Origin Firing Research Articles

Coordinating transcription and replication to mitigate their conflicts in early Drosophila embryos.

Collisions between transcribing RNA polymerases and DNA replication forks are disruptive. The threat of collisions is particularly acute during the rapid early embryonic cell cycles of Drosophila when S phase occupies the entirety of interphase. We hypothesize that collision-avoidance mechanisms safeguard this early transcription. Real-time imaging of endogenously tagged RNA polymerase II (RNAPII) and a reporter for nascent transcripts in unperturbed embryos shows clustering of RNAPII at around 2min after mitotic exit, followed by progressive dispersal as associated nascent transcripts accumulate later in interphase. Abrupt inhibition of various steps in DNA replication, including origin licensing, origin firing, and polymerization, suppresses post-mitotic RNAPII clustering and transcription in nuclear cycles. We propose that replication dependency defers the onset of transcription so that RNAPII transcribes behind advancing replication forks. The resulting orderly progression can explain how early embryos circumvent transcription-replication conflicts to express essential developmental genes.

The Impact of Reduced Fire Risk Cigarettes Regulation on Residential Fire Incidents, Mortality and Health Service Utilisation in New South Wales, Australia.

Smoking materials are a common ignition source for residential fires. In Australia, reduced fire risk (RFR) cigarettes regulation was implemented in 2010. However, the impact of this regulation on residential fires is unknown. This paper examines the impact of the RFR cigarettes regulation on the severity and health outcomes of fire incidents in New South Wales (NSW), Australia, from 2005 to 2014. Fire department data from 2005 to 2014 were linked with ambulance, emergency department, hospital, outpatient burns clinic and mortality datasets for NSW. Negative binomial regression analysis was performed to assess the changes to fire incidents’ severity pre- and post-RFR cigarettes regulation. There was an 8% reduction in total fire incidents caused by smokers’ materials post-RFR cigarettes regulation. Smokers’ materials fire incidents that damaged both contents and structure of the building, where fire flames extended beyond the room of fire origin, with over AUD 1000 monetary damage loss, decreased by 18, 22 and 12%, respectively. RFR cigarettes regulation as a fire risk mitigation has positively impacted the residential fire incident outcomes. This provides support for regulation of fire risk protective measures and bestows some direction for other fire safety policies and regulations.

Rpd3 regulates single-copy origins independently of the rDNA array by opposing Fkh1-mediated origin stimulation

Eukaryotic chromosomes are organized into structural and functional domains with characteristic replication timings, which are thought to contribute to epigenetic programming and genome stability. Differential replication timing results from epigenetic mechanisms that positively and negatively regulate the competition for limiting replication initiation factors. Histone deacetylase Sir2 negatively regulates initiation of the multicopy (∼150) rDNA origins, while Rpd3 histone deacetylase negatively regulates firing of single-copy origins. However, Rpd3's effect on single-copy origins might derive indirectly from a positive function for Rpd3 in rDNA origin firing shifting the competitive balance. Our quantitative experiments support the idea that origins compete for limiting factors; however, our results show that Rpd3's effect on single-copy origin is independent of rDNA copy-number and of Sir2's effects on rDNA origin firing. Whereas RPD3 deletion and SIR2 deletion alter the early S phase dynamics of single-copy and rDNA origin firings in opposite fashion, unexpectedly only RPD3 deletion suppresses overall rDNA origin efficiency across S phase. Increased origin activation in rpd3Δ requires Fkh1/2, suggesting that Rpd3 opposes Fkh1/2-origin stimulation, which involves recruitment of Dbf4-dependent kinase (DDK). Indeed, Fkh1 binding increases at Rpd3-regulated origins in rpd3Δ cells in G1, supporting a mechanism whereby Rpd3 influences initiation timing of single-copy origins directly through modulation of Fkh1-origin binding. Genetic suppression of a DBF4 hypomorphic mutation by RPD3 deletion further supports the conclusion that Rpd3 impedes DDK recruitment by Fkh1, revealing a mechanism of Rpd3 in origin regulation.

