Integrated molecular mechanism directing nucleosome reorganization by human FACT.

Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3-H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular ß structure with H4. At the other site, the Mid-H2A steric collision on the H2A-docking surface of the H3-H4 tetramer within the nucleosome induces H2A-H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.

Mbf1 ensures Polycomb silencing by protecting E(z) mRNA from degradation by Pacman.

Under stress conditions, the coactivator Multiprotein bridging factor 1 (Mbf1) translocates from the cytoplasm into the nucleus to induce stress-response genes. However, its role in the cytoplasm, where it is mainly located, has remained elusive. Here, we show that Drosophila Mbf1 associates with E(z) mRNA and protects it from degradation by the exoribonuclease Pacman (Pcm), thereby ensuring Polycomb silencing. In genetic studies, loss of mbf1 function enhanced a Polycomb phenotype in Polycomb group mutants, and was accompanied by a significant reduction in E(z) mRNA expression. Furthermore, a pcm mutation suppressed the Polycomb phenotype and restored the expression level of E(z) mRNA, while pcm overexpression exhibited the Polycomb phenotype in the mbf1 mutant but not in the wild-type background. In vitro, Mbf1 protected E(z) RNA from Pcm activity. Our results suggest that Mbf1 buffers fluctuations in Pcm activity to maintain an E(z) mRNA expression level sufficient for Polycomb silencing.

The transcriptional factor Apt regulates neuroblast differentiation through activating CycE expression.

In Drosophila, the thoracic neuroblast 6-4 (NB6-4T) divides asymmetrically into a glial precursor and a neuronal precursor, while the abdominal neuroblast 6-4 (NB6-4A) divides symmetrically to produce two glial cells. The underlying mechanism by which NB6-4T and NB6-4A undergo distinct differentiation is still elusive. Here, we find that the transcription factor Apontic (Apt) exclusively expresses in NB6-4T cells and is involved in regulating NB6-4T differentiation. Loss of Apt results in neuronal precursor loss. Epistasis analysis shows that Apt controls NB6-4T differentiation through activating CycE expression. On the other hand, Gcm suppresses Apt expression in the NB6-4A cell, thus inhibiting CycE expression. Taken together, our findings reveal a Gcm-Apt-CycE axis that regulates neuroblast and glia cell differentiation.

Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducing cyclin E during eye development.

During Drosophila eye development, differentiation initiates in the posterior region of the eye disk and progresses anteriorly as a wave marked by the morphogenetic furrow (MF), which demarcates the boundary between anterior undifferentiated cells and posterior differentiated photoreceptors. However, the mechanism underlying the regulation of gene expression immediately before the onset of differentiation remains unclear. Here, we show that Apontic (Apt), which is an evolutionarily conserved transcription factor, is expressed in the differentiating cells posterior to the MF. Moreover, it directly induces the expression of cyclin E and is also required for the G1-to-S phase transition, which is known to be essential for the initiation of cell differentiation at the MF. These observations identify a pathway crucial for eye development, governed by a mechanism in which Cyclin E promotes the G1-to-S phase transition when regulated by Apt.

Midline governs axon pathfinding by coordinating expression of two major guidance systems.

Formation of the neural network requires concerted action of multiple axon guidance systems. How neurons orchestrate expression of multiple guidance genes is poorly understood. Here, we show that Drosophila T-box protein Midline controls expression of genes encoding components of two major guidance systems: Frazzled, ROBO, and Slit. In midline mutant, expression of all these molecules are reduced, resulting in severe axon guidance defects, whereas misexpression of Midline induces their expression. Midline is present on the promoter regions of these genes, indicating that Midline controls transcription directly. We propose that Midline controls axon pathfinding through coordinating the two guidance systems.

Gprk2 adjusts Fog signaling to organize cell movements in Drosophila gastrulation.

