A chromatin-based signalling mechanism directs the switch from mutagenic to error-free repair of DNA double strand breaks

Mutations caused by DNA damage are a main driver of cancer. We discovered that recognition of newly synthesised histone H4 directs breast cancer type 1 susceptibility protein (BRCA1) to post-replicative chromatin. The switch from mutagenic to error-free DNA double strand break repair by homologous recombination is therefore controlled by chromatin

Charakterisierung von BRUCE als antiapoptotisches IAP

Der programmierte Zelltod, oder Apoptose, ist ein physiologischer Vorgang mit zentraler Bedeutung für die Entwicklung und Homöostase mehrzelliger Organismen. Die Auslösung der Apoptose führt zur Aktivierung von Caspasen. Dies sind Cysteinproteasen, die gezielte Substratproteine spalten und so die koordinierte Zerstörung der Zelle herbeiführen. Apoptose wird durch pro- und antiapoptotische Proteine reguliert, die die Aktivierung von Caspasen stimulieren bzw. unterdrücken. Da diese Proteine sich gegenseitig beeinflussen, wird das Schicksal einer Zelle durch die relative Aktivität pro- und antiapoptotischer Faktoren bestimmt. BRUCE (BIR repeat-containing ubiquitin-conjugating enzyme) ist ein konserviertes, 528 kDa großes, peripheres Membranprotein des trans-Golgi Netzwerks. Seine charakteristischen Merkmale sind eine N-terminale BIR-Domäne und eine C-terminale UBC-Domäne, die dem Molekül Ubiquitin-Konjugationsaktivität verleiht. Diese Arbeit demonstriert, dass BRUCE Zellen vor der Apoptose schützt und als ein inhibitor of apoptosis protein (IAP) wirkt, indem es an aktive Caspasen bindet und diese inhibiert. Die Verwendung von Wildtyp und Mutanten des BRUCE Proteins zeigt, dass diese Aktivitäten von der BIR-Domäne abhängen. Während der Apoptose wird BRUCE durch unterschiedliche Mechanismen blockiert. Zum einen wird BRUCE durch Caspasen und HtrA2 proteolytisch gespalten und dadurch inaktiviert. Zum anderen bindet der mitochondriale IAP-Antagonist Smac an die BIR-Domäne von BRUCE und unterdrückt dessen Caspase-inhibitorische Aktivität, indem es die Bindung von BRUCE an Caspasen verhindert. Aufgrund seiner Lokalisierung an Membranen des trans-Golgi Netzwerks könnte BRUCE ein spezialisiertes, antiapoptotisches Protein mit räumlich begrenzter Aktivität sein. Wie die stark negative Regulation verdeutlicht, scheint außerdem die Entfernung von BRUCE aus der Zelle während der Apoptose wichtig zu sein. Räumlich und zeitlich begrenzte Inhibition von Caspasen während der Apoptose könnte daher für einen geordneten Ablauf apoptotischer Prozesse, wie zum Beispiel den Abbau des Golgi-Apparates und seine Verpackung in apoptotische Vesikel, notwendig sein

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

SummaryModifications on histones or on DNA recruit proteins that regulate chromatin function. Here, we use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify “crosstalk” between these two distinct classes of modification. Our analysis reveals proteins whose binding to nucleosomes is regulated by methylation of CpGs, H3K4, H3K9, and H3K27 or a combination thereof. We identify the origin recognition complex (ORC), including LRWD1 as a subunit, to be a methylation-sensitive nucleosome interactor that is recruited cooperatively by DNA and histone methylation. Other interactors, such as the lysine demethylase Fbxl11/KDM2A, recognize nucleosomes methylated on histones, but their recruitment is disrupted by DNA methylation. These data establish SILAC nucleosome affinity purifications (SNAP) as a tool for studying the dynamics between different chromatin modifications and provide a modification binding “profile” for proteins regulated by DNA and histone methylation

KDM2A integrates DNA and histone modification signals through a CXXC/PHD module and direct interaction with HP1.

Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromatin recognition by the lysine demethylase KDM2A. Using biochemical approaches we identify a nucleosome interaction module within KDM2A consisting of a CXXC type zinc finger, a PHD domain and a newly identified Heterochromatin Protein 1 (HP1) interaction motif that mediates direct binding between KDM2A and HP1. This nucleosome interaction module enables KDM2A to decode nucleosomal H3K9me3 modification in addition to CpG methylation signals. The multivalent engagement with DNA and HP1 results in a nucleosome binding circuit in which KDM2A can be recruited to H3K9me3-modified chromatin through HP1, and HP1 can be recruited to unmodified chromatin by KDM2A. A KDM2A mutant deficient in HP1-binding is inactive in an in vivo overexpression assay in zebrafish embryos demonstrating that the HP1 interaction is essential for KDM2A function. Our results reveal a complex regulation of chromatin binding for both KDM2A and HP1 that is modulated by DNA- and H3K9-methylation, and suggest a direct role for KDM2A in chromatin silencing

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon-intron boundaries and the 3'UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome

Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish.

KDM2A is a histone demethylase associated with transcriptional silencing, however very little is known about its in vivo role in development and disease. Here we demonstrate that loss of the orthologue kdm2aa in zebrafish causes widespread transcriptional disruption and leads to spontaneous melanomas at a high frequency. Fish homozygous for two independent premature stop codon alleles show reduced growth and survival, a strong male sex bias, and homozygous females exhibit a progressive oogenesis defect. kdm2aa mutant fish also develop melanomas from early adulthood onwards which are independent from mutations in braf and other common oncogenes and tumour suppressors as revealed by deep whole exome sequencing. In addition to effects on translation and DNA replication gene expression, high-replicate RNA-seq in morphologically normal individuals demonstrates a stable regulatory response of epigenetic modifiers and the specific de-repression of a group of zinc finger genes residing in constitutive heterochromatin. Together our data reveal a complex role for Kdm2aa in regulating normal mRNA levels and carcinogenesis. These findings establish kdm2aa mutants as the first single gene knockout model of melanoma biology

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

Quantitative mass spectrometry enables the proteome-wide assessment of biomolecular binding affinities. While previous approaches mainly focused on protein–small molecule interactions, the authors here present a method to probe protein–DNA and protein–nucleosome binding affinities at proteome scale

Basic surface features of nuclear FKBPs facilitate chromatin binding

The nucleoplasmin family of histone chaperones is identified by a pentamer-forming domain and multiple acidic tracts that mediate histone binding and chaperone activity. Within this family, a novel domain organization was recently discovered that consists of an N-terminal nucleoplasmin-like (NPL) domain and a C-terminal FKBP peptidyl-proline isomerase domain. Saccharomyces cerevisiae Fpr4 is one such protein. Here we report that in addition to its known histone prolyl isomerase activities, the Fpr4 FKBP domain binds to nucleosomes and nucleosome arrays in vitro. This ability is mediated by a collection of basic patches that enable the enzyme to stably associate with linker DNA. The interaction of the Fpr4 FKBP with recombinant chromatin complexes condenses nucleosome arrays independently of its catalytic activity. Based on phylogenetic comparisons we propose that the chromatin binding ability of ‘basic’ FKBPs is shared amongst related orthologues present in fungi, plants, and insects. Thus, a subclass of FKBP prolyl isomerase enzymes is recruited to linker regions of chromatin

LETTERS JAK2 phosphorylates histone H3Y41 and excludes HP1a from chromatin

Activation of Janus kinase 2 (JAK2) by chromosomal translocations or point mutations is a frequent event in haematological malignancies To explore the role of JAK2 within the nucleus we investigated the possibility that histones could be a substrate. Among all core histones, we found that recombinant JAK2 specifically phosphorylated histone H3, a reaction inhibited by the JAK2 inhibitor TG101209 (ref. 16)