This study presents the first global protein interaction network for all 11 human HDACs in T cells and an integrative mass spectrometry approach for profiling relative interaction stability within isolated protein complexes.

In order to explore the defense mechanism by which retrotransposons are repressed, we assessed the ability of methyl-CpG-binding protein 2, MeCP2, to influence LINE-1 (L1) and Alu transcription and, furthermore, L1 retrotransposition. In transient transfection assays, targeting of the transcriptional-repression domain (TRD) of MeCP2 (via a linked Gal4 DNA-binding domain) to the transcriptional start site of L1 promoter-driven reporter constructs efficiently repressed transcription. The Gal4-linked TRD of the related methyl-CpG-binding protein MBD1 also repressed transcription but not that of MBD2. Furthermore, full-length MeCP2 effectively repressed transcription of a HpaII-methylated L1 reporter. Secondly, we used a genetic assay employing a full-length neo-marked L1 reporter construct to study L1 retrotransposition. We found the Gal4-linked TRD of MeCP2 to repress effectively L1 retrotransposition when targeted to the retrotransposition reporter. Retrotransposition was also reduced in response to in vitro HpaII methylation of the reporter and was further decreased by co-expressed full-length MeCP2. In striking contrast expression of the Gal4-linked TRD of MeCP2 had no inhibiting effect on transcription of an AluSx reporter tagged with a 7S-upstream sequence. Furthermore, full-length MeCP2 abrogated the methylation-induced repression of this reporter. Our results indicate that MeCP2 serves a role in repression of L1 expression and retrotransposition but has no inhibiting effect on Alu transcription.

SUMMARYCompared with the well-studied biochemical function of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) as a histone chaperone in nucleosome assembly/disassembly, the physiological roles of NAP1 remain largely uncharacterized. Here, we define the NAP1 gene family members in Arabidopsis, examine their molecular properties, and use reverse genetics to characterize their biological roles. We show that the four AtNAP1-group proteins can form homodimers and heterodimers, can bind histone H2A, and are localized abundantly in the cytoplasm and weakly in the nucleus at steady state. AtNAP1;4 differs from the others by showing inhibitorsensitive nucleocytoplasmic shuttling and tissue-specific expression, restricted to root segments and pollen grains. The other three AtNAP1 genes are ubiquitously expressed in plants and the AtNAP1;3 protein is detected as the major isoform in seedlings. We show that disruption of the AtNAP1-group genes does not affect normal plant growth under our laboratory conditions. Interestingly, two allelic triple mutants, Atnap1;1-1 Atnap1;2-1 Atnap1;3-1 and Atnap1;1-1 Atnap1;2-1 Atnap1;3-2, exhibit perturbed genome transcription, and show hypersensitivity to DNA damage caused by UV-C irradiation. We show that AtNAP1;3 binds chromatin, with enrichment at some genes involved in the nucleotide excision repair (NER) pathway, and that the expression of these genes is downregulated in the triple mutants. Taken together, our results highlight conserved and isoform-specific properties of AtNAP1 proteins, and unravel their function in the NER pathway of DNA damage repair.