Gastrulation of Drosophila melanogaster proceeds through sequential cell movements: ventral mesodermal (VM) cells are induced by secreted Fog protein to constrict their apical surfaces to form the ventral furrow, and subsequently lateral mesodermal (LM) cells involute toward the furrow. How these cell movements are organized remains elusive. Here, we observed that LM cells extended apical protrusions and then underwent accelerated involution movement, confirming that VM and LM cells display distinct cell morphologies and movements. In a mutant for the GPCR kinase Gprk2, apical constriction was expanded to all mesodermal cells and the involution movement was abolished. In addition, the mesodermal cells halted apical constriction prematurely in accordance with the aberrant accumulation of Myosin II. Epistasis analyses revealed that the Gprk2 mutant phenotypes were dependent on the fog gene. Overexpression of Gprk2 suppressed the effects of excess Cta, a downstream component of Fog signaling. Based on these findings, we propose that Gprk2 attenuates and tunes Fog-Cta signaling to prevent apical constriction in LM cells and to support appropriate apical constriction in VM cells. Thus, the two distinct cell movements in mesoderm invagination are not predetermined, but rather are organized by the adjustment of cell signaling.

Ash1l methylates Lys36 of histone H3 independently of transcriptional elongation to counteract polycomb silencing.

Molecular mechanisms for the establishment of transcriptional memory are poorly understood. 5,6-dichloro-1-D-ribofuranosyl-benzimidazole (DRB) is a P-TEFb kinase inhibitor that artificially induces the poised RNA polymerase II (RNAPII), thereby manifesting intermediate steps for the establishment of transcriptional activation. Here, using genetics and DRB, we show that mammalian Absent, small, or homeotic discs 1-like (Ash1l), a member of the trithorax group proteins, methylates Lys36 of histone H3 to promote the establishment of Hox gene expression by counteracting Polycomb silencing. Importantly, we found that Ash1l-dependent Lys36 di-, tri-methylation of histone H3 in a coding region and exclusion of Polycomb group proteins occur independently of transcriptional elongation in embryonic stem (ES) cells, although both were previously thought to be consequences of transcription. Genome-wide analyses of histone H3 Lys36 methylation under DRB treatment have suggested that binding of the retinoic acid receptor (RAR) to a certain genomic region promotes trimethylation in the RAR-associated gene independent of its ongoing transcription. Moreover, DRB treatment unveils a parallel response between Lys36 methylation of histone H3 and occupancy of either Tip60 or Mof in a region-dependent manner. We also found that Brg1 is another key player involved in the response. Our results uncover a novel regulatory cascade orchestrated by Ash1l with RAR and provide insights into mechanisms underlying the establishment of the transcriptional activation that counteracts Polycomb silencing.

The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions.

Establishment and maintenance of epigenetic memories are essential for development. Replacement of canonical histone H3 by its variant H3.3 has been implicated in cellular memory. Drosophila sequence-specific DNA-binding protein GAGA factor and a chromatin factor FACT direct H3.3 replacement in conjunction with H3.3-specific chaperone HIRA at chromatin boundaries to counteract the spreading of silent chromatin. However, little is known about which ATP-driven chromatin remodeling factor is responsible for the H3.3 replacement at chromatin boundaries. Here, we report that GAGA factor associates with the Polybromo-associated Brm (PBAP) remodeling complex, which consists of many Trithorax group proteins, and recruits this complex to chromatin boundaries d1 (which is downstream of w), the Fab-7 DNase-hypersensitive site (HS) 1 of Abd-B and the bxd region of Ubx. Trl-encoding GAGA factor, brm and polybromo/bap180 mutations compromise the H3.3 replacement and boundary functions in a synergistic manner. Furthermore, Polybromo is necessary for generation of the DNase HS at d1, and HIRA functions to restore the alteration. Taken together, we propose that FACT and PBAP complexes are recruited to chromatin boundaries in a GAGA factor-dependent manner, and are needed for H3.3 replacement to execute boundary functions. Our results provide new insight into the function of the trithorax group during development.

RSF governs silent chromatin formation via histone H2Av replacement.

Human remodeling and spacing factor (RSF) consists of a heterodimer of Rsf-1 and hSNF2H, a counterpart of Drosophila ISWI. RSF possesses not only chromatin remodeling activity but also chromatin assembly activity in vitro. While no other single factor can execute the same activities as RSF, the biological significance of RSF remained unknown. To investigate the in vivo function of RSF, we generated a mutant allele of Drosophila Rsf-1 (dRsf-1). The dRsf-1 mutant behaved as a dominant suppressor of position effect variegation. In dRsf-1 mutant, the levels of histone H3K9 dimethylation and histone H2A variant H2Av were significantly reduced in an euchromatic region juxtaposed with heterochromatin. Furthermore, using both genetic and biochemical approaches, we demonstrate that dRsf-1 interacts with H2Av and the H2Av-exchanging machinery Tip60 complex. These results suggest that RSF contributes to histone H2Av replacement in the pathway of silent chromatin formation.

