Methylated mammalian promoters are transcriptionally silenced by nuclear factors, but the identity of these factors and the molecular mechanism of methylation-induced repression have long been elusive. We show here that methylated promoters recruit...
John Greally@cshperspectives Consensus? In #epigenetics?
The inability of chromatin/DNA modifiers to choose loci is the real weakness in the modifier-centric perspective.
The psychological workaround is to think of all these modifiers looping without TFs, like Tim Bestor's latest
Polycomb repressive complex 2 (PRC2) catalyzes tri-methylation of histone H3 on lysine 27 and is required for normal development of complex eukaryotes. The requirement for H3K27me3 in various aspects of mammalian differentiation is not clear. Though...
John GreallyNot really surprising, if you regard polycomb as a mechanism for locking in transcriptional regulatory programs, but nice to demonstrate.
H3K27me3 is dispensable for early differentiation but required to maintain differentiated cell identity biorxiv.org/content/10.110… #epigenetics
Exposure to certain chemicals early in life can reprogram the liver epigenome so that the organism becomes more vulnerable to diet-triggered metabolic problems later in life.
John GreallyHow to write an outstandingly awful press release about an #epigenetics study, from the PR office at @bcmhouston
Is it really necessary to use analogies like ‘sleeper cells’ and ‘ticking time bombs’? Ugly.
Decreasing the DNA-binding affinity of a transcription factor via MAPK-stimulated
p300/CBP-mediated acetylation of a lysine contacting the DNA-phosphate backbone paradoxically
increases its functional output by promoting release from a genome-wide...
John GreallyTranscription factor post-translational modifications.
Another source of variability of transcriptional regulation.
My feeling: hugely important emerging field.
Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution
John GreallyYes, but with caveats:
Ireland needs informed oversight of genomics research.
Privacy and legal issues need to be addressed legislatively.
A coherent genomics health strategy is essential.
Covid-19 – a national research biobank is urgently needed
The identity of dividing cells is challenged during mitosis, as transcription is halted and chromatin architecture drastically altered. How cell type-specific gene expression and genomic organization are faithfully reset upon G1 entry in daughter...
John GreallyEffie @efapostolou29@WeillCornell is on a bit of a roll at present, another interesting preprint.
Mitotic retention of H3K27 acetylation promotes rapid topological and transcriptional resetting of stem cell-related genes and enhancers upon G1 entry
Local activity of the DNA methylation machinery remains poorly understood. Here, the authors present a theoretical and experimental framework to infer methylation and demethylation rates at genome scale in mouse embryonic stem cells, finding that...
We apply long-read nanopore sequencing and a new tool, TLDR (Transposons from Long Dirty Reads), to directly infer CpG methylation of new and extant human transposable element (TE) insertions in hippocampus, heart, and liver, as well as paired...
Nanopore sequencing +
TLDR (Transposons from Long Dirty Reads)=
CpG methylation of new and extant human transposable element insertions
Nanopore sequencing enables comprehensive transposable element epigenomic profiling
Dysregulation of imprinted gene loci also referred to as loss of imprinting (LOI) can result in severe developmental defects and other diseases, but the molecular mechanisms that ensure imprint stability remain incompletely understood. Here, we...
John GreallyDissection of the Dlk1-Dio3 imprinted locus by @efapostolou29. Nice to see genomic imprinting still a focus for #epigenetics research.
A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus
John GreallyIf you are black/other under-represented group, and you would like get experience reviewing #epigenetics (biologue.plos.org/2020/05/14/epi…) submissions at @PLOSGenetics, DM me your name/email and I'll add you to the system.
Not much, I know, but even small steps may help foster equity.
A four-part strategy of hygiene, distancing, screening, and masks will not return us to normal life. But, when signs indicate that the virus is under control, it could get people out of their homes and moving again.
John GreallyFrom @Atul_Gawande in the @NewYorker, everything you need to know about meeting the challenge of #COVID19 as a society. Worth sharing as an education aid.
Amid the Coronavirus Crisis, a Regimen for Reëntry
I. Viruses, in the sense of filterable, replicable and transmissible (infective) particles in the cytoplasm, containing nucleoprotein, cause a number of tumours, such as Rous sarcoma in fowls, avian ...
John GreallyWeekend challenge: 1957.
That’s the year of the earliest publication I can find describing both #cancer and #epigenetics. Julian Huxley the author.
Can anyone find an earlier mention of cancer/epigenetics?
The inequities of New York City’s health care system are clear at a public hospital in a section of Brooklyn hit hard by the coronavirus pandemic.
John GreallyAs health care disparities go, so do research disparities. Rich health care systems are the ones testing local populations. Poor health care systems, which care for the disadvantaged, barely scrape by. Research is very secondary #ResearchDisparities
Human Phenotype Ontology (HPO)-based analysis has become standard for genomic diagnostics of rare diseases. Current algorithms use a variety of semantic and statistical approaches to prioritize the typically long lists of genes with candidate...
John GreallyThis looks very intriguing from Peter Robinson @jacksonlab and colleagues, their update on Exomiser, LIRICAL. Includes ability to use HPO terms *not* present, promises to be very useful.
Interpretable Clinical Genomics with a Likelihood Ratio Paradigm