Modern Dimensional Analysis-Based Steel Column Heat Transfer Evaluation Using Multiple Experiments

In order to foresee the response during the fire of a real symmetrical structure (prototype), nowadays engineers apply methods which involve the associated reduced-scale model’s behaviors, mainly dimensional analysis behaviors. Between the dimensional analysis methods, the so-called Modern Dimensional Analysis (MDA), developed by Szirtes, fulfills all engineering requirements compared with the classical one. The authors used this new proposed method to describe their original electric fire simulation testing bench, as well as the Model Law (using MDA) for the heat transfer in tubular rectangular bars. So, a validation of the Model Law was performed based on several scrupulous experimental investigations both on a real column’s segment and its associated reduced-scale models manufactured at 1:2; 1:4, as well as 1:10 scales. The original heating system, the elaborated protocol, the deduced Model Law, and the results of the experimental investigations represent the contributions of the authors in the field of metallic structures subject to fires. The results validate the possibility of using MDA in the case of heat transmission.

Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-α/β expression.

ATR kinase is a central regulator of the DNA damage response (DDR) and cell cycle checkpoints. ATR kinase inhibitors (ATRi's) combine with radiation to generate CD8+ Tcell-dependent responses in mouse models of cancer. We show that ATRi's induce cyclin-dependent kinase 1 (CDK1)-dependent origin firing across active replicons in CD8+ Tcells activated exvivo while simultaneously decreasing the activity of rate-limiting enzymes for nucleotide biosynthesis. These pleiotropic effects of ATRi induce deoxyuridine (dU) contamination in genomic DNA, R loops, RNA-DNA polymerase collisions, and interferon-α/β (IFN-α/β). Remarkably, thymidine rescues ATRi-induced dU contamination and partially rescues death and IFN-α/β expression in proliferating CD8+ Tcells. Thymidine also partially rescues ATRi-induced cancer cell death. We propose that ATRi-induced dU contamination contributes to dose-limiting leukocytopenia and inflammation in the clinic and CD8+ Tcell-dependent anti-tumor responses in mouse models. We conclude that ATR is essential to limit dU contamination in genomic DNA and IFN-α/β expression.

The TRESLIN-MTBP complex couples completion of DNA replication with S/G2 transition

SummaryIt has been proposed that ATR kinase senses the completion of DNA replication to initiate the S/G2 transition. In contrast to this model, we show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ATR/CHK1 kinases. TRESLIN-MTBP acts transiently at pre-replication complexes (preRCs) to initiate origin firing and is released after the subsequent recruitment of CDC45. This dynamic behavior of TRESLIN-MTBP implements a monitoring system that checks the activation of replication forks and senses the rate of origin firing to prevent the entry into G2. This system detects the decline in the number of origins of replication that naturally occurs in very late S, which is the signature that cells use to determine the completion of DNA replication and permit the S/G2 transition. Our work introduces TRESLIN-MTBP as a key player in cell-cycle control independent of canonical checkpoints.

Targeting Replication Stress Response Pathways to Enhance Genotoxic Chemo- and Radiotherapy.

Proliferating cells regularly experience replication stress caused by spontaneous DNA damage that results from endogenous reactive oxygen species (ROS), DNA sequences that can assume secondary and tertiary structures, and collisions between opposing transcription and replication machineries. Cancer cells face additional replication stress, including oncogenic stress that results from the dysregulation of fork progression and origin firing, and from DNA damage induced by radiotherapy and most cancer chemotherapeutic agents. Cells respond to such stress by activating a complex network of sensor, signaling and effector pathways that protect genome integrity. These responses include slowing or stopping active replication forks, protecting stalled replication forks from collapse, preventing late origin replication firing, stimulating DNA repair pathways that promote the repair and restart of stalled or collapsed replication forks, and activating dormant origins to rescue adjacent stressed forks. Currently, most cancer patients are treated with genotoxic chemotherapeutics and/or ionizing radiation, and cancer cells can gain resistance to the resulting replication stress by activating pro-survival replication stress pathways. Thus, there has been substantial effort to develop small molecule inhibitors of key replication stress proteins to enhance tumor cell killing by these agents. Replication stress targets include ATR, the master kinase that regulates both normal replication and replication stress responses; the downstream signaling kinase Chk1; nucleases that process stressed replication forks (MUS81, EEPD1, Metnase); the homologous recombination catalyst RAD51; and other factors including ATM, DNA-PKcs, and PARP1. This review provides an overview of replication stress response pathways and discusses recent pre-clinical studies and clinical trials aimed at improving cancer therapy by targeting replication stress response factors.

Impact of Chromosomal Context on Origin Selection and the Replication Program.

Eukaryotic DNA replication is regulated by conserved mechanisms that bring about a spatial and temporal organization in which distinct genomic domains are copied at characteristic times during S phase. Although this replication program has been closely linked with genome architecture, we still do not understand key aspects of how chromosomal context modulates the activity of replication origins. To address this question, we have exploited models that combine engineered genomic rearrangements with the unique replication programs of post-quiescence and pre-meiotic S phases. Our results demonstrate that large-scale inversions surprisingly do not affect cell proliferation and meiotic progression, despite inducing a restructuring of replication domains on each rearranged chromosome. Remarkably, these alterations in the organization of DNA replication are entirely due to changes in the positions of existing origins along the chromosome, as their efficiencies remain virtually unaffected genome wide. However, we identified striking alterations in origin firing proximal to the fusion points of each inversion, suggesting that the immediate chromosomal neighborhood of an origin is a crucial determinant of its activity. Interestingly, the impact of genome reorganization on replication initiation is highly comparable in the post-quiescent and pre-meiotic S phases, despite the differences in DNA metabolism in these two physiological states. Our findings therefore shed new light on how origin selection and the replication program are governed by chromosomal architecture.

Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation.

Replication of the human genome initiates within broad zones of ∼150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq), based on density substitution. Newly replicated DNA is rendered ‘heavy-light’ (HL) by incorporation of BrdUTP while unreplicated DNA remains ‘light-light’ (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within early initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.

Temporal control of late replication and coordination of origin firing by self-stabilizing Rif1-PP1 hubs in Drosophila

In the metazoan S phase, coordinated firing of clusters of origins replicates different parts of the genome in a temporal program. Despite advances, neither the mechanism controlling timing nor that coordinating firing of multiple origins is fully understood. Rif1, an evolutionarily conserved inhibitor of DNA replication, recruits protein phosphatase 1 (PP1) and counteracts firing of origins by S-phase kinases. During the midblastula transition (MBT) in Drosophila embryos, Rif1 forms subnuclear hubs at each of the large blocks of satellite sequences and delays their replication. Each Rif1 hub disperses abruptly just prior to the replication of the associated satellite sequences. Here, we show that the level of activity of the S-phase kinase, DDK, accelerated this dispersal program, and that the level of Rif1-recruited PP1 retarded it. Further, Rif1-recruited PP1 supported chromatin association of nearby Rif1. This influence of nearby Rif1 can create a "community effect" counteracting kinase-induced dissociation such that an entire hub of Rif1 undergoes switch-like dispersal at characteristic times that shift in response to the balance of Rif1-PP1 and DDK activities. We propose a model in which the spatiotemporal program of late replication in the MBT embryo is controlled by self-stabilizing Rif1-PP1 hubs, whose abrupt dispersal synchronizes firing of associated late origins.

Abstract 1832: CHK1 inhibitor prexasertib induces NOXA-dependent apoptosis in ovarian cancer

Abstract Background: The kinases ataxia-telangiectasia-mutated-and-Rad3-related (ATR), checkpoint kinase 1 (CHK1) and WEE1 participate in the response to replication stress. Inhibitors of ATR, WEE1 and CHK1 are being tested for antineoplastic activity as monotherapies and in combination with chemotherapy. Although these agents impair cell cycle checkpoints, fork stabilization, origin firing and homologous recombination (HR), little is known about the apoptotic pathways that are engaged and the critical mediators activating cell death mechanisms. The present study utilizes high grade serous ovarian cancer (HGSOC) cell lines and patient derived xenografts (PDXs) to identify the primary mechanism of cell death in ovarian cancer and assess changes involved in the resistance setting after treatment with these inhibitors. Methods: A panel of HGSOC cell lines was examined for responses to ceralasertib (ATRi), prexasertib (CHK1i) or adavosertib (WEE1i) using colony forming assays, immunoblotting and assays for apoptosis. Mechanisms involved in acquired resistance and downstream changes in cell fate were evaluated by generating prexasertib-resistant HGSOC cell lines. Subsequent NGS analysis was performed in the sensitive and resistant pairs. Results: Irrespective of the homologous recombination (HR) status, ovarian cell lines and PDXs underwent cell death during prolonged exposure at clinically achievable concentrations. Treatment of ovarian cancer cell lines with ATRi, CHK1i or WEE1i activated the replication checkpoint, consistent with previously published reports. The subsequent apoptotic response involved PMAIP1 and BCL2L11 upregulation rather than the TNFa-induced death receptor-mediated apoptosis we recently described in acute leukemia (Cancer Res. PMID: 33414171). Additionally, ovarian lines selected for CHK1i resistance failed to die in response to either ATRi or WEE1i. Conclusions: Prexasertib, ceralasertib, and adavosertib exhibit monotherapy activity in both HR deficient and proficient HGSOC cell lines and PDX models. Unlike AML, death receptor mediated apoptosis was not observed; instead, the primary mechanism of cell killing in HGSOC lines involves activation of the mitochondrial apoptotic pathway. Cross-resistance of these DNA damage repair modulators is likely multifactorial and mainly involves diminished replication stress response. Citation Format: Annapoorna Venkatachalam, Kevin L. Peterson, Cristina Correia, Karen S. Flatten, Xianon Hou, Paula A. Schneider, Emily Balczewski, Cordelia McGehee, Rachel M. Hurley, Xue W. Meng, Chance Sine, Rameen Shah, Nicole Vincelettte, Husheng Ding, Hu Li, Saravut (John) Weroha, Scott H. Kaufmann. CHK1 inhibitor prexasertib induces NOXA-dependent apoptosis in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1832.

The Role of MTBP as a Replication Origin Firing Factor.

Simple SummaryCopying the chromosomal DNA completely and faithfully during the process of DNA replication is key to inheriting the genetic information in an unaltered state. To achieve this, replication initiation, which generates the complex molecular machines on the chromosomes that copy the DNA, must be precisely regulated. Despite our profound understanding of bacterial and viral DNA replication, our knowledge about the molecular processes and cellular regulation of replication initiation in eukaryotic cells was surprisingly scarce for a long time. Recently, fundamental progress has been made by studying purified replication initiation proteins structurally and biochemically. The MTBP protein (Mdm2-binding protein) was the last replication initiation factor to be identified in higher multicellular eukaryotes. MTBP is the counterpart of the Sld7 protein found in the simpler eukaryote budding yeast. MTBP is essential for replication initiation in cultured human cells and is emerging as a molecular relay for signals that control replication initiation at origins, such as initiation efficiency, placement and timing. We here discuss recent progress to unravel the molecular initiation processes and the role of MTBP. The initiation step of replication at replication origins determines when and where in the genome replication machines, replisomes, are generated. Tight control of replication initiation helps facilitate the two main tasks of genome replication, to duplicate the genome accurately and exactly once each cell division cycle. The regulation of replication initiation must ensure that initiation occurs during the S phase specifically, that no origin fires more than once per cell cycle, that enough origins fire to avoid non-replicated gaps, and that the right origins fire at the right time but only in favorable circumstances. Despite its importance for genetic homeostasis only the main molecular processes of eukaryotic replication initiation and its cellular regulation are understood. The MTBP protein (Mdm2-binding protein) is so far the last core replication initiation factor identified in metazoan cells. MTBP is the orthologue of yeast Sld7. It is essential for origin firing, the maturation of pre-replicative complexes (pre-RCs) into replisomes, and is emerging as a regulation focus targeted by kinases and by regulated degradation. We present recent insight into the structure and cellular function of the MTBP protein in light of recent structural and biochemical studies revealing critical molecular details of the eukaryotic origin firing reaction. How the roles of MTBP in replication and other cellular processes are mutually connected and are related to MTBP’s contribution to tumorigenesis remains largely unclear.

Forest Fire Monitoring and Positioning Improvement at Subpixel Level: Application to Himawari-8 Fire Products

Forest fires are among the biggest threats to forest ecosystems and forest resources, and can lead to ecological disasters and social crises. Therefore, it is imperative to detect and extinguish forest fires in time to reduce their negative impacts. Satellite remote sensing, especially meteorological satellites, has been a useful tool for forest-fire detection and monitoring because of its high temporal resolution over large areas. Researchers monitor forest fires directly at pixel level, which usually presents a mixture of forest and fire, but the low spatial resolution of such mixed pixels cannot accurately locate the exact position of the fire, and the optimal time window for fire suppression can thus be missed. In order to improve the positioning accuracy of the origin of forest fire (OriFF), we proposed a mixed-pixel unmixing integrated with pixel-swapping algorithm (MPU-PSA) model to monitor the OriFFs in time. We then applied the model to the Japanese Himawari-8 Geostationary Meteorological Satellite data to obtain forest-fire products at subpixel level. In this study, the ground truth data were provided by the Department of Emergency Management of Hunan Province, China. To validate the positioning accuracy of MPU-PSA for OriFFs, we applied the model to the Himawari-8 satellite data and then compared the derived fire results with fifteen reference forest-fire events that occurred in Hunan Province, China. The results show that the extracted forest-fire locations using the proposed method, referred to as forest fire locations at subpixel (FFLS) level, were far closer to the actual OriFFs than those from the modified Himawari-8 Wild Fire Product (M-HWFP). This improvement will help to reduce false fire claims in the Himawari-8 Wild Fire Product (HWFP). We conducted a comparative study of M-HWFP and FFLS products using three accuracy-evaluation indexes, i.e., Euclidean distance, RMSE, and MAE. The mean distances between M-HWFP fire locations and OriFFs and between FFLS fire locations and OriFFs were 3362.21 m and 1294.00 m, respectively. The mean RMSEs of the M-HWFP and FFLS products are 1225.52 m and 474.93 m, respectively. The mean MAEs of the M-HWFP and FFLS products are 992.12 m and 387.13 m, respectively. We concluded that the newly proposed MPU-PSA method can extract forest-fire locations at subpixel level, providing higher positioning accuracy of forest fires for their suppression.

High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control

DNA replication initiates from replication origins firing throughout S phase. Debate remains about whether origins are a fixed set of loci, or a loose agglomeration of potential sites used stochastically in individual cells, and about how consistent their firing time is. We develop an approach to profile DNA replication from whole-genome sequencing of thousands of single cells, which includes in silico flow cytometry, a method for discriminating replicating and non-replicating cells. Using two microfluidic platforms, we analyze up to 2437 replicating cells from a single sample. The resolution and scale of the data allow focused analysis of replication initiation sites, demonstrating that most occur in confined genomic regions. While initiation order is remarkably similar across cells, we unexpectedly identify several subtypes of initiation regions in late-replicating regions. Taken together, high throughput, high resolution sequencing of individual cells reveals previously underappreciated variability in replication initiation and progression.

