. L. The relationship between cell size and cell fate in Volvox carteri. J Cell Biol. 1993 Oct;123(1):191–208. doi: 10.1083/jcb.123.1.191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kongsuwan K., Yu Q., Vincent A., Frisardi M. C., Rosbash M., Lengyel J. A., Merriam J. A Drosophila Minute gene encodes a ribosomal protein. Nature. 1985 Oct 10;317(6037):555–558. doi: 10.1038/317555a0. [DOI] [PubMed] [Google Scholar]
  29. Kuo C. J., Conley P. B., Chen L., Sladek F. M., Darnell J. E., Jr, Crabtree G. R. A transcriptional hierarchy involved in mammalian cell-type specification. Nature. 1992 Jan 30;355(6359):457–461. doi: 10.1038/355457a0. [DOI] [PubMed] [Google Scholar]
  30. Labarca C., Paigen K. A simple, rapid, and sensitive DNA assay procedure. Anal Biochem. 1980 Mar 1;102(2):344–352. doi: 10.1016/0003-2697(80)90165-7. [DOI] [PubMed] [Google Scholar]
  31. Lavery D. J., Schibler U. Circadian transcription of the cholesterol 7 alpha hydroxylase gene may involve the liver-enriched bZIP protein DBP. Genes Dev. 1993 Oct;7(10):1871–1884. doi: 10.1101/gad.7.10.1871. [DOI] [PubMed] [Google Scholar]
  32. Lebherz H. G., Rutter W. J. Glyceraldehyde-3-phosphate dehydrogenase variants in phyletically diverse organisms. Science. 1967 Sep 8;157(3793):1198–1200. doi: 10.1126/science.157.3793.1198. [DOI] [PubMed] [Google Scholar]
  33. Li X. Y., Hooft van Huijsduijnen R., Mantovani R., Benoist C., Mathis D. Intron-exon organization of the NF-Y genes. Tissue-specific splicing modifies an activation domain. J Biol Chem. 1992 May 5;267(13):8984–8990. [PubMed] [Google Scholar]
  34. Lichtsteiner S., Schibler U. A glycosylated liver-specific transcription factor stimulates transcription of the albumin gene. Cell. 1989 Jun 30;57(7):1179–1187. doi: 10.1016/0092-8674(89)90055-x. [DOI] [PubMed] [Google Scholar]
  35. Maity S. N., Sinha S., Ruteshouser E. C., de Crombrugghe B. Three different polypeptides are necessary for DNA binding of the mammalian heteromeric CCAAT binding factor. J Biol Chem. 1992 Aug 15;267(23):16574–16580. [PubMed] [Google Scholar]
  36. Mantovani R., Pessara U., Tronche F., Li X. Y., Knapp A. M., Pasquali J. L., Benoist C., Mathis D. Monoclonal antibodies to NF-Y define its function in MHC class II and albumin gene transcription. EMBO J. 1992 Sep;11(9):3315–3322. doi: 10.1002/j.1460-2075.1992.tb05410.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Miwa K., Doyle C., Strominger J. L. Sequence-specific interactions of nuclear factors with conserved sequences of human class II major histocompatibility complex genes. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4939–4943. doi: 10.1073/pnas.84.14.4939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Mueller C. R., Maire P., Schibler U. DBP, a liver-enriched transcriptional activator, is expressed late in ontogeny and its tissue specificity is determined posttranscriptionally. Cell. 1990 Apr 20;61(2):279–291. doi: 10.1016/0092-8674(90)90808-r. [DOI] [PubMed] [Google Scholar]
  39. Müller M. M., Ruppert S., Schaffner W., Matthias P. A cloned octamer transcription factor stimulates transcription from lymphoid-specific promoters in non-B cells. Nature. 1988 Dec 8;336(6199):544–551. doi: 10.1038/336544a0. [DOI] [PubMed] [Google Scholar]
  40. Nadal C., Zajdela F. Polyploïdie somatique dans le foie de rat. I. Le röle des cellules binuclées dans la genèse des cellules polyploïdes. Exp Cell Res. 1966 Apr;42(1):99–116. doi: 10.1016/0014-4827(66)90324-7. [DOI] [PubMed] [Google Scholar]
  41. Olmo E. Nucleotype and cell size in vertebrates: a review. Basic Appl Histochem. 1983;27(4):227–256. [PubMed] [Google Scholar]
  42. Ossipow V., Laemmli U. K., Schibler U. A simple method to renature DNA-binding proteins separated by SDS-polyacrylamide gel electrophoresis. Nucleic Acids Res. 1993 Dec 25;21(25):6040–6041. doi: 10.1093/nar/21.25.6040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Roeder R. G. Multiple forms of deoxyribonucleic acid-dependent ribonucleic acid polymerase in Xenopus laevis. Levels of activity during oocyte and embryonic development. J Biol Chem. 1974 Jan 10;249(1):249–256. [PubMed] [Google Scholar]
  44. Roth G., Blanke J., Wake D. B. Cell size predicts morphological complexity in the brains of frogs and salamanders. Proc Natl Acad Sci U S A. 1994 May 24;91(11):4796–4800. doi: 10.1073/pnas.91.11.4796. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Schibler U., Hagenbüchle O., Wellauer P. K., Pittet A. C. Two promoters of different strengths control the transcription of the mouse alpha-amylase gene Amy-1a in the parotid gland and the liver. Cell. 1983 Jun;33(2):501–508. doi: 10.1016/0092-8674(83)90431-2. [DOI] [PubMed] [Google Scholar]
