Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Nucleosome organization in the Drosophila genome


Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: H2A.Z nucleosomal organization around the 5′ end of Drosophila genes.
Figure 2: Organization of conserved DNA motifs around TSSs (left) and nucleosomes (right).
Figure 3: Positioning properties of Drosophila nucleosomes and DNA.
Figure 4: H2A.Z nucleosomal organization around the 3′ end of Drosophila genes.
Figure 5: Distribution of Pol II and Pol II-engaged nucleosomes around the 5′ end of genes.

Accession codes

Primary accessions


Data deposits

Sequence data are deposited in the NCBI Trace Archives TI SRA000283 under the Sequencing Center designation ‘CCGB’, and microarray data are deposited in the ArrayExpress under accession numbers E-MEXP-1515, E-MEXP-1519 and E-MEXP-1520.


  1. 1

    Albert, I. et al. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446, 572–576 (2007)

    CAS  ADS  Article  Google Scholar 

  2. 2

    Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007)

    CAS  Article  Google Scholar 

  3. 3

    Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007)

    CAS  Article  Google Scholar 

  4. 4

    Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genet. 39, 1235–1244 (2007)

    CAS  Article  Google Scholar 

  5. 5

    Mito, Y., Henikoff, J. G. & Henikoff, S. Genome-scale profiling of histone H3.3 replacement patterns. Nature Genet. 37, 1090–1097 (2005)

    CAS  Article  Google Scholar 

  6. 6

    Pokholok, D. K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005)

    CAS  Article  Google Scholar 

  7. 7

    Yuan, G. C. et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626–630 (2005)

    CAS  ADS  Article  Google Scholar 

  8. 8

    Leach, T. J. et al. Histone H2A.Z is widely but nonrandomly distributed in chromosomes of Drosophila melanogaster. J. Biol. Chem. 275, 23267–23272 (2000)

    CAS  Article  Google Scholar 

  9. 9

    Updike, D. L. & Mango, S. E. Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA. PLoS Genet. 2, e161 (2006)

    Article  Google Scholar 

  10. 10

    Swaminathan, J., Baxter, E. M. & Corces, V. G. The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin. Genes Dev. 19, 65–76 (2005)

    CAS  Article  Google Scholar 

  11. 11

    Lieb, J. D. & Clarke, N. D. Control of transcription through intragenic patterns of nucleosome composition. Cell 123, 1187–1190 (2005)

    CAS  Article  Google Scholar 

  12. 12

    Raisner, R. M. et al. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123, 233–248 (2005)

    CAS  Article  Google Scholar 

  13. 13

    Zhang, H., Roberts, D. N. & Cairns, B. R. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123, 219–231 (2005)

    CAS  Article  Google Scholar 

  14. 14

    Li, B. et al. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc. Natl Acad. Sci. USA 102, 18385–18390 (2005)

    CAS  ADS  Article  Google Scholar 

  15. 15

    Hild, M. et al. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 5, R3 (2003)

    CAS  Article  Google Scholar 

  16. 16

    Tomancak, P. et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 8, R145 (2007)

    Article  Google Scholar 

  17. 17

    Bruce, K. et al. The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken. Nucleic Acids Res. 33, 5633–5639 (2005)

    CAS  Article  Google Scholar 

  18. 18

    Purnell, B. A., Emanuel, P. A. & Gilmour, D. S. TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes. Genes Dev. 8, 830–842 (1994)

    CAS  Article  Google Scholar 

  19. 19

    Kutach, A. K. & Kadonaga, J. T. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20, 4754–4764 (2000)

    CAS  Article  Google Scholar 

  20. 20

    Lim, C. Y. et al. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 18, 1606–1617 (2004)

    CAS  Article  Google Scholar 

  21. 21

    Biggin, M. D. & Tjian, R. Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts. Cell 53, 699–711 (1988)

    CAS  Article  Google Scholar 

  22. 22

    Soeller, W. C., Oh, C. E. & Kornberg, T. B. Isolation of cDNAs encoding the Drosophila GAGA transcription factor. Mol. Cell. Biol. 13, 7961–7970 (1993)

