Posts categorized under: misc

Enhancer Journal Club: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

I've been thinking a lot about super-enhancers recently and I found this paper¹ from Jennifer Mitchell's lab very interesting, especially as whether and how super-enhancers are distinct from "normal" enhancers has been generating a lot of discussion in the enhancer/gene-regulation literature recently²,³

Here's the abstract:

Transcriptional …

Enhancer Journal Club: Enhancer runaway and the evolution of diploid gene expression

I came across this very interesting theoretical paper about enhancer evolution a couple of months ago¹ and thought it was worth a little discussion. The paper comes from Frederic Fyon and others at the CNRS in Montpellier. The original paper can be found at PLOS Genetics, and it's well …

Enhancer Journal Club: Functional annotation of native enhancers with a Cas9-histone demethylase fusion

I really enjoyed Eric Mendenhall's 2013 paper in Nature Biotechnology¹, where he was able to target LSD1 histone demethylase activity to endogenous enhancers using TALE fusion proteins (read my thoughts on that paper here). So I was very interested to see a similar approach published earlier this year in …

Enhancer Journal Club: Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

I read a neat little paper in Nature just before Christmas about enhancer hijacking, which I think is a particularly interesting topic. The original paper can be found at: http://www.nature.com/nature/journal/v511/n7510/full/nature13379.html

The abstract is as follows:

Medulloblastoma is a highly malignant …

Enhancer Journal Club: Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

I noticed a nice paper this week in Nature Neuroscience from Michael Greenberg's lab at Harvard Medical School. The paper discusses the identification of enhancers in neurons which are activated (or deactivated) when those neurons are stimulated by membrane de-polarization. The original paper can be found at: http://www.nature …

Enhancer Journal Club: Global view of enhancer–promoter interactome in human cells

One of the key hypotheses which is driving interest in enhancer biology right now is that mutations in enhancer sequences may cause medically relevant changes in gene expression (e.g. in cancer). There has been a great deal of progress in recent years towards high throughput identification of enhancers, genome …

Enhancer Journal Club: Genome-scale functional characterization of Drosophila developmental enhancers in vivo

Following on from last month's journal club, there was a new paper this month from the Stark lab in Vienna also dealing with large-scale characterisation of enhancer activity patterns. The original paper can be found at www.nature.com/doifinder/10.1038/nature13395, and the abstract is as follows:

Transcriptional …

Enhancer Journal Club: Functional and topological characteristics of mammalian regulatory domains

This month, I'm going to do a short journal club on a paper called "Functional and topological characteristics of mammalian regulatory domains", which comes from François Spitz's group at the EMBL. The original paper can be found at http://genome.cshlp.org/content/early/2014/01/07/gr.163519.113 …

Enhancer (sort of) Journal Club: Detection and replication of epistasis influencing transcription in humans

I thought I would write a short journal club on a paper that I really enjoyed reading recently. It isn't as directly related to enhancers as previous papers I've covered, but I think it has some interesting implications for the field. The paper is called "Detection and replication of epistasis …

Enhancer Journal Club: Polycomb potentiates meis2 activation in midbrain by mediating interaction of the promoter...

Much of the tissue specific gene-expression required for development appears to be driven by cis-regulatory elements like enhancers, but I think the field has a long way to go in understanding how these elements work mechanistically. One nice paper on this subject has recently been published by Haruhiko Koseki's lab …