Mammalian Polycomb-mediated repression of Hox genes requires the essential spliceosomal protein Sf3b1

Polycomb group (PcG) proteins are responsible for the stable repression of homeotic (Hox) genes by forming multimeric protein complexes. We show (1) physical interaction between components of the U2 small nuclear ribonucleoprotein particle (U2 snRNP), including Sf3b1 and PcG proteins Zfp144 and Rnf2; and (2) that Sf3b1 heterozygous mice exhibit skeletal transformations concomitant with ectopic Hox expressions. These alterations are enhanced by Zfp144 mutation but repressed by Mll mutation (a trithorax-group gene). Importantly, the levels of Sf3b1 in PcG complexes were decreased in Sf3b1-heterozygous embryos. These findings suggest that Sf3b1-PcG protein interaction is essential for true PcG-mediated repression of Hox genes

Overlapping Roles for Homeodomain-Interacting Protein Kinases Hipk1 and Hipk2 in the Mediation of Cell Growth in Response to Morphogenetic and Genotoxic Signals

Homeodomain-interacting protein kinase 1 (Hipk1), 2, and 3 genes encode evolutionarily conserved nuclear serine/threonine kinases, which were originally identified as interacting with homeodomain-containing proteins. Hipks have been repeatedly identified as interactors for a vast range of functional proteins, including not only transcriptional regulators and chromatin modifiers but also cytoplasmic signal transducers, transmembrane proteins, and the E2 component of SUMO ligase. Gain-of-function experiments using cultured cells indicate growth regulatory roles for Hipks on receipt of morphogenetic and genotoxic signals. However, Hipk1 and Hipk2 singly deficient mice were grossly normal, and this is expected to be due to a functional redundancy between Hipk1 and Hipk2. Therefore, we addressed the physiological roles of Hipk family proteins by using Hipk1 Hipk2 double mutants. Hipk1 Hipk2 double homozygotes are progressively lost between 9.5 and 12.5 days postcoitus and frequently fail to close the anterior neuropore and exhibit exencephaly. This is most likely due to defective proliferation in the neural fold and underlying paraxial mesoderm, particularly in the ventral region, which may be attributed to decreased responsiveness to Sonic hedgehog signals. The present study indicated the overlapping roles for Hipk1 and Hipk2 in mediating cell proliferation and apoptosis in response to morphogenetic and genotoxic signals during mouse development

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

SummaryThe Polycomb-group (PcG) repressive complex-1 (PRC1) forms microscopically visible clusters in nuclei; however, the impact of this cluster formation on transcriptional regulation and the underlying mechanisms that regulate this process remain obscure. Here, we report that the sterile alpha motif (SAM) domain of a PRC1 core component Phc2 plays an essential role for PRC1 clustering through head-to-tail macromolecular polymerization, which is associated with stable target binding of PRC1/PRC2 and robust gene silencing activity. We propose a role for SAM domain polymerization in this repression by two distinct mechanisms: first, through capturing and/or retaining PRC1 at the PcG targets, and second, by strengthening the interactions between PRC1 and PRC2 to stabilize transcriptional repression. Our findings reveal a regulatory mechanism mediated by SAM domain polymerization for PcG-mediated repression of developmental loci that enables a robust yet reversible gene repression program during development

Splicing factor 3b subunit 1 (Sf3b1) haploinsufficient mice display features of low risk Myelodysplastic syndromes with ring sideroblasts

The presence of somatic mutations in splicing factor 3b subunit 1 (SF3B1) in patients with Myelodysplastic syndromes with ring sideroblasts (MDS-RS) highlights the importance of the RNA-splicing machinery in MDS. We previously reported the presence of bone marrow (BM) RS in Sf3b1 heterozygous (Sf3b1 (+/-)) mice which are rarely found in mouse models of MDS. Sf3b1 (+/-) mice were originally engineered to study the interaction between polycomb genes and other proteins. We used routine blood tests and histopathologic analysis of BM, spleen, and liver to evaluate the hematologic and morphologic characteristics of Sf3b1 (+/-) mice in the context of MDS by comparing the long term follow-up (15 months) of Sf3b1 (+/-) and Sf3b1 (+/+) mice. We then performed a comprehensive RNA-sequencing analysis to evaluate the transcriptome of BM cells from Sf3b1 (+/-) and Sf3b1 (+/+) mice. Sf3b1 (+/-) exhibited macrocytic anemia (MCV: 49.5 ± 1.6 vs 47.2 ± 1.4; Hgb: 5.5 ± 1.7 vs 7.2 ± 1.0) and thrombocytosis (PLTs: 911.4 ± 212.1 vs 878.4 ± 240.9) compared to Sf3b1 (+/+) mice. BM analysis showed dyserythropoiesis and occasional RS in Sf3b1 (+/-) mice. The splenic architecture showed increased megakaryocytes with hyperchromatic nuclei, and evidence of extramedullary hematopoiesis. RNA-sequencing showed higher expression of a gene set containing Jak2 in Sf3b1 (+/-) compared to Sf3b1 (+/+). Our study indicates that Sf3b1 (+/-) mice manifest features of low risk MDS-RS and may be relevant for preclinical therapeutic studies

Polycomb Group Protein Ezh2 Regulates Hepatic Progenitor Cell Proliferation and Differentiation in Murine Embryonic Liver

<div><p>In embryonic liver, hepatic progenitor cells are actively proliferating and generate a fundamental cellular pool for establishing parenchymal components. However, the molecular basis for the expansion of the progenitors maintaining their immature state remains elusive. Polycomb group proteins regulate gene expression throughout the genome by modulating of chromatin structure and play crucial roles in development. <i>Enhancer of zeste homolog 2</i> (<i>Ezh2</i>), a key component of polycomb group proteins, catalyzes tri-methylation of lysine 27 of histone H3 (H3K27me3), which trigger the gene suppression. In the present study, we investigated a role of <i>Ezh2</i> in the regulation of the expanding hepatic progenitor population <i>in vivo</i>. We found that Ezh2 is highly expressed in the actively proliferating cells at the early developmental stage. Using a conditional knockout mouse model, we show that the deletion of the SET domain of <i>Ezh2</i>, which is responsible for catalytic induction of H3K27me3, results in significant reduction of the total liver size, absolute number of liver parenchymal cells, and hepatic progenitor cell population in size. A clonal colony assay in the hepatic progenitor cells directly isolated from <i>in vivo</i> fetal livers revealed that the bi-potent clonogenicity was significantly attenuated by the Ezh2 loss of function. Moreover, a marker expression based analysis and a global gene expression analysis showed that the knockout of Ezh2 inhibited differentiation to hepatocyte with reduced expression of a number of liver-function related genes. Taken together, our results indicate that Ezh2 is required for the hepatic progenitor expansion <i>in vivo</i>, which is essential for the functional maturation of embryonic liver, through its activity for catalyzing H3K27me3.</p></div

Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure

Summary: NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies’ function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with MLL1/CRM1 and co-localized on chromatin. Furthermore, whole-genome chromatin-conformation capture analysis reveals that NUP98::HOXA9 induces a drastic alteration in high-order genome structure at target regions concomitant with the generation of chromatin loops and/or rearrangement of topologically associating domains in a phase-separation-dependent manner. Collectively, these results show that the phase-separated nuclear bodies of nucleoporin fusion proteins can enhance the activation of target genes by promoting the condensation of MLL1/CRM1 and rearrangement of the 3D genome structure

Splicing Factor 3b Subunit 1 (SF3B1) Heterozygous Mice Manifest a Hematologic Phenotype Similar To Low Risk Myelodysplastic Syndromes With Ring Sideroblasts

Abstract The link between SF3B1 mutation and the ring sideroblast (RS) phenotype in myelodysplastic syndromes (MDS) was solidified by the identification of RS in Sf3b1 heterozygous (Sf3b1+/-) mice. The identification of SF3B1 mutations in refractory anemia with RS (RARS) and RARS with thrombocytosis (RARS-T) showed the importance of RNA splicing in MDS biology. Furthermore, it opened the possibility of targeted therapy using spliceosome inhibitors in RARS/-T. However, many questions remain unanswered in linking SF3B1 dysfunction to MDS biology like the downstream targets of this gene. The identification of a robust murine model is essential to study a specific molecularly defined disease-phenotype and develop targeted therapies. We identified occasional RS in the bone marrow (BM) of Sf3b1+/- which are rarely found in current mouse models of MDS (Beachy SH, Hematol Oncol Clin North Am, 2010). However, aside from RS in the BM no other MDS features were found. Sf3b1+/- mice were originally engineered as a means to study the interaction between polycomb (PcG) genes and other protein-complexes (Isono K, Genes Dev, 2005). Homozygous Sf3b1-/- mice died at the stage of pre-implantation of the embryos while Sf3b1+/- appear healthy. Several tools have been tested to model MDS in genetically engineered mice targeting key genes in MDS. However, the creation of an ideal mouse model resembling distinct morphologic MDS subtypes is still lacking. To define a mouse model useful for preclinical therapeutic studies, we evaluated the hematologic features of Sf3b1+/- and Sf3b1+/+ mice during a long term follow-up. Five Sf3b1+/- and 5 Sf3b1+/+ mice were followed over time until 12 months of age. Blood was drawn from the retro-orbital vein every month starting from 6 months of age. Using two-sample Wilcoxon test we compared standard hematologic parameters finding a significant difference over the time between Sf3b1+/- and Sf3b1+/+: hemoglobin (g/dL) 6.9 ±0.73 vs 10.0 ±1.6 (P=0.008), red blood cells (M/uL) 8.3±0.5 vs 5.9±1.0 (P=0.008), platelets (K/uL) 731±105 vs 579±93 (P=0.008), and mean corpuscular volume (fL) 47.8±1.5 vs 45.1±1.1 (P=0.032). We did not detect any significant difference in other parameters although lymphocytes were more represented vs neutrophils, eosinophils and monocytes in Sf3b1+/- vs Sf3b1+/+ (6.3K/uL ±3.1 vs 5.8 ±1.8; P=1). Analysis of the BM, showed no difference in cell number between Sf3b1+/- (n=7) and Sf3b1+/+ (n=7) (44.1±9.1 vs 43.2 ±11; P=0.62). However, distinct dyserythropoiesis such as nuclear budding or irregular nuclei in Wright-Giemsa and occasional RS in Prussian blue stains were noted in Sf3b1+/- which were not present in Sf3b1+/+. In support of the iron overload seen in SF3B1 mutant patients (pts), a similar observation was made in Sf3b1+/- by light microscopy and rhodamine based- flow cytometry to quantify mitochondrial iron (Visconte, Abstract #64897). We also characterized the transcriptome of Sf3b1+/- and Sf3b1+/+. Total RNA was isolated from BM of age/gender matched mice, polyA cDNA was prepared from 3ug of RNA and Mouse RNA-sequencing was run on Illumina HiSeq2000. 200 exons were found differentially used in Sf3b1+/- vs Sf3b1+/+. Chromosome 1 contains the highest number of genes with at least 1 exon alternatively used similar to what we observed in SF3B1 mutant pts. In total 22 genes showed stronger differential expression in Sf3b1+/- vs Sf3b1+/+. Sf3b1 was down-regulated as expected (MFC: 0.74) in Sf3b1+/-. Studies in Sf3b1+/- mice show that Sf3b1 protein physically interacts with Class II PcG proteins (PRC1) which are relevant in MDS. When we interrogated PcG genes and others, we found lower mRNA levels of ezh2 (MFC: 0.06) and npm1 and tpr53 (MFC: 0.01 and 0.28) and no difference in asxl1 and runx1 (MFC:1.22 and 1.1) in Sf3b1+/- vs Sf3b1+/+. Jak2, dock8, and uhrf2 showed significant (P=.0003) higher expression in Sf3b1+/-. MDS is a heterogeneous disease characterized by genetic and non-genetic causes. Introduction of secondary events implicated in MDS pathogenesis can modify the phenotype of Sf3b1+/- mice. In sum, Sf3b1+/- mice after 6 months of follow-up developed macrocytic anemia, thrombocytosis, RS and dyserythropoiesis akin to human RARS/-T. Furthermore, transcriptome analysis shows exon usage/ gene expression changes similar to human SF3B1 mutants lending support that Sf3b1+/- can serve as a mouse model for studying the biology of human low risk MDS specifically that of RARS/-T. Disclosures: No relevant conflicts of interest to declare

Negative regulators of cell cycle were significantly up-regulated in the Ezh2 SET domain depleted fetal livers.

<p>A: The G1_to_S_Cell_Cycle_Control pathway (WP413_41269) from analysis using the WikiPathways platform is shown, in which gene hits with more than 2-fold change up to 8-fold change (<i>P</i> = 0.0018) are highlighted in yellow and hits with more than 8-fold change (<i>P</i> = 0.0046) in red in the Ezh2-KO CD45⁻ TER119⁻ liver cells at ED 13.5 compared with WT control. B: ChIP-PCR analysis with the anti-Ezh2 antibody and the primer sets detecting promoter regions of Cdkn1a, Cdkn2a, and Cdkn2b in the CD45⁻ TER119⁻ liver cells from WT livers at ED 13.5 are shown. C: ChIP-PCR analysis with the anti-H3K27me3 antibody and the primer sets detecting promoter regions of Cdkn1a, Cdkn2a, and Cdkn2b in the CD45⁻ TER119⁻ liver cells from the WT control livers at ED 13.5 are shown. D: Immunohistochemical analysis of Cdkn1a protein in the WT control and Ezh2 KO liver tissues at ED 13.5. Scale bar = 50 µm.</p