    CAS  Article  Google Scholar 

  23. 23

    Stark, A. et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219–232 (2007)

    CAS  ADS  Article  Google Scholar 

  24. 24

    Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M. & Trifonov, E. N. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262, 129–139 (1996)

    CAS  Article  Google Scholar 

  25. 25

    Ioshikhes, I. P., Albert, I., Zanton, S. J. & Pugh, B. F. Nucleosome positions predicted through comparative genomics. Nature Genet. 38, 1210–1215 (2006)

    CAS  Article  Google Scholar 

  26. 26

    Johnson, S. M., Tan, F. J., McCullough, H. L., Riordan, D. P. & Fire, A. Z. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 16, 1505–1516 (2006)

    CAS  Article  Google Scholar 

  27. 27

    Kogan, S. B., Kato, M., Kiyama, R. & Trifonov, E. N. Sequence structure of human nucleosome DNA. J. Biomol. Struct. Dyn. 24, 43–48 (2006)

    CAS  Article  Google Scholar 

  28. 28

    Gilmour, D. S. & Lis, J. T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 6, 3984–3989 (1986)

    CAS  Article  Google Scholar 

  29. 29

    Law, A., Hirayoshi, K., O'Brien, T. & Lis, J. T. Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila. Nucleic Acids Res. 26, 919–924 (1998)

    CAS  Article  Google Scholar 

  30. 30

    Lee, C. et al. NELF and GAGA factor are linked to promoter proximal pausing at many genes in Drosophila. Mol. Cell. Biol. (in the press)

  31. 31

    Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507–1511 (2007)

    CAS  Article  Google Scholar 

  32. 32

    Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512–1516 (2007)

    CAS  Article  Google Scholar 

  33. 33

    Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science 292, 1876–1882 (2001)

    CAS  ADS  Article  Google Scholar 

  34. 34

    Brown, S. A., Imbalzano, A. N. & Kingston, R. E. Activator-dependent regulation of transcriptional pausing on nucleosomal templates. Genes Dev. 10, 1479–1490 (1996)

    CAS  Article  Google Scholar 

  35. 35

    Brown, S. A. & Kingston, R. E. Disruption of downstream chromatin directed by a transcriptional activator. Genes Dev. 11, 3116–3121 (1997)

    CAS  Article  Google Scholar 

  36. 36

    Carey, M., Li, B. & Workman, J. L. RSC exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation. Mol. Cell 24, 481–487 (2006)

    CAS  Article  Google Scholar 

  37. 37

    Bondarenko, V. A. et al. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. Mol. Cell 24, 469–479 (2006)

    CAS  Article  Google Scholar 

  38. 38

    Renner, D. B., Yamaguchi, Y., Wada, T., Handa, H. & Price, D. H. A highly purified RNA polymerase II elongation control system. J. Biol. Chem. 276, 42601–42609 (2001)

    CAS  Article  Google Scholar 

  39. 39

    Wu, C. H. et al. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev. 17, 1402–1414 (2003)

    CAS  Article  Google Scholar 

  40. 40

    Kornberg, R. The location of nucleosomes in chromatin: specific or statistical. Nature 292, 579–580 (1981)

    CAS  ADS  Article  Google Scholar 

  41. 41

    Kornberg, R. D. & Stryer, L. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 16, 6677–6690 (1988)

    CAS  Article  Google Scholar 

  42. 42

    Lehmann, M. Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure. Trends Genet. 20, 15–22 (2004)

    CAS  Article  Google Scholar 

  43. 43

    Mito, Y., Henikoff, J. G. & Henikoff, S. Histone replacement marks the boundaries of cis-regulatory domains. Science 315, 1408–1411 (2007)

    CAS  ADS  Article  Google Scholar 

  44. 44

    Lis, J. T. Imaging Drosophila gene activation and polymerase pausing in vivo. Nature 450, 198–202 (2007)

    CAS  ADS  Article  Google Scholar 

  45. 45

    Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)

