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Characterization of the Drosophila melanogaster genome at the nuclear lamina

Abstract

The nuclear lamina binds chromatin in vitro and is thought to function in its organization, but genes that interact with it are unknown. Using an in vivo approach, we identified 500 Drosophila melanogaster genes that interact with B-type lamin (Lam). These genes are transcriptionally silent and late replicating, lack active histone marks and are widely spaced. These factors collectively predict lamin binding behavior, indicating that the nuclear lamina integrates variant and invariant chromatin features. Consistently, proximity of genomic regions to the nuclear lamina is partly conserved between cell types, and induction of gene expression or active histone marks reduces Lam binding. Lam target genes cluster in the genome, and these clusters are coordinately expressed during development. This genome-wide analysis gives clear insight into the nature and dynamic behavior of the genome at the nuclear lamina, and implies that intergenic DNA functions in the global organization of chromatin in the nucleus.

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Figure 1: Generation of genome-wide binding maps by expression of Dam-fused Lam proteins.
Figure 2: Lam targets identified by DamID are enriched at the nuclear envelope (NE).
Figure 3: Lam-associated genes are repressed.
Figure 4: Lam binding genes are identified by a combination of DNA and chromatin properties.
Figure 5: Global loss of Lam binding upon inhibition of histone deacetylation.
Figure 6: Lamina-associated gene clusters are units of developmental regulation.
Figure 7: Changes in nuclear lamina binding of gene clusters during differentiation.
Figure 8: Model summarizing factors involved in the association of Lam binding genes to the nuclear lamina.

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Acknowledgements

We thank J. Delrow and M. Aronszajn (Genomics facility, Fred Hutchinson Cancer Research Center) for providing and annotating of cDNA arrays; N. Stuurman for plasmids, antibodies and helpful suggestions; F. Greil and C. Moorman for valuable technical advice; G. Hart for advice on statistical methods; M. Heimerikx and the NKI microarray facility for technical support; L. Guelen, H. van der Velde, J. Hendriksen and D. Engelsma for scoring of the FISH images; and J.M. Boer, S. Nijman, F. van Leeuwen, J. Neefjes, M. van Lohuizen and members of the van Steensel and Fornerod labs for helpful discussions and critical reading of the manuscript. This work was supported by a Marie Curie European Community Training and Mobility grant to H.P. and an European Young Investigator Award to B.v.S.

Author information

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Authors

Contributions

H.P., M.F. and B.v.S. conceived and designed the project; H.P. performed DamID, expression profiling and microscopy experiments and designed FISH probes; B.K. developed and performed FISH experiments; W.T. performed ChIP; E.d.W., M.F. and B.v.S. designed and performed computational analyses and H.P., M.F. and B.v.S. wrote the manuscript with help from B.K. and E.d.W.

Corresponding authors

Correspondence to Maarten Fornerod or Bas van Steensel.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Estimate of DNA content in the nuclear periphery. (PDF 273 kb)

Supplementary Fig. 2

Genomic Lamin binding in embryonic cells shows significant correspondence to polytene chromosome nuclear envelope contacts in larvae. (PDF 116 kb)

Supplementary Fig. 3

Genes bound by Lam are repressed, lack active histone marks and are late replicating. (PDF 157 kb)

Supplementary Fig. 4

The binding pattern of Lam is distinct from that of HP1 and Su(var)3-9. (PDF 1100 kb)

Supplementary Fig. 5

Developmental expression profiles of Lam target gene clusters. (PDF 99 kb)

Supplementary Table 1

Excel spreadsheet containing DamID data, clustering data, expression profiling, flanking intergenic region lengths, probe annotation and gene ontology analysis of Lam-binding genes. (XLS 6469 kb)

Supplementary Table 2

Characteristics of FISH probes. (PDF 86 kb)

Supplementary Table 3

Multiple regression analysis of Lam binding. (PDF 64 kb)

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Pickersgill, H., Kalverda, B., de Wit, E. et al. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38, 1005–1014 (2006). https://doi.org/10.1038/ng1852

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