Patrick J. Murphy
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Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis Open
Aging is characterized by a decline in the functionality and number of stem cells across the organism. In this study, we uncovered a mechanism by which systemic inflammation drives muscle stem cell (MuSC) aging through epigenetic erosion. …
View article: Barriers to Paramedic Professionalisation: A Qualitative Enquiry Across the UK, Canada, Australia, USA and the Republic of Ireland.
Barriers to Paramedic Professionalisation: A Qualitative Enquiry Across the UK, Canada, Australia, USA and the Republic of Ireland. Open
Background – Paramedicine is in the midst of a transformative shift, as paramedics move beyond traditional emergency roles toward recognition as healthcare professionals. Central to this evolution is the pursuit of professionalisation—seek…
View article: Opposing effects of histone H2A.Z on memory, transcription and pathology in male and female Alzheimer’s disease mice and patients
Opposing effects of histone H2A.Z on memory, transcription and pathology in male and female Alzheimer’s disease mice and patients Open
Alzheimer’s disease (AD) is a devastating neurodegenerative disease that disproportionately impacts women, but underlying mechanisms for sex-divergent outcomes are unknown. Here, we show that the histone variant H2A.Z is a novel sex-specif…
CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays Open
Summary Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, th…
Loss-of-function of RNA-binding protein PRRC2B causes translational defects and congenital cardiovascular malformation Open
Alternative splicing generates variant forms of proteins for a given gene and accounts for functional redundancy or diversification. A novel RNA-binding protein, Pro-rich Coiled-coil Containing Protein 2B (PRRC2B), has been reported by mul…
The Effects of Perfluorooctanesulfonic acid (PFOS) on Human Umbilical Vein Endothelial Cells (HUVECs) Proliferation and Gene Expression and its Implications on Fetal Development Open
Polyfluoro-alkyl substances (PFAS) are widely distributed environmental contaminants linked to human toxicity and developmental delays, especially low birthweight (LBW). In this study, Human Umbilical Vein Endothelial Cells (HUVECs) were e…
CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration Open
Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epi…
CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration Open
Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epi…
Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis. Open
Aging is associated with a decline in stem cell functionality and number across the organism. In this study, we aimed to further unravel Muscle Stem Cells (MuSCs) aging by assessing how systemic factors influence MuSC fate decisions throug…
<i>Smad4</i> restricts injury-provoked biliary proliferation and carcinogenesis Open
Cholangiocarcinoma (CCA) is a deadly and heterogeneous type of cancer characterized by a spectrum of epidemiologic associations as well as genetic and epigenetic alterations. We seek to understand how these features inter-relate in the ear…
View article: Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification
Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification Open
Creating long-lasting memories requires learning-induced changes in gene expression, which are impacted by epigenetic modifications of DNA and associated histone proteins. Post-translational modifications (PTMs) of histones are key regulat…
Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation Open
Epigenetic regulation of chromatin states is crucial for proper gene expression programs and progression during development, but precise mechanisms by which epigenetic factors influence differentiation remain poorly understood. Here we fin…
The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations Open
We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as ‘sources’ to produce or provide a resource and compete with each other to occupy separate ‘sinks’. In th…
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression Open
The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of …
Supplementary Figures from TAp73 Modifies Metabolism and Positively Regulates Growth of Cancer Stem–Like Cells in a Redox-Sensitive Manner Open
Supplementary Figures
NURF301 contributes to <i>gypsy</i> chromatin insulator-mediated nuclear organization Open
Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex co…
Competition for H2A.Z between genes and repetitive elements establishes response to anti-viral immune activation Open
Activation of endogenous retroviruses leads to widespread transcriptional reprograming, affecting innate immune activation, metabolic control, and development. We find that the histone variant H2A.Z plays a central role in orchestrating th…
Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos Open
Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal the order of…
Author response: Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Vertebrate embryos ach…
Identification of chromatin states during zebrafish gastrulation using <span>CUT</span> & <span>RUN</span> and <span>CUT</span> &Tag Open
Background Cell fate decisions are governed by interactions between sequence‐specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices,…
Inflammatory vaginitis in women on long-term rituximab treatment for autoimmune disorders Open
Background Consequences of long-term B cell depletion with rituximab are not well understood. We describe inflammatory vaginitis as a potential side effect of long-term rituximab treatment, distinct from previously described vulvovaginal p…
Chromatin Patterns Distinguish Breast Tumor Subtypes and Disease Progression in Association with<i>ANP32E</i>levels Open
Despite highly advanced diagnosis and treatment strategies, breast cancer patient outcomes vary extensively, even among individuals with the same diagnosis. Thus, a better understanding of the unique molecular characteristics that underlie…
Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag Open
Background Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices,…