    CAS  ADS  Article  Google Scholar 

  46. 46

    Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863–14868 (1998)

    CAS  ADS  Article  Google Scholar 

  47. 47

    Fyrberg, E. & Goldstein, L. Drosophila melanogaster: Practical Uses in Cell and Molecular Biology. Methods Cell Biol. 44, 1–732 (1994)

    Google Scholar 

  48. 48

    Orlando, V., Jane, E. P., Chinwalla, V., Harte, P. J. & Paro, R. Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J. 17, 5141–5150 (1998)

    CAS  Article  Google Scholar 

  49. 49

    David, L. et al. A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA 103, 5320–5325 (2006)

    CAS  ADS  Article  Google Scholar 

  50. 50

    Zhang, Z. & Dietrich, F. S. Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE. Nucleic Acids Res. 33, 2838–2851 (2005)

    CAS  Article  Google Scholar 

  51. 51

    Johnson, W. E. et al. Model-based analysis of tiling-arrays for ChIP–chip. Proc. Natl Acad. Sci. USA 103, 12457–12462 (2006)

    CAS  ADS  Article  Google Scholar 

  52. 52

    van Steensel, B., Delrow, J. & Bussemaker, H. J. Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding. Proc. Natl Acad. Sci. USA 100, 2580–2585 (2003)

    CAS  ADS  Article  Google Scholar 

  53. 53

    Li, X. Y. et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 6, e27 (2008)

    Article  Google Scholar 

  54. 54

    Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005)

    CAS  ADS  Article  Google Scholar 

Download references


This work was supported by grants HG004160 (B.F.P.) and GM47477 (D.S.G.). We thank M. Biggin for early access to the Pol II chromatin immunoprecipitation (ChIP)–chip data, R. Fan for supplying the antibody raised against the Drosophila Pol II subunit Rpb3, and C. Lee for help in identifying paused Pol II.

Author Contributions T.N.M. prepared and purified the nucleosomes including Pol II-bound nucleosomes; C.J. analysed the nucleosome-mapping data and its relationship to other genomic features; I.P.I. performed computational analyses related to nucleosome-positioning sequences; X.L. conducted ChIP–chip on Pol II; B.J.V. conducted ChIP–chip and analysis on GAF; S.J.Z. provided bioinformatics support; L.P.T. constructed libraries and sequenced nucleosomal DNA; J.Q. mapped sequencing reads to the yeast genome; R.L.G. provided H2A.Z antibodies; S.C.S. directed the DNA-sequencing phase; D.S.G. directed embryo preparations and helped to interpret the data; I.A. developed computational approaches to derive nucleosome maps from the read locations and developed the associated browser; and B.F.P. directed the project, interpreted the data and wrote the paper.

Author information



Corresponding author

Correspondence to B. Franklin Pugh.

Supplementary information

Supplementary information

The file contains Supplementary Figures 1-19 with Legends. (PDF 3877 kb)

Supplementary information

The file contains Supplementary Table S1 including H2A.Z nucleosome consensus start and end points, peak height, read counts, and standard deviation of read distribution. (TXT 40634 kb)

Supplementary information

The file contains Supplementary Table S2 - TAB file containing all gene lists used in this study. (DOC 954 kb)

Supplementary information

The file contains Supplementary Table S3 - TAB file containing the genomic coordinates of all GAGA motifs. (DOC 4329 kb)

Supplementary information

The file contains Supplementary Table S4 - XLS file containing the plotted data for Fig. 2 (XLS 3111 kb)

Supplementary information

The file contains Supplementary Table S5 - TAB file containing the start and end coordinates of bulk nucleosomes. (DOC 9676 kb)

Supplementary information

The file contains Supplementary Table S6 - TXT file containing the start and end coordinates of Pol II peaks. (TXT 21615 kb)

Supplementary information

The file contains Supplementary Table S7 - TAB file containing the start and end coordinates of Pol II bound nucleosomes. (DOC 1936 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Mavrich, T., Jiang, C., Ioshikhes, I. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358–362 (2008).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing