Peeping in on Dynamic All-or-None Single-Cell Chromatin RepressionMarch 6, 2016Ever dream of knowing the single-cell details of chromatin regulators in real-time only to awake trapped in the static world of heterogenous cell populations? Well, dream no longer because thanks to the efforts of the Elowitz laboratory at Caltech researchers now have the ability to see just how some of our favorite epigenetic repressors (HDAC4, KRAB, DNMT3B […]
DNA Methylation and Transcription Data from Single Stem CellsJanuary 28, 2016Ever wanted to be able to do two things at the same time? Like work and have a social life? Eat pizza and still fit in your new purchases? Pat your head and rub your belly? While these highly important combinations remain almost impossible (at least for the EpiGenie staff), a stellar cast of scientists […]
Viva in vivo Gene Editing: A Roundup of the Latest CRISPR HitsJanuary 28, 2016Gene editing with CRISPR/Cas9 is here, there, and everywhere. We have seen gene editing in human somatic cells, pluripotent stem cells, and even embryos. However, we should also be looking at CRISPR-based gene editing somewhere else: in a living, breathing human. The question is – where does the current technology stand on the in vivo […]
LobChIP: A Single Day ChIP-Seq Library Preparation HackJanuary 9, 2016With the speed and power of today’s high-throughput sequencers it seems that chromatin immunoprecipitation is the ‘limiting reagent’ in your ChIP-Seq reaction. Usually ChIP-Seq immunoprecipitation and library preparation takes 4 or 5 days, but now a talented team from Uppsala University in Sweden bring forth the library-on-beads ChIP (lobChIP) protocol, which wraps that up into […]
CRISPR-Enhanced Enhancer MappingNovember 29, 2015Enhancers are hugely important regulatory regions of DNA that control gene expression. New techniques are telling us a lot about enhancer structure and function, but the study of enhancers could still use some enhancement. Enhancers are currently defined by what they look like (local DNA methylation, histone modifications, and chromatin availability) or by pulling them […]
Linking RNA Modifications and Stem Cell PluripotencyNovember 12, 2015Recent studies reported here at Epigenie have identified N6-methyladenosine (m6A) as a highly dynamic RNA modification that influences all aspects of RNA biology. Furthermore, an interesting study in mouse and human embryonic stem cells (ESCs) has indicated a role for N6-methyladenosine in the switch between ESC pluripotency and differentiation. Cool stuff indeed, but whate regulates N6-methyladenosine deposition […]
More Insights into Sperm Epigenomics: Histone Methylation Takes It Solo TransgenerationallyNovember 12, 2015While CpG methylation has received the seminal fame of transgenerational epigenetic inheritance, it seems that other players in the epigenome are just as capable. Sperm miRNAs have taken the solo spotlight in highlighting the mechanisms and distinction between transgenerational inheritance and intergenerational effect, but now histone methylation steps up to the plate leading us to […]
Single Cell “Drop ChIP” Reveals Epigenetic Heterogeneity in Cell PopulationsOctober 22, 2015Being average isn’t all that bad, but it’s far from good. Since its very beginning, chromatin immunoprecipitation (ChIP) has been plagued with the problem of averages: chromatin profiles based on ChIP data are an average of the many thousands of cells required to perform this experiment. This gives us a rough overview of the chromatin […]
Validating GWAS with Epigenome EditingOctober 10, 2015GWASs (genome-wide association studies) have found a lot of genetic variants associated with various traits and diseases. But GWASs suffer from that old weakness, the mantra of every good scientist: correlation does not imply causation. The problem gets even worse when you find out most GWAS variants are in non-coding regions of DNA, meaning they […]
Microfluidic ChIP Makes a Few Cells Go a Long WaySeptember 11, 2015Chromatin immunoprecipitation (or ChIP) is a handy technique to study epigenetic profiles, but only if you have enough cells. The main problem with ChIP is that it can be a “greedy” technique that uses large numbers of cells while giving back the bare minimum of DNA as a result. This is problematic for the study of genome-wide […]