Chromatin Segregation Research Articles

CDK phosphorylation of Sfr1 downregulates Rad51 function in late-meiotic homolog invasions.

Meiosis is the developmental program that generates gametes. To produce healthy gametes, meiotic recombination creates reciprocal exchanges between each pair of homologous chromosomes that facilitate faithful chromosome segregation. Using fission yeast and biochemical, genetic, and cytological approaches, we have studied the role of CDK (cyclin-dependent kinase) in the control of Swi5-Sfr1, a Rad51-recombinase auxiliary factor involved in homolog invasion during recombination. We show that Sfr1 is a CDK target, and its phosphorylation downregulates Swi5-Sfr1 function in the meiotic prophase. Expression of a phospho-mimetic sfr1-7D mutant inhibits Rad51 binding, its robust chromosome loading, and subsequently decreases interhomolog recombination. On the other hand, the non-phosphorylatable sfr1-7A mutant alters Rad51 dynamics at late prophase, and exacerbates chromatin segregation defects and Rad51 retention observed in dbl2 deletion mutants when combined with them. We propose Sfr1 phospho-inhibition as a novel cell-cycle-dependent mechanism, which ensures timely resolution of recombination intermediates and successful chromosome distribution into the gametes. Furthermore, the N-terminal disordered part of Sfr1, an evolutionarily conserved feature, serves as a regulatory platform coordinating this phospho-regulation, protein localization and stability, with several CDK sites and regulatory sequences being conserved.

Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus.

The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution,which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This "inversion" is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP1α-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.

Hepatocyte-specific METTL3 ablation by Alb-iCre mice (GPT), but not by Alb-Cre mice (JAX), resulted in acute liver failure (ALF) and postnatal lethality.

In 2019, to examine the functions of METTL3 in liver and underlying mechanisms, we generated mice with hepatocyte-specific METTL3 homozygous knockout (METTL3Δhep) by simultaneously crossing METTL3fl/fl mice with Alb-iCre mice (GPT) or Alb-Cre mice (JAX), respectively. In this study, we explored the potential reasons why hepatocyte-specific METTL3 homozygous disruption by Alb-iCre mice (GPT), but not by Alb-Cre mice (JAX), resulted in acute liver failure (ALF) and then postnatal lethality. Mice with hepatocyte-specific METTL3 knockout were generated by simultaneously crossing METTL3fl/fl mice with Alb-iCre mice (GPT; Strain No. T003814) purchased from the GemPharmatech Co., Ltd., (Nanjing, China) or with Alb-Cre mice (JAX; Strain No. 003574) obtained from The Jackson Laboratory, followed by combined-phenotype analysis. The publicly available RNA-sequencing data deposited in the NCBI Gene Expression Omnibus (GEO) database under the accession No.: GSE198512 (postnatal lethality), GSE197800 (postnatal survival) and GSE176113 (postnatal survival) were mined to explore the potential reasons why hepatocyte-specific METTL3 homozygous deletion by Alb-iCre mice (GPT), but not by Alb-Cre mice (JAX), leads to ALF and then postnatal lethality. Firstly, we observed that hepatocyte-specific METTL3 homozygous deficiency by Alb-iCre mice (GPT) or by Alb-Cre mice (JAX) caused liver injury, abnormal lipid accumulation and apoptosis. Secondly, we are surprised to find that hepatocyte-specific METTL3 homozygous deletion by Alb-iCre mice (GPT), but not by Alb-Cre mice (JAX), led to ALF and then postnatal lethality. Our findings clearly demonstrated that METTL3Δhep mice (GPT), which are about to die, exhibited the severe destruction of liver histological structure, suggesting that METTL3Δhep mice (GPT) nearly lose normal liver function, which subsequently contributes to ALF, followed by postnatal lethality. Finally, we unexpectedly found that as the compensatory growth responses of hepatocytes to liver injury induced by METTL3Δhep (GPT), the proliferation of METTL3Δhep hepatocytes (GPT), unlike METTL3Δhep hepatocytes (JAX), was not evidenced by the significant increase of Ki67-positive hepatocytes, not accompanied by upregulation of cell-cycle-related genes. Moreover, GO analysis revealed that upregulated genes in METTL3Δhep livers (GPT), unlike METTL3Δhep livers (JAX), are not functionally enriched in terms associated with cell cycle, cell division, mitosis, microtubule cytoskeleton organization, spindle organization, chromatin segregation and organization, and nuclear division, consistent with the loss of compensatory proliferation of METTL3Δhep hepatocytes (GPT) observed in vivo. Thus, obviously, the loss of the compensatory growth capacity of METTL3Δhep hepatocytes (GPT) in response to liver injury might contribute to, at least partially, ALF and subsequently postnatal lethality of METTL3Δhep mice (GPT). These findings from this study and other labs provide strong evidence that these phenotypes (i.e., ALF and postnatal lethality) of METTL3Δhep mice (GPT) might be not the real functions of METTL3, and closely related with Alb-iCre mice (GPT), suggesting that we should remind researchers to use Alb-iCre mice (GPT) with caution to knockout gene in hepatocytes in vivo.

Chromatin Organization during C. elegans Early Development

Embryogenesis is characterized by dynamic chromatin remodeling and broad changes in chromosome architecture. These changes in chromatin organization are accompanied by transcriptional changes, which are crucial for the proper development of the embryo. Several independent mechanisms regulate this process of chromatin reorganization, including the segregation of chromatin into heterochromatin and euchromatin, deposition of active and repressive histone modifications, and the formation of 3D chromatin domains such as TADs and LADs. These changes in chromatin structure are directly linked to developmental milestones such as the loss of developmental plasticity and acquisition of terminally differentiated cell identities. In this review, we summarize these processes that underlie this chromatin reorganization and their impact on embryogenesis in the nematode C. elegans.

Calreticulin and JAK2V617F driver mutations induce distinct mitotic defects in myeloproliferative neoplasms.

Myeloproliferative neoplasms (MPNs) encompass a diverse group of hematologic disorders driven by mutations in JAK2, CALR, or MPL. The prevailing working model explaining how these driver mutations induce different disease phenotypes is based on the decisive influence of the cellular microenvironment and the acquisition of additional mutations. Here, we report increased levels of chromatin segregation errors in hematopoietic cells stably expressing CALRdel52 or JAK2V617F mutations. Our investigations employing murine 32DMPL and human erythroleukemic TF-1MPL cells demonstrate a link between CALRdel52 or JAK2V617F expression and a compromised spindle assembly checkpoint (SAC), a phenomenon contributing to error-prone mitosis. This defective SAC is associated with imbalances in the recruitment of SAC factors to mitotic kinetochores upon CALRdel52 or JAK2V617F expression. We show that JAK2 mutant CD34 + MPN patient-derived cells exhibit reduced expression of the master mitotic regulators PLK1, aurora kinase B, and PP2A catalytic subunit. Furthermore, the expression profile of mitotic regulators in CD34 + patient-derived cells allows to faithfully distinguish patients from healthy controls, as well as to differentiate primary and secondary myelofibrosis from essential thrombocythemia and polycythemia vera. Altogether, our data suggest alterations in mitotic regulation as a potential driver in the pathogenesis in MPN.

Genome Doubling Weakens DNA Organization and Supports Tumorigenesis

Whole-genome doubling (WGD) induces loss of chromatin segregation, which promotes cancer development.

Whole-genome doubling drives oncogenic loss of chromatin segregation

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies1–8. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here we show that in p53-deficient cells, WGD induces loss of chromatin segregation (LCS). This event is characterized by reduced segregation between short and long chromosomes, A and B subcompartments and adjacent chromatin domains. LCS is driven by the downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primes genomic regions for subcompartment repositioning in WGD cells. This results in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Notably, subcompartment repositioning events were largely independent of chromosomal alterations, which indicates that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, which suggests that chromatin evolution is a hallmark of WGD-driven cancer.

Genomic instability caused by Arp2/3 complex inactivation results in micronucleus biogenesis and cellular senescence.

The Arp2/3 complex is an actin nucleator with well-characterized activities in cell morphogenesis and movement, but its roles in nuclear processes are relatively understudied. We investigated how the Arp2/3 complex affects genomic integrity and cell cycle progression using mouse fibroblasts containing an inducible knockout (iKO) of the ArpC2 subunit. We show that permanent Arp2/3 complex ablation results in DNA damage, the formation of cytosolic micronuclei, and cellular senescence. Micronuclei arise in ArpC2 iKO cells due to chromatin segregation defects during mitosis and premature mitotic exits. Such phenotypes are explained by the presence of damaged DNA fragments that fail to attach to the mitotic spindle, abnormalities in actin assembly during metaphase, and asymmetric microtubule architecture during anaphase. In the nuclei of Arp2/3-depleted cells, the tumor suppressor p53 is activated and the cell cycle inhibitor Cdkn1a/p21 mediates a G1 arrest. In the cytosol, micronuclei are recognized by the DNA sensor cGAS, which is important for stimulating a STING- and IRF3-associated interferon response. These studies establish functional requirements for the mammalian Arp2/3 complex in mitotic spindle organization and genome stability. They also expand our understanding of the mechanisms leading to senescence and suggest that cytoskeletal dysfunction is an underlying factor in biological aging.

Dynamic SUMOylation of MORC2 orchestrates chromatin remodelling and DNA repair in response to DNA damage and drives chemoresistance in breast cancer.

Rationale: SUMOylation regulates a plethora of biological processes, and its inhibitors are currently under investigation in clinical trials as anticancer agents. Thus, identifying new targets with site-specific SUMOylation and defining their biological functions will not only provide new mechanistic insights into the SUMOylation signaling but also open an avenue for developing new strategy for cancer therapy. MORC family CW-type zinc finger 2 (MORC2) is a newly identified chromatin-remodeling enzyme with an emerging role in the DNA damage response (DDR), but its regulatory mechanism remains enigmatic. Methods: In vivo and in vitro SUMOylation assays were used to determine the SUMOylation levels of MORC2. Overexpression and knockdown of SUMO-associated enzymes were used to detect their effects on MORC2 SUMOylation. The effect of dynamic MORC2 SUMOylation on the sensitivity of breast cancer cells to chemotherapeutic drugs was examined through in vitro and in vivo functional assays. Immunoprecipitation, GST pull-down, MNase, and chromatin segregation assays were used to explore the underlying mechanisms. Results: Here, we report that MORC2 is modified by small ubiquitin-like modifier 1 (SUMO1) and SUMO2/3 at lysine 767 (K767) in a SUMO-interacting motif dependent manner. MORC2 SUMOylation is induced by SUMO E3 ligase tripartite motif containing 28 (TRIM28) and reversed by deSUMOylase sentrin-specific protease 1 (SENP1). Intriguingly, SUMOylation of MORC2 is decreased at the early stage of DNA damage induced by chemotherapeutic drugs that attenuate the interaction of MORC2 with TRIM28. MORC2 deSUMOylation induces transient chromatin relaxation to enable efficient DNA repair. At the relatively late stage of DNA damage, MORC2 SUMOylation is restored, and SUMOylated MORC2 interacts with protein kinase CSK21 (casein kinase II subunit alpha), which in turn phosphorylates DNA-PKcs (DNA-dependent protein kinase catalytic subunit), thus promoting DNA repair. Notably, expression of a SUMOylation-deficient mutant MORC2 or administration of SUMO inhibitor enhances the sensitivity of breast cancer cells to DNA-damaging chemotherapeutic drugs. Conclusions: Collectively, these findings uncover a novel regulatory mechanism of MORC2 by SUMOylation and reveal the intricate dynamics of MORC2 SUMOylation important for proper DDR. We also propose a promising strategy to sensitize MORC2-driven breast tumors to chemotherapeutic drugs by inhibition of the SUMO pathway.

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Whole genome doubling drives oncogenic loss of chromatin segregation (part 2)

Whole genome doubling drives oncogenic loss of chromatin segregation (part 2)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 1)

Whole genome doubling drives oncogenic loss of chromatin segregation (part 1)

Whole genome doubling drives oncogenic loss of chromatin segregation (part 1)

CC-92480 Enhances Cell-Autonomous Cytotoxicity through Blockade of G 2/M Transition When Combined with Bortezomib/Dexamethasone in Pre-Clinical Multiple Myeloma

Background: Pomalidomide (POM) is an established agent in relapsed/refractory (R/R) multiple myeloma (MM). CC-92480, a novel cereblon E3 ligase modulator (CELMoD ®) agent, is being investigated in R/R MM patients in combination with the proteasome inhibitor (PI) bortezomib (BTZ) and steroid dexamethasone (DEX) (NCT03374085/NCT03989414). Previously, we showed mechanistic synergy of POM/BTZ/DEX in MM cell line models (Bjorklund et al). Here we analyzed the cell autonomous cytotoxic activities of CC-92480 or POM alone and in combination with BTZ/DEX to compare and differentiate their mechanisms of action (MOA).Results:Comparative analysis of the anti-proliferative activity against H929 and MM1.S cell lines revealed that CC-92480 demonstrated a more potent inhibition of proliferation by 100-fold lower dose compared to POM. Combination experiments utilizing a titration of POM or CC-92480 in combination with a 1 hr BTZ pulse, to mimic the clinical pharmacokinetics (+/- DEX co-treatment) showed an enhancement of antiproliferative capacity in both doublet and triplet combinations compared to single agents. Combination indices for POM/BTZ/DEX or CC-92480/BTZ/DEX resulted in values <1 for most combinations indicating a synergistic effect. Additionally, POM or CC-92480 in combination with BTZ or DEX, or in triplet combinations increased induction of apoptosis (>90% for each triplet compared to POM (20%) and CC-92480 (40%). Flow cytometric analysis of Aiolos and Ikaros protein level in MM cells treated with POM/BTZ/DEX or CC-92480/BTZ/DEX resulted in a slight kinetic delay in substrate depletion at early time points (1-4 hr), where the effect is less apparent with CC-92480, and indistinguishable at 24 hr compared to single agent POM or CC-92480 in the clinically relevant concentrations.We performed transcriptomic analyses of H929 cells treated with POM/BTZ/DEX or CC-92480/BTZ/DEX for 24 hrs to identify key pathways responsible for the observed synergistic combination effect. Common pathways dysregulated by POM or CC-92480 included previously identified interferon, protein homeostasis and proliferation gene sets. Gene set enrichment analysis (GSEA) showed many significant pathway differences when comparing the triplets, including general cell cycle progression, cell division and chromatin segregation. Interestingly, genes involved in negative regulation of G 2/M transition were identified as one of the most significant differences between POM/BTZ/DEX and CC-92480/BTZ/DEX.To understand how these pathways contributed to cell cycle effects and apoptosis, we assessed DNA fragmentation by TUNEL in conjunction with cell cycle flow cytometry to examine cell cycle specific apoptotic induction. Temporal assessment (6, 12, 18, 24, and 48 hr treatments) demonstrated accumulation of BrdU incorporation in all cell cycle phases when treated with POM/BTZ/DEX or CC-92480/BTZ/DEX indicating cell death was occurring within all phases. However, there was a marked enhancement of G 2/M BrdU incorporation (80% vs. 40% of G 2/M population) at 18-24 hr when treated with CC-92480/BTZ/DEX compared to POM/BTZ/DEX, or other single agent treatments. Additionally, G 2/M transition-dependent cyclins A and B were shown to be dysregulated by CC-92480. These data indicate that CC-92480 potentiates a G 2/M arrest in combination with BTZ in MM cells.Conclusions: These results demonstrate that CC-92480 alone or in combination with BTZ/DEX elicits a more potent cytotoxic effect on MM cells compared to POM. Importantly, the combination of either POM or CC-92480 with a PI, like BTZ, does not appreciatively affect single agent MOA. We have also identified a key differentiating mechanism of cell autonomous activity for CC-92480 in combination with BTZ/DEX where MM cells enhance apoptotic induction at the G 2/M stage compared to POM. Clinically, this added mechanistic difference suggests a more cytotoxic response in patients treated with CC-92480/BTZ/DEX compared to POM/BTZ/DEX. DisclosuresBjorklund: BMS: Current Employment, Current equity holder in publicly-traded company. Amatangelo: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Kang: BMS: Current equity holder in publicly-traded company. Chiu: Bristol Myers Squibb: Current Employment, Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company. Pourdehnad: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company, Patents & Royalties: No royalty. Hagner: BMS: Current Employment, Current equity holder in publicly-traded company. Thakurta: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company.

Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations

We examine the relationship between the size of domains of epigenetic marks and the stability of those domains using our theoretical model that captures the physical mechanisms governing the maintenance of epigenetic modifications. We focus our study on histone H3 lysine-9 trimethylation, one of the most common and consequential epigenetic marks with roles in chromatin compaction and gene repression. Our model combines the effects of methyl spreading by methyltransferases and chromatin segregation into heterochromatin and euchromatin because of preferential heterochromatin protein 1 (HP1) binding. Our model indicates that, although large methylated domains are passed successfully from one chromatin generation to the next, small alterations to the methylation sequence are not maintained during chromatin replication. Using our predictive model, we investigate the size required for an epigenetic domain to persist over chromatin generations while surrounded by a much larger domain of opposite methylation and compaction state. We find that there is a critical size threshold in the hundreds-of-nucleosomes scale above which an epigenetic domain will be reliably maintained over generations. The precise size of the threshold differs for heterochromatic and euchromatic domains. Our results are consistent with natural alterations to the epigenetic sequence occurring during embryonic development and due to age-related epigenetic drift.