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"Miles, K"
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Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments
Although enhancers are central regulators of mammalian gene expression, the mechanisms underlying enhancer–promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively capture large-scale three-dimensional (3D) genome structure but struggle to achieve the depth necessary to resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining micrococcal nuclease (MNase)-based 3C with a tiling region-capture approach and generate the deepest 3D genome maps reported with only modest sequencing. By applying RCMC in mouse embryonic stem cells and reaching the genome-wide equivalent of ~317 billion unique contacts, RCMC reveals previously unresolvable patterns of highly nested and focal 3D interactions, which we term microcompartments. Microcompartments frequently connect enhancers and promoters, and although loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. We therefore propose that many E-P interactions form through a compartmentalization mechanism, which may partially explain why acute cohesin depletion only modestly affects global gene expression.
Region Capture Micro-C (RCMC) combines MNase-based 3C with a tiling region-capture method. Profiling mouse embryonic stem cells with RCMC identifies nested microcompartments, which connect enhancers and promoters.
Journal Article
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy
Polycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. How PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here, we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We observe that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, suggesting that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.
How PRC1 recognises and interacts with its target genes remains poorly understood. Here, the authors use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells, revealing that this repressor is highly dynamic, with only a small fraction stably interacting with chromatin.
Journal Article
Temperature effects on food supply and chick mortality in tree swallows (Tachycineta bicolor)
Tree swallow (Tachycineta bicolor) breeding success in Ithaca, NY, USA, over the past quarter century has shown generally healthy fledgling production punctuated by years of high nestling mortality. This study tested the potential effects that temperature may have on the food supply and breeding success of swallows. Data from 17 years of daily insect samples were used to relate flying insect abundances to daily maximum temperatures and to define \"cold snaps\" as strings of consecutive days when the maximum temperatures did not exceed critical temperatures. The distributions of cold snaps and chick mortality events were investigated both through detailed reconstructions of the fates and fate dates of individual chicks, focused on the three breeding seasons of lowest fledging success, and with less detailed brood-level analyses of a larger 11-year dataset including years of more moderate mortality. Mark—recapture analyses of daily brood survival rate (DSR) reveal very strong support for the effects of cold temperatures on brood survival rates, and all the top models agree on a critical temperature of 18.5 °C for insect flight activity in Ithaca. The individual-level analyses, focused on years of higher mortality, favored a 3-day cold snap definition as the most predictive of DSR effects, whereas the larger-scale brood-level analyses revealed 1- and 2-day cold snaps as having the most significant effects on DSR. Regardless, all analyses reveal that, in an age of generally warmer climates, the largest effect of weather on swallow fledgling production is from cold temperatures.
Journal Article
YAP activation protects urothelial cell carcinoma from treatment-induced DNA damage
Current standard of care for muscle-invasive urothelial cell carcinoma (UCC) is surgery along with perioperative platinum-based chemotherapy. UCC is sensitive to cisplatin-based regimens, but acquired resistance eventually occurs, and a subset of tumors is intrinsically resistant. Thus, there is an unmet need for new therapeutic approaches to target chemotherapy-resistant UCC. Yes-associated protein (YAP) is a transcriptional co-activator that has been associated with bladder cancer progression and cisplatin resistance in ovarian cancer. In contrast, YAP has been shown to induce DNA damage associated apoptosis in non-small cell lung carcinoma. However, no data have been reported on the YAP role in UCC chemo-resistance. Thus, we have investigated the potential dichotomous role of YAP in UCC response to chemotherapy utilizing two patient-derived xenograft models recently established. Constitutive expression and activation of YAP inversely correlated
with in vitro
and
in vivo
cisplatin sensitivity. YAP overexpression protected while YAP knockdown sensitized UCC cells to chemotherapy and radiation effects via increased accumulation of DNA damage and apoptosis. Furthermore, pharmacological YAP inhibition with verteporfin inhibited tumor cell proliferation and restored sensitivity to cisplatin. In addition, nuclear YAP expression was associated with poor outcome in UCC patients who received perioperative chemotherapy. In conclusion, these results suggest that YAP activation exerts a protective role and represents a pharmacological target to enhance the anti-tumor effects of DNA damaging modalities in the treatment of UCC.
Journal Article
Partner gaze shapes the relationship between symptoms of psychopathology and interpersonal coordination
Interpersonal coordination is a key determinant of successful social interaction but can be disrupted when people experience symptoms related to social anxiety or autism. Effective coordination rests on individuals directing their attention towards interaction partners. Yet little is known about the impact of the attentional behaviours of the partner themselves. As the gaze of others has heightened salience for those experiencing social anxiety or autism, addressing this gap can provide insight into how symptoms of these disorders impact coordination. Using a novel virtual reality task, we investigated whether partner gaze (i.e., direct vs. averted) influenced the emergence of interpersonal coordination. Results revealed: (i) spontaneous coordination was diminished in the averted (cf. direct) gaze condition; (ii) spontaneous coordination was positively related to symptoms of social anxiety, but only when partner gaze was averted. This latter finding contrasts the extant literature and points to the importance of social context in shaping the relationship between symptoms of psychopathology and interpersonal coordination.