  46. Schmidt E. E., Merrill G. F. Changes in dihydrofolate reductase (DHFR) mRNA levels can account fully for changes in DHFR synthesis rates during terminal differentiation in a highly amplified myogenic cell line. Mol Cell Biol. 1991 Jul;11(7):3726–3734. doi: 10.1128/mcb.11.7.3726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Schmidt E. E., Merrill G. F. Transcriptional repression of the mouse dihydrofolate reductase gene during muscle cell commitment. J Biol Chem. 1989 Dec 15;264(35):21247–21256. [PubMed] [Google Scholar]
  48. Schöler H. R., Hatzopoulos A. K., Balling R., Suzuki N., Gruss P. A family of octamer-specific proteins present during mouse embryogenesis: evidence for germline-specific expression of an Oct factor. EMBO J. 1989 Sep;8(9):2543–2550. doi: 10.1002/j.1460-2075.1989.tb08392.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Scott M. L., Fujita T., Liou H. C., Nolan G. P., Baltimore D. The p65 subunit of NF-kappa B regulates I kappa B by two distinct mechanisms. Genes Dev. 1993 Jul;7(7A):1266–1276. doi: 10.1101/gad.7.7a.1266. [DOI] [PubMed] [Google Scholar]
  50. Seglen P. O. Preparation of isolated rat liver cells. Methods Cell Biol. 1976;13:29–83. doi: 10.1016/s0091-679x(08)61797-5. [DOI] [PubMed] [Google Scholar]
  51. Seyfert H. M., Hipke H., Schmidt W. Isolation and phenotypic characterization of Tetrahymena thermophila size mutants: the relationship between cell size and regulation of DNA content. J Cell Sci. 1984 Apr;67:203–215. doi: 10.1242/jcs.67.1.203. [DOI] [PubMed] [Google Scholar]
  52. Sturm R. A., Das G., Herr W. The ubiquitous octamer-binding protein Oct-1 contains a POU domain with a homeo box subdomain. Genes Dev. 1988 Dec;2(12A):1582–1599. doi: 10.1101/gad.2.12a.1582. [DOI] [PubMed] [Google Scholar]
  53. Sun S. C., Ganchi P. A., Ballard D. W., Greene W. C. NF-kappa B controls expression of inhibitor I kappa B alpha: evidence for an inducible autoregulatory pathway. Science. 1993 Mar 26;259(5103):1912–1915. doi: 10.1126/science.8096091. [DOI] [PubMed] [Google Scholar]
  54. Suzuki N., Peter W., Ciesiolka T., Gruss P., Schöler H. R. Mouse Oct-1 contains a composite homeodomain of human Oct-1 and Oct-2. Nucleic Acids Res. 1993 Jan 25;21(2):245–252. doi: 10.1093/nar/21.2.245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Szarski H. Cell size and the concept of wasteful and frugal evolutionary strategies. J Theor Biol. 1983 Nov 21;105(2):201–209. doi: 10.1016/s0022-5193(83)80002-2. [DOI] [PubMed] [Google Scholar]
  56. Tanaka M., Lai J. S., Herr W. Promoter-selective activation domains in Oct-1 and Oct-2 direct differential activation of an snRNA and mRNA promoter. Cell. 1992 Feb 21;68(4):755–767. doi: 10.1016/0092-8674(92)90150-b. [DOI] [PubMed] [Google Scholar]
  57. Thayer M. J., Tapscott S. J., Davis R. L., Wright W. E., Lassar A. B., Weintraub H. Positive autoregulation of the myogenic determination gene MyoD1. Cell. 1989 Jul 28;58(2):241–248. doi: 10.1016/0092-8674(89)90838-6. [DOI] [PubMed] [Google Scholar]
  58. Tian J. M., Schibler U. Tissue-specific expression of the gene encoding hepatocyte nuclear factor 1 may involve hepatocyte nuclear factor 4. Genes Dev. 1991 Dec;5(12A):2225–2234. doi: 10.1101/gad.5.12a.2225. [DOI] [PubMed] [Google Scholar]
  59. Vuorio T., Maity S. N., de Crombrugghe B. Purification and molecular cloning of the "A" chain of a rat heteromeric CCAAT-binding protein. Sequence identity with the yeast HAP3 transcription factor. J Biol Chem. 1990 Dec 25;265(36):22480–22486. [PubMed] [Google Scholar]
  60. Way J. C., Chalfie M. The mec-3 gene of Caenorhabditis elegans requires its own product for maintained expression and is expressed in three neuronal cell types. Genes Dev. 1989 Dec;3(12A):1823–1833. doi: 10.1101/gad.3.12a.1823. [DOI] [PubMed] [Google Scholar]
  61. Wuarin J., Falvey E., Lavery D., Talbot D., Schmidt E., Ossipow V., Fonjallaz P., Schibler U. The role of the transcriptional activator protein DBP in circadian liver gene expression. J Cell Sci Suppl. 1992;16:123–127. doi: 10.1242/jcs.1992.supplement_16.15. [DOI] [PubMed] [Google Scholar]
  62. Wuarin J., Mueller C., Schibler U. A ubiquitous CCAAT factor is required for efficient in vitro transcription from the mouse albumin promoter. J Mol Biol. 1990 Aug 20;214(4):865–874. doi: 10.1016/0022-2836(90)90341-I. [DOI] [PubMed] [Google Scholar]
  63. Wuarin J., Schibler U. Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell. 1990 Dec 21;63(6):1257–1266. doi: 10.1016/0092-8674(90)90421-a. [DOI] [PubMed] [Google Scholar]
  64. Wuarin J., Schibler U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol Cell Biol. 1994 Nov;14(11):7219–7225. doi: 10.1128/mcb.14.11.7219. [DOI] [PMC free article] [PubMed] [Google Scholar]

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