G9a Responds to KRAS‐Mediated Replication Stress by Increased Origin Licensing

Pancreatic Ductal Adenocarcinoma (PDAC) remains as one of the leading causes of cancer death in the US. KRAS mutations are recognized as the leading oncogenic driver of PDAC growth. Activation of KRAS causes increased proliferation that requires a level of adaptation during processes, such as DNA replication. This rapid duplication of the genome and epigenome generates havoc in the timing and coordination of replication origin firing, triggering a response known as replication stress (RS). The epigenomic regulator G9a is responsible for catalyzing histone H3 lysine 9 mono‐ and di‐methylation (H3K9me1 and H3K9me2). G9a is abundantly present in many forms of cancer, including PDAC, and because of its interaction with replication proteins, such as RPA and PCNA, it is known to have an important role during DNA replication. DNA replication happens at the S phase of the cell cycle, which requires that replication origins are recognized at late G1 phase by the origin recognition complex (ORC) followed by assembly of the pre‐replication complex (pre‐RC), comprised of CDC6, cdt1 and mini chromosome maintenance (MCM) proteins, to allow origin licensing and subsequent firing. We have shown that the G9a complex increases in response to KRAS activation and is critical to the growth‐promoting effects of this oncogene in PDAC. Though it is known that KRAS reduces distances between replication origins, there has been a paucity of knowledge regarding the role of G9a during replication origin licensing and whether it is directly involved with the pre‐RC. In the current study, we aim to better understand whether G9a interacts with the replication origins and the pre‐RC to increase origin licensing under conditions of KRAS‐mediated RS. To simulate the early events in oncogene‐induced RS to study compensatory mechanisms, we generated an inducible KRAS model (iKRAS‐HPNE) in an hTERT‐immortalized human non‐cancerous pancreatic ductal cell line, hTERT‐HPNE E6/E7. We found that KRAS induction for 48h in this iKRAS‐HPNE model activated the ATR RS‐response pathway, indicated by increased levels of P‐T1989‐ATR, P‐S345‐CHK1 and P‐S33‐RPA32 by western blot and immunofluorescence‐based microscopy. Concurrently, members of the G9a epigenomic complex (G9a, GLP and WIZ) significantly increased along with two subunits of the ORC (ORC1 and ORC2) and several other pre‐RC proteins (Cdt1, MCM2, MCM5 and MCM7). Co‐immunoprecipitation of G9a in the iKRAS‐HPNE cells revealed that G9a interacts with ORC2 protein under conditions of oncogene‐induced RS. Pharmacological inhibition of G9a with UNC0642 during KRAS‐induced RS resulted in a decrease of chromatin‐bound ORC1 and ORC2 as well as pre‐RC proteins in subcellular fractionation experiments, suggesting that functional G9a is critical for enhanced origin licensing. In summary, our results demonstrate that G9a directly interacts with replication origins and the pre‐RC during origin licensing under conditions of RS. Our study reveals one potential mechanism by which cancerous cells with KRAS mutation meet the demands for rapid cellular proliferation during RS and reinforces the role of G9a as a promising therapeutic target for PDAC.

Small Molecule Inhibitor Targeting CDT1/Geminin Protein Complex Promotes DNA Damage and Cell Death in Cancer Cells.

DNA replication initiation requires the loading of MCM2-7 complexes at the origins of replication during G1. Replication licensing renders chromatin competent for DNA replication and its tight regulation is essential to prevent aberrant DNA replication and genomic instability. CDT1 is a critical factor of licensing and its activity is controlled by redundant mechanisms, including Geminin, a protein inhibitor of CDT1. Aberrant CDT1 and Geminin expression have been shown to promote tumorigenesis in vivo and are also evident in multiple human tumors. In this study, we developed an in vitro AlphaScreen™ high-throughput screening (HTS) assay for the identification of small-molecule inhibitors targeting the CDT1/Geminin protein complex. Biochemical characterization of the most potent compound, AF615, provided evidence of specific, dose-dependent inhibition of Geminin binding to CDT1 both in-vitro and in cells. Moreover, compound AF615 induces DNA damage, inhibits DNA synthesis and reduces viability selectively in cancer cell lines, and this effect is CDT1-dependent. Taken together, our data suggest that AF615 may serve as a useful compound to elucidate the role of CDT1/Geminin protein complex in replication licensing and origin firing as well as a scaffold for further medicinal chemistry optimisation.

Co-expression patterns explain how a basic transcriptional role for MYC modulates Wnt and MAPK pathways in colon and lung adenocarcinomas