Prevalence and prognostic implications of malnutrition as defined by GLIM criteria in elderly patients with heart failure.

BACKGROUND & AIMS: Although the Global Leadership Initiative on Malnutrition (GLIM) proposed a consensus scheme for diagnosing malnutrition in adults in clinical settings globally, the prevalence and prognostic value of malnutrition defined by GLIM criteria have yet to be evaluated in elderly patients with heart failure. This study aimed to determine the prevalence and prognostic implication of malnutrition as defined by GLIM criteria in comparison to those for a pre-existing definition of malnutrition, the geriatric nutritional risk index (GNRI), in elderly patients with heart failure METHODS: We evaluated malnutrition by two metrics, the GLIM criteria and geriatric nutritional risk index (GNRI), in 890 hospitalized patients with decompensation of heart failure aged ≥65 years, able to ambulate at discharge. The primary outcome was all-cause death within 1 year of discharge. RESULTS: According to GLIM criteria and GNRI <92, 42.4% and 46.5% of participants, respectively, had malnutrition, with moderate agreement (Cohen's kappa coefficient: 0.46 [95% confidence interval: 0.40-0.51]). During 1 year of follow-up, 101 (11.4%) deaths were observed, and malnutrition defined by either the GLIM criteria or GNRI was associated with a higher mortality rate, independent of other prognostic factors (GNRI: hazard ratio, 1.45, P = 0.031; GLIM: hazard ratio, 1.57, P = 0.016). Although malnutrition defined by either criterion showed additive prognostic value when added to a model incorporating pre-existing prognostic factors, defining malnutrition by GLIM criteria instead of the GNRI yielded a statistically significant improvement in model prognostic predictive ability (net-reclassification improvement, 0.44, P < 0.001; integrated discrimination index, 0.013, P < 0.001). CONCLUSIONS: In elderly patients with heart failure, 42.4% are malnourished according to the GLIM criteria, which is associated with a poor prognosis, independent of known prognostic factors. CLINICAL TRIAL REGISTRATION: University Hospital Medical Information Network (UMIN-CTR, https://www.umin.ac.jp/ctr/index.htm, study unique identifier: UMIN000023929).

Evolutionarily Conserved Roles for Apontic in Induction and Subsequent Decline of Cyclin E Expression.

Cyclin E is a key factor for S phase entry, and deregulation of Cyclin E results in developmental defects and tumors. Therefore, proper cycling of Cyclin E is crucial for normal growth. Here we found that transcription factors Apontic (Apt) and E2f1 cooperate to induce cyclin E in Drosophila. Functional binding motifs of Apt and E2f1 are clustered in the first intron of Drosophila cyclin E and directly contribute to the cyclin E transcription. Knockout of apt and e2f1 together abolished Cyclin E expression. Furthermore, Apt up-regulates Retinoblastoma family protein 1 (Rbf1) for proper chromatin compaction, which is known to repress cyclin E. Notably, Apt-dependent up-regulation of Cyclin E and Rbf1 is evolutionarily conserved in mammalian cells. Our findings reveal a unique mechanism underlying the induction and subsequent decline of Cyclin E expression.

Impact of the Geriatric Nutritional Risk Index on In-Hospital Mortality and Length of Hospitalization in Patients with Acute Decompensated Heart Failure with Preserved or Reduced Ejection Fraction.

In patients with heart failure (HF), the impact of the Geriatric Nutritional Risk Index (GNRI) on in-hospital mortality and length of hospital stay remains unclear. We aimed to identify the factors associated with increased in-hospital mortality and longer length of hospital stay considering the GNRI in acute decompensated HF with reduced and preserved ejection fraction (HFrEF and HFpEF, respectively). Patients with acute decompensated HF who were admitted to our institution between 2007 and 2011 were investigated. A total of 451 (201, HFrEF; 250, HFpEF) patients were divided into the following: patients with GNRI < 92 and ≥92. In HFrEF, there were no significant differences in in-hospital mortality and length of hospital stay between patients with GNRI < 92 and ≥92 (median (interquartile range), 24.0 (23.8) days and 20.0 (15.0) days, respectively, p = 0.32). In HFpEF, despite no differences in in-hospital mortality, patients with GNRI < 92 had significantly longer length of hospital stay than those with GNRI ≥ 92 (median (interquartile range), 20.0 (22.3) days and 17.0 (16.0) days, respectively, p = 0.04). In HFpEF, GNRI < 92, along with lower hemoglobin, higher B-type natriuretic peptide, and elevated C-reactive protein levels, were the independent factors for longer length of hospital stay. Among patients with acute decompensated HF, assessment of nutritional status with GNRI is useful for stratifying patients at high risk for longer length of hospital stay in HFpEF but not in HFrEF. These observations are particularly important when considering the increasing elderly population and prevalence of HFpEF.

Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy.

Intrinsically disordered (ID) regions of proteins are recognized to be involved in biological processes such as transcription, translation, and cellular signal transduction. Despite the important roles of ID regions, effective methods to observe these thin and flexible structures directly were not available. Herein, we use high-speed atomic force microscopy (AFM) to observe the heterodimeric FACT (facilitates chromatin transcription) protein, which is predicted to have large ID regions in each subunit. Successive AFM images of FACT on a mica surface, captured at rates of 5-17 frames per second, clearly reveal two distinct tail-like segments that protrude from the main body of FACT and fluctuate in position. Using deletion mutants of FACT, we identify these tail segments as the two major ID regions predicted from the amino acid sequences. Their mechanical properties estimated from the AFM images suggest that they have more relaxed structures than random coils. These observations demonstrate that this state-of-the-art microscopy method can be used to characterize unstructured protein segments that are difficult to visualize with other experimental techniques.

Crucial roles for chromatin dynamics in cellular memory.

Cellular memory is defined as a long-term maintenance of a particular pattern of gene expression through many rounds of cell division or even after cell division. It is critical for development and differentiation of multicellular organisms. Chromatin dynamics including histone modification, histone replacement and chromatin remodeling play key roles in cellular memory.

Apontic directly activates hedgehog and cyclin E for proper organ growth and patterning.

Hedgehog (Hh) signaling pathway and Cyclin E are key players in cell proliferation and organ development. Hyperactivation of hh and cyclin E has been linked to several types of cancer. However, coordination of the expression of hh and cyclin E was not well understood. Here we show that an evolutionarily conserved transcription factor Apontic (Apt) directly activates hh and cyclin E through its binding site in the promoter regions of hh and cyclin E. This Apt-dependent proper expression of hh and cyclin E is required for cell proliferation and development of the Drosophila wing. Furthermore, Fibrinogen silencer-binding protein (FSBP), a mammalian homolog of Apt, also positively regulates Sonic hh (Shh), Desert hh (Dhh), Cyclin E1 (CCNE1) and Cyclin E2 (CCNE2) in cultured human cells, suggesting evolutionary conservation of the mechanism. Apt-mediated expression of hh and cyclin E can direct proliferation of Hh-expressing cells and simultaneous growth, patterning and differentiation of Hh-recipient cells. The discovery of the simultaneous expression of Hh and principal cell-cycle regulator Cyclin E by Apt implicates insight into the mechanism by which deregulated hh and cyclin E promotes tumor formation.

The potato transcriptional co-activator StMBF1 is up-regulated in response to oxidative stress and interacts with the TATA-box binding protein.

To gain a better understanding on the function of the potato Solanum tuberosum Multiprotein Bridging Factor 1 protein (StMBF1) its interaction with the TATA box binding protein (TBP) was demonstrated. In addition we reported that StMBF1 rescues the yeast mbf1 mutant phenotype, indicating its role as a plant co-activator. These data reinforce the hypothesis that MBF1 function is also conserved among non closely related plant species. In addition, measurement of StMBF1 protein level by Western blot using anti-StMBF1 antibodies indicated that the protein level increased upon H(2)O(2) and heat shock treatments. However, the potato beta-1,3-glucanase protein level was not changed under the same experimental conditions. These data indicate that StMBF1 participates in the cell stress response against oxidative stress allowing us to suggest that MBF1 genes from different plant groups may share similar functions.

Identification of the human IAI.3B promoter element and its use in the construction of a replication-selective adenovirus for ovarian cancer therapy.

