DNA double-strand breaks (DSBs) are highly toxic lesions that can drive genetic instability. To preserve genome integrity, organisms have evolved several DSB repair mechanisms, of which nonhomologous ...end-joining (NHEJ) and homologous recombination (HR) represent the two most prominent. It has recently become apparent that multiple layers of regulation exist to ensure these repair pathways are accurate and restricted to the appropriate cellular contexts. Such regulation is crucial, as failure to properly execute DSB repair is known to accelerate tumorigenesis and is associated with several human genetic syndromes. Here, we review recent insights into the mechanisms that influence the choice between competing DSB repair pathways, how this is regulated during the cell cycle, and how imbalances in this equilibrium result in genome instability.
Force fields developed with machine learning methods in tandem with quantum mechanics are beginning to find merit, given their (i) low cost, (ii) accuracy, and (iii) versatility. Recently, we ...proposed one such approach, wherein, the vectorial force on an atom is computed directly from its environment. Here, we discuss the multistep workflow required for their construction, which begins with generating diverse reference atomic environments and force data, choosing a numerical representation for the atomic environments, down selecting a representative training set, and lastly the learning method itself, for the case of Al. The constructed force field is then validated by simulating complex materials phenomena such as surface melting and stress–strain behavior, that truly go beyond the realm of ab initio methods, both in length and time scales. To make such force fields truly versatile an attempt to estimate the uncertainty in force predictions is put forth, allowing one to identify areas of poor performance and paving the way for their continual improvement.
Plant hormones control most aspects of the plant life cycle by regulating genome expression. Expression of auxin-responsive genes involves interactions among auxin-responsive DNA sequence elements, ...transcription factors and trans-acting transcriptional repressors. Transcriptional output from these auxin signaling complexes is regulated by proteasome-mediated degradation that is triggered by interaction with auxin receptor-E3 ubiquitin ligases such SCF(TIR1). Auxin signaling components are conserved throughout land plant evolution and have proliferated and specialized to control specific developmental processes.
The testing and rapid detection of pathogenic organisms is a crucial protocol in the prevention and identification of crises related to health, safety and wellbeing. Pathogen detection has become one ...of the most challenging aspects in the food and water industries, because of the rapid spread of waterborne and foodborne diseases in the community and at significant costs. With the prospect of inevitable population growth, and an influx of tourism to certain water bodies testing will become a requirement to control and prevent possible outbreaks of potentially fatal illnesses. The legislation is already particularly rigorous in the food industry, where failure to detect pathogenic materials represents a catastrophic event, particularly for the elderly, very young or immune-compromised population types. In spite of the need and requirement for rapid analytical testing, conventional and standard bacterial detection assays may take up to seven days to yield a result. Given the advent of new technologies, biosensors, chemical knowledge and miniaturisation of instrumentation this timescale is not acceptable. This review presents an opportunity to fill a knowledge gap for an extremely important research area; discussing the main techniques, biology, chemistry, miniaturisation, sensing and the emerging state-of-the-art research and developments for detection of pathogens in food, water, blood and faecal samples.
Genotoxic DNA double-strand breaks (DSBs) can be repaired by error-free homologous recombination (HR) or mutagenic non-homologous end-joining
. HR supresses tumorigenesis
, but is restricted to the S ...and G2 phases of the cell cycle when a sister chromatid is present
. Breast cancer type 1 susceptibility protein (BRCA1) promotes HR by antagonizing the anti-resection factor TP53-binding protein 1(53BP1) (refs.
), but it remains unknown how BRCA1 function is limited to the S and G2 phases. We show that BRCA1 recruitment requires recognition of histone H4 unmethylated at lysine 20 (H4K20me0), linking DSB repair pathway choice directly to sister chromatid availability. We identify the ankyrin repeat domain of BRCA1-associated RING domain protein 1 (BARD1)-the obligate BRCA1 binding partner
-as a reader of H4K20me0 present on new histones in post-replicative chromatin
. BARD1 ankyrin repeat domain mutations disabling H4K20me0 recognition abrogate accumulation of BRCA1 at DSBs, causing aberrant build-up of 53BP1, and allowing anti-resection activity to prevail in S and G2. Consequently, BARD1 recognition of H4K20me0 is required for HR and resistance to poly (ADP-ribose) polymerase inhibitors. Collectively, this reveals that BRCA1-BARD1 monitors the replicative state of the genome to oppose 53BP1 function, routing only DSBs within sister chromatids to HR.
This paper investigates the precedents, policies and factors relevant to a successful energy regime transition which may be applied in the Japanese case, through a review of national leaders in ...renewable energy deployment. The examples of Germany, Italy and Spain are of particular note for their progress along the transition pathway toward a low carbon energy regime. Transition theory is used as a framework to enable this assessment, and exogenous impacts specific to Japan such as recent and ongoing market liberalization and the Fukushima nuclear incident are considered as pertinent factors which impact upon the transition landscape. Through a comparative assessment of policy approaches, technologies deployed, and social factors impacting upon deployment, lessons are drawn for comparison with current Japanese transition progress, identifying factors critical to the future estimation of the Japanese transition pathway. Future energy transition pathway projections will need to incorporate policy approaches and mechanisms as well as being cognizant of Japan's geographic and cost-competitive RE resource deployment limitations. These limitations alongside existing generation assets (including nuclear energy) are expected to have a significant impact upon Japan's transition from the current pre-development phase toward take-off, acceleration and the stabilization of a new, low-carbon energy regime.