Journal Article
Influence of the grounding zone on the internal structure of ice shelves
Antarctic ice shelves typically comprise continental meteoric ice, in situ-accumulated meteoric ice, and marine ice accumulated at the shelf base. Using borehole optical televiewer logs from across Larsen C Ice Shelf, Antarctic Peninsula, we identify and report an intermediate ice unit, located between continental and in situ meteoric ice, that is tens of metres thick and formed of layers that progressively increase in dip (by ~60°) with depth. The unit’s stratigraphic position and depth, supported by flowline modelling, indicate formation at the grounding zone. We hypothesise that the unit forms due to changes in the surface slope of feeder glaciers at the grounding zone, resulting in both variable surface accumulation and intense deformation. The top of the unit also marks the depth at which lateral consistency in radar layering is lost from radargrams, which may, to some degree, mark the depth of grounding zone ice across all ice shelves.
Borehole optical televiewer logs from across Larsen C Ice Shelf, Antarctic Peninsula, reveal an ice unit formed during transport over the grounding zone, the upper depth of which coincides with a loss in lateral consistency of radar layering.
Journal Article
Current status and guidelines for the assessment of tumour vascular support with dynamic contrast-enhanced computed tomography
Dynamic contrast-enhanced computed tomography (DCE-CT) assesses the vascular support of tumours through analysis of temporal changes in attenuation in blood vessels and tissues during a rapid series of images acquired with intravenous administration of iodinated contrast material. Commercial software for DCE-CT analysis allows pixel-by-pixel calculation of a range of validated physiological parameters and depiction as parametric maps. Clinical studies support the use of DCE-CT parameters as surrogates for physiological and molecular processes underlying tumour angiogenesis. DCE-CT has been used to provide biomarkers of drug action in early phase trials for the treatment of a range of cancers. DCE-CT can be appended to current imaging assessments of tumour response with the benefits of wide availability and low cost. This paper sets out guidelines for the use of DCE-CT in assessing tumour vascular support that were developed using a Delphi process. Recommendations encompass CT system requirements and quality assurance, radiation dosimetry, patient preparation, administration of contrast material, CT acquisition parameters, terminology and units, data processing and reporting. DCE-CT has reached technical maturity for use in therapeutic trials in oncology. The development of these consensus guidelines may promote broader application of DCE-CT for the evaluation of tumour vascularity.
Key Points
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DCE-CT can robustly assess tumour vascular support
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DCE-CT has reached technical maturity for use in therapeutic trials in oncology
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This paper presents consensus guidelines for using DCE-CT in assessing tumour vascularity
Journal Article
Neurogenomic insights into paternal care and its relation to territorial aggression
Motherhood is characterized by dramatic changes in brain and behavior, but less is known about fatherhood. Here we report that male sticklebacks—a small fish in which fathers provide care—experience dramatic changes in neurogenomic state as they become fathers. Some genes are unique to different stages of paternal care, some genes are shared across stages, and some genes are added to the previously acquired neurogenomic state. Comparative genomic analysis suggests that some of these neurogenomic dynamics resemble changes associated with pregnancy and reproduction in mammalian mothers. Moreover, gene regulatory analysis identifies transcription factors that are regulated in opposite directions in response to a territorial challenge versus during paternal care. Altogether these results show that some of the molecular mechanisms of parental care might be deeply conserved and might not be sex-specific, and suggest that tradeoffs between opposing social behaviors are managed at the gene regulatory level.
Compared to motherhood, the molecular changes associated with fatherhood are less understood. Here, the authors investigate gene expression changes associated with paternal care in male stickleback fish, and compare them with patterns in territorial aggression.
Journal Article
Apoptotic cells protect mice from autoimmune inflammation by the induction of regulatory B cells
The maintenance of immune tolerance to apoptotic cells (AC) within an inflammatory milieu is vital to prevent autoimmunity. To investigate this, we administered syngeneic AC i.v. into mice carrying a cohort of ovalbumin (OVA)-specific transgenic T cells (DO11.10) along with OVA peptide and complete Freund's adjuvant, observing a dramatic increase in OVA-specific IL-10 secretion. Activated splenic B cells responded directly to AC, increasing secretion of IL-10, and this programming by AC was key to inducing T cell-derived IL-10. We went on to ask whether AC are able to modulate the course of autoimmune-mediated, chronic inflammation. AC given up to 1 month before the clinical onset of collagen-induced arthritis protected mice from severe joint inflammation and bone destruction. Antigen-specific CD4⁺ T cells again secreted significantly more IL-10, associated with a reduced titer of pathogenic anti-collagen II antibodies. Inhibition of IL-10 in vivo reversed the beneficial effects of AC. Passive transfer of B cells from AC-treated mice provided significant protection from arthritis. These data demonstrate that AC exert a profound influence on an adaptive immune response through the generation of CD19⁺ regulatory B cells, which in turn are able to influence the cytokine profile of antigen-specific effector T cells.
Journal Article