HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle

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Abstract

Cornelia de Lange syndrome (CdLS) is a dominantly inherited congenital malformation disorder, caused by mutations in the cohesin-loading protein NIPBL1,2 for nearly 60% of individuals with classical CdLS3,4,5, and by mutations in the core cohesin components SMC1A (5%) and SMC3 (<1%) for a smaller fraction of probands6,7. In humans, the multisubunit complex cohesin is made up of SMC1, SMC3, RAD21 and a STAG protein. These form a ring structure that is proposed to encircle sister chromatids to mediate sister chromatid cohesion8 and also has key roles in gene regulation9. SMC3 is acetylated during S-phase to establish cohesiveness of chromatin-loaded cohesin10,11,12,13, and in yeast, the class I histone deacetylase Hos1 deacetylates SMC3 during anaphase14,15,16. Here we identify HDAC8 as the vertebrate SMC3 deacetylase, as well as loss-of-function HDAC8 mutations in six CdLS probands. Loss of HDAC8 activity results in increased SMC3 acetylation and inefficient dissolution of the ‘used’ cohesin complex released from chromatin in both prophase and anaphase. SMC3 with retained acetylation is loaded onto chromatin, and chromatin immunoprecipitation sequencing analysis demonstrates decreased occupancy of cohesin localization sites that results in a consistent pattern of altered transcription seen in CdLS cell lines with either NIPBL or HDAC8 mutations.

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Figure 1: HDAC8 is an SMC3 deacetylase.
Figure 2: Cohesin and SMC3-ac localization sites in control and HDAC8 RNAi-treated HeLa cells.
Figure 3: HDAC8 mutations in CdLS.
Figure 4: Retention of RAD21-N and sororin on cohesin in the absence of HDAC8.

Accession codes

Primary accessions

Sequence Read Archive

Data deposits

ChIP-Seq and RNA-Seq data from this study are available from the Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra) under the accession number SRP011927.

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Acknowledgements

We are grateful to the individuals and families with Cornelia de Lange syndrome who participated in this study, as well as to the referring physicians and colleagues who have contributed samples and clinical information. We thank Riken Omics Science Center, K. Nakagawa, S. Watanabe, M. Albrecht and J. Eckhold for technical support. We thank J.-M. Peters for the sororin and RAD21 antibodies. We thank F. Beckouët and K. Nasmyth for sharing unpublished results. We are indebted to the continued support of the US and International Cornelia de Lange Syndrome Foundations. This work was supported by National Institutes of Health grants K08HD055488 (NICHD, M.A.D.), GM49758 (D.W.C.) and P01 HD052860 (NICHD; I.D.K.), research grants from the US CdLS Foundation, institutional funds from the Children’s Hospital of Philadelphia, Intramural funding from the University of Lübeck (Schwerpunktprogramm, Medizinische Genetik: Von seltenen Varianten zur Krankheitsentstehung; F.J.K., G.G.-K.), Research Program of Innovative Cell Biology by Innovative Technology, Grant-in-Aid for Scientific Research (S) and for innovative science from MEXT (K.Sh.).

Author information

M.B. and K.Sh. designed and performed the biochemical analyses; M.B., E.W., C.J., L.M.-J. and K.Sh. performed HDAC screening. M.B., K.Sa., E.W. and L.M.-J. performed chromatin spreading assays; N.N. monoclonal isolation; M.B., R.N., T.I., M.K., Y.K. and K.Sh. the ChIP sequencing and analysis; M.B., R.N. and Y.S. RNA sequencing; M.M., K.T. and T.H. microscopy. M.A.D., G.G.-K., L.G.J., F.J.K. and I.D.K. initiated the human studies. M.A.D., D.C., E.D.B., G.R.M., V.M.S., P.W., N.T., Y.G., M.B.P., G.G.-K. and I.D.K. identified and characterized clinical data. M.A.D., M.K., S.E., L.J.F., M.H. and F.J.K. performed mutation screening, inactivation and lymphoblastoid expression studies. K.H., T.K. and H.S. established fibroblast cell lines. M.A.D., J.J.W., K.E.C., P.M.L., C.D. and D.W.C. performed enzymatic and structural analysis. M.A.D., M.B. and K.Sh. drafted the manuscript. All authors analysed data, discussed the results and commented on the manuscript.

Correspondence to Matthew A. Deardorff or Ian D. Krantz or Katsuhiko Shirahige.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-10, a Supplementary Discussion, Supplementary Tables 1-6 and 8-9, Supplementary References and full scan images for all Western-blotting data presented in both the main article figures and supplementary figures. (PDF 5189 kb)

Supplementary Data

This file contains Nanostring data and calculations for 32-gene CdLS lymphoblastoid expression profiling. (XLS 174 kb)

Supplementary Data

This file contains Supplementary Table 7, which shows RNA sequencing data from Fibroblast experiments. (XLS 1594 kb)

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