Following irradiation, numerous DNA-damage-responsive proteins rapidly redistribute into microscopically visible subnuclear aggregates, termed ionising-radiation-induced foci (IRIF). How the ...enrichment of proteins on damaged chromatin actually relates to DNA repair remains unclear. Here, we use super-resolution microscopy to examine the spatial distribution of BRCA1 and 53BP1 proteins within single IRIF at subdiffraction-limit resolution, yielding an unprecedented increase in detail that was not previously apparent by conventional microscopy. Consistent with a role for 53BP1 in promoting DNA double-strand break repair by non-homologous end joining, 53BP1 enrichment in IRIF is most prominent in the G0/G1 cell cycle phases, where it is enriched in dense globular structures. By contrast, as cells transition through S phase, the recruitment of BRCA1 into the core of IRIF is associated with an exclusion of 53BP1 to the focal periphery, leading to an overall reduction of 53BP1 occupancy at DNA damage sites. Our data suggest that the BRCA1-associated IRIF core corresponds to chromatin regions associated with repair by homologous recombination, and the enrichment of BRCA1 in IRIF represents a temporal switch in the DNA repair program. We propose that BRCA1 antagonises 53BP1-dependent DNA repair in S phase by inhibiting its interaction with chromatin proximal to damage sites. Furthermore, the genomic instability exhibited by BRCA1-deficient cells might result from a failure to efficiently exclude 53BP1 from such regions during S phase.
Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the ...administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.
Calcineurin inhibitor (CNI) nephrotoxicity was recognized in Cambridge in the late 1970s. The vasoconstrictor impact of cyclosporine (CsA) and to a lesser extent tacrolimus, in both acute and chronic ...settings, results from a decrease in vasodilators and increase in vasconconstrictors while direct tubular toxicity results from blockade of mitochondrial permeability transition pores and inhibition of prolyl isomerase. A biopsy of native kidneys of recipients of CNIs reveals nephrotoxicity as the most common pathological diagnosis with chronic CNI toxicity and hypertension the primary problems. A long‐term study of randomized clinical trials with up to 20 years of follow‐up shows inferiority of both renal function and graft survival for continuous CsA compared to either CsA withdrawal or continuous azathioprine and prednisolone. Pathological hallmarks of chronic CNI nephrotoxicity include stripped interstitial fibrosis, arteriolar hyalinosis and glomerular sclerosis, but with the exception of nodular arteriolar hyalinosis the findings are non specific. The model for chronic renal allograft loss must be multifactorial with both immune and nonimmune factors operating dependent upon an individual's risk factors for cell and/or antibody‐mediated rejection, CNI nephrotoxicity and recurrent disease. Better outcomes will require early diagnosis and individualization of therapy dependent upon the dominant mechanisms impacting each patient. The revisionist view put forward by some senior, experienced and thoughtful individuals, challenges the concept of chronic CNI nephrotoxicity as an important clinical entity. By implication, the view that appears to be promoted is as follows: we need not fear‐prolonged exposure to CNIs, and in seeking better long‐term solutions for transplant recipients, we have forgotten alloimmunity. It is thus apparent that we must revisit the data and again question the basis for chronic CNI nephrotoxicity in current clinical practice. This contribution to the debate will focus on the evidence that CNIs are nephrotoxic and that their impact needs to be limited if we are to improve long‐term outcomes after transplantation, leaving others to promote the contrary perspective and perhaps also to reflect on the largely unproven impact of the steroid avoidance and other minimization strategies so prevalent today.
Reviewing the data that lead to the conclusion that chronic CNI nephrotoxicity contributes to loss of kidneys in the long term, the author reviews data from the last 3 decades to understand the issues of today. See rhetorical viewpoint by Matas on page 687.
The tumor suppressor protein 53BP1, a pivotal regulator of DNA double-strand break (DSB) repair, was first identified as a p53-interacting protein over two decades ago. However, its direct ...contributions to p53-dependent cellular activities remain undefined. Here, we reveal that 53BP1 stimulates genome-wide p53-dependent gene transactivation and repression events in response to ionizing radiation (IR) and synthetic p53 activation. 53BP1-dependent p53 modulation requires both auto-oligomerization and tandem-BRCT domain-mediated bivalent interactions with p53 and the ubiquitin-specific protease USP28. Loss of these activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Furthermore, we demonstrate 53BP1-USP28 cooperation to be essential for normal p53-promoter element interactions and gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data provide a mechanistic explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell-fate decisions and reveal these activities to be distinct and separable from 53BP1’s regulation of DNA double-strand break repair pathway choice.
Display omitted
•53BP1 enhances genome-wide p53-dependent transcriptional responses•53BP1’s DNA repair and p53-regulatory roles are distinct and separable•Regulation requires 53BP1 oligomerization and BRCT domain interactions with p53 and USP28•53BP1-USP28 complexes function to stimulate p53 DNA-binding activity
53BP1 was first identified as p53 binding protein 1, yet the function of the p53-53BP1 interaction was unclear. Cuella-Martin et al. show that 53BP1 bridges interactions between p53 and the deubiquitinating enzyme USP28, promoting p53-DNA interactions to globally enhance p53-dependent transcriptional programs.
PDF