Little is known concerning promoters or gene therapy specific for ovarian cancer. To explore the potential use of IAI.3B isolated from ovarian cancer cells in gene therapy for ovarian cancer, we identified the promoter region of the IAI.3B gene and created a replication-selective adenovirus, AdE3-IAI.3B, driven by the promoter. Transient transfection experiments showed that the DNA segment located between -1816 and -1 bp resulted in preferential expression in ovarian cancer cells with negligible expression in squamous cell carcinoma and normal cells. The promoter activity of IAI.3B was almost the same as that of cytomegalovirus and an order of magnitude higher than those of midkine and cyclooxygenase-2 in ovarian cancer cells. AdE3-IAI.3B replicated as efficiently as the wild-type adenovirus and caused extensive cell killing in a panel of ovarian cancer cells in vitro. In contrast, squamous cell carcinoma and normal cells were not able to support AdE3-IAI.3B replication. In animal studies, AdE3-IAI.3B administered to flank and i.p. xenografts of ovarian cancer cells led to a significant therapeutic effect. These results demonstrate the usefulness of the IAI.3B promoter for generation of ovarian cancer-specific adenoviral vectors and provide a potential for the development of ovarian cancer-specific oncolytic viral therapies.

The T-box transcription factor Midline regulates wing development by repressing wingless and hedgehog in Drosophila.

Wingless (Wg) and Hedgehog (Hh) signaling pathways are key players in animal development. However, regulation of the expression of wg and hh are not well understood. Here, we show that Midline (Mid), an evolutionarily conserved transcription factor, expresses in the wing disc of Drosophila and plays a vital role in wing development. Loss or knock down of mid in the wing disc induced hyper-expression of wingless (wg) and yielded cocked and non-flat wings. Over-expression of mid in the wing disc markedly repressed the expression of wg, DE-Cadherin (DE-Cad) and armadillo (arm), and resulted in a small and blistered wing. In addition, a reduction in the dose of mid enhanced phenotypes of a gain-of-function mutant of hedgehog (hh). We also observed repression of hh upon overexpression of mid in the wing disc. Taken together, we propose that Mid regulates wing development by repressing wg and hh in Drosophila.

Introduction of p16INK4a inhibits telomerase activity through transcriptional suppression of human telomerase reverse transcriptase expression in human gliomas.

The p16 and p53 tumor suppressor proteins, which are frequently altered in malignant gliomas, have been noted as regulators of telomerase activity. However, the link between telomerase regulation and these suppressor proteins has not been adequately clarified. In the present study, we demonstrated that p16, as well as p53, suppress telomerase activity through transcriptional regulation of human telomerase reverse transcriptase (hTERT) in malignant glioma. To examine the effect of p16 and p53 on telomerase activity, we utilized wild-type p16 or p53 expression plasmid and three human glioma cell lines differing in their p53 and p16 status. Restoring p16 significantly reduced the level of telomerase activity of glioma cells. Furthermore, cotransfection of the p16 gene with 5'-deletion constructs of the hTERT promoter carrying Sp1 binding sites, repressed the transcriptional activity of hTERT promoter in p16-deleted cells. In addition, electrophoretic mobility shift assay revealed that p16 expression inhibited the binding of Sp1 to the consensus Sp1 responsive element, indicating that the recruitment of Sp1 to the hTERT proximal core promoter is inhibited by p16 protein. These results were similar to those from a p53 transfection study in p53-mutated cells. These findings implicate p16 in the transcriptional regulation of telomerase activity by inhibiting the function of Sp1 in human malignant gliomas.

Heterotrimeric G protein signaling governs the cortical stability during apical constriction in Drosophila gastrulation.

During gastrulation in Drosophila melanogaster, coordinated apical constriction of the cellular surface drives invagination of the mesoderm anlage. Forces generated by the cortical cytoskeletal network have a pivotal role in this cellular shape change. Here, we show that the organisation of cortical actin is essential for stabilisation of the cellular surface against contraction. We found that mutation of genes related to heterotrimeric G protein (HGP) signaling, such as Gß13F, Gγ1, and ric-8, results in formation of blebs on the ventral cellular surface. The formation of blebs is caused by perturbation of cortical actin and induced by local surface contraction. HGP signaling mediated by two Gα subunits, Concertina and G-iα65A, constitutively regulates actin organisation. We propose that the organisation of cortical actin by HGP is required to reinforce the cortex so that the cells can endure hydrostatic stress during tissue folding.