ABSTRACT A subset of proliferation genes that are associated with origin licensing, firing, and DNA synthesis has been compared to known drivers of colon (COAD) and lung (LUAD) adenocarcinomas using Spearman’s rank correlation coefficients. The frequency with which APC, CTNNB1, KRAS, MYC, Braf, TP53, Rb1, EGFR, and cell cycle components have direct or indirect co-expression with the proliferation factors permits identification of their expression relative to the G1-S phase of the cell cycle. Here, adenomatous polyposis coli (APC), a negative regulator of Wnt signaling known to function through MYC, indirectly co-expresses at the same frequency as proliferation genes in both COAD and LUAD, consistent with M phase expression. However, APC is indirectly co-expressed with MYC and is found mutated only in COAD. MYC is thought to function at the interface of transcription and replication, acting through the SWI/SNF chromatin remodeling complex, and increased or decreased expression of MYC can induce or repress tumorigenesis, respectively. These data suggest that transcription of APC during the M phase with low MYC co-expression contributes by an unknown mechanism to APC mutations and Wnt pathway deregulation in COAD and that upper and lower limits of MYC expression, enforced by the cell cycle, may influence cancer differentially. Other Wnt signaling components co-expressed in the low MYC context in COAD also have significantly higher mutation frequencies, supporting the hypothesis. Additionally, Braf is found here to have direct co-expression with multiple proliferation factors in non-EGFR activated LUAD, and EGFR-activated LUAD are completely deregulated with respect to E2F(s) 4/5/6 expression, potentially explaining the low proliferation rates seen in LUAD. Abbreviations: TCGA: The cancer genome atlas; PANCAN: Pan cancer; CDK: Cyclin-dependent kinase; COAD: Colon adenocarcinoma; LUAD: Lung adenocarcinoma; Wnt: Wingless/integrated signaling; MAPK: Mitogen-activated protein kinase; APC: Adenomatous polyposis coli gene; CIN: Chromosomal instability; GS: Genome stabile; MMR: Mismatch repair; mRNA: Messenger RNA; RPKM: Reads per kilobase of transcription per million mapped reads; RSEM: RNA Seq by expectation maximization; FDR: False discovery rate; GTEx: Genotype-Tissue Expression portal; MPF: Maturation-promoting factor; SCF: Skp1-Cul1-F-box; HH: Hedgehog; EMT: Epithelial mesenchymal transition; RB: Retinoblastoma; EGFR: Epidermal growth factor receptor; rs or ρ: Spearman’s correlation

LSD1 is required for euchromatic origin firing and replication timing

The chromatin-based rule governing the selection and activation of replication origins remains to be elucidated. It is believed that DNA replication initiates from open chromatin domains; thus, replication origins reside in open and active chromatin. However, we report here that lysine-specific demethylase 1 (LSD1), which biochemically catalyzes H3K4me1/2 demethylation favoring chromatin condensation, interacts with the DNA replication machinery in human cells. We find that LSD1 level peaks in early S phase, when it is required for DNA replication by facilitating origin firing in euchromatic regions. Indeed, euchromatic zones enriched in H3K4me2 are the preferred sites for the pre-replicative complex (pre-RC) binding. Remarkably, LSD1 deficiency leads to a genome-wide switch of replication from early to late. We show that LSD1-engaged DNA replication is mechanistically linked to the loading of TopBP1-Interacting Checkpoint and Replication Regulator (TICRR) onto the pre-RC and subsequent recruitment of CDC45 during origin firing. Together, these results reveal an unexpected role for LSD1 in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. As selective inhibitors of LSD1 are being exploited as potential cancer therapeutics, our study supports the importance of leveraging an appropriate level of LSD1 to curb the side effects of anti-LSD1 therapy.

Separating function of timber floor and wall assemblies

Abstract The basic concern on the fire compartmentation is focused on to limit the spread of the fire and smoke outside of the room of the fire origin. Where the fire compartmentation is required, the elements forming the boundaries of the fire compartment should be designed and constructed in such a way that they maintain their separating function during the relevant fire exposure [1]. The general accepted method for assessing the fire resistance of a structural or non-structural member is the full-scale testing of the fire performance, however, several calculation methods for verification of the separation function of timber assemblies can also be used in order to prove compliance with the code regulations [2].

A Delphi study to identify and prioritize research gaps for the incorporation of a fire into life cycle assessment of structures

The current life cycle assessment (LCA) methodology used in structural engineering does not consider hazards like fires within its scope. Various efforts have been made to identify research gaps that need to be filled in order to accomplish a Fire-LCA. This study presented research gaps from literature to experts to determine the research gap's impact, desirability, and probability of occurrence by the year 2030. The study provides insight into what researchers should prioritize to accomplish the proposed Fire-LCA methodology. In each round the experts were asked to evaluate and comment on the impact, desirability, and probability of occurrence by the year 2030 of each identified research gap. The results of the Delphi questionnaire identified high priority research gaps for the implementation of the proposed Fire-LCA methodology. The most prioritized research gap was statistical data that would describe the number and severity of fires, fire origin, and extent of fire spread in different types of building. The results of this study can guide researchers and funding agencies to prioritize research that will fill key gaps in knowledge that prevent the implementation of a Fire-LCA methodology for building structures.