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Getting started with Chromatin Conformation Capture (3C)

February 15, 2015

The concept of chromatin contact mapping, or determining the three-dimensional structure conformation and interactions of chromatin domains, is now a reality because of Chromatin Conformation Capture (3C) and subsequent methods born out of that approach. Several new 3C-based techniques have emerged, each with particular strengths and applications, but the sheer variety creates a challenge when […]

New Transcriptional Repressors for Pick ‘N’ Mix Synthetic Gene Circuits

February 15, 2015

As a kid there was no greater feeling on a weekend shopping trip than being set loose on the Pick ‘N’ Mix, carefully choosing from the wealth of candy to create the perfect selection. Lucky for you synthetic biology promises the same thrill, by providing a selection of ready-to-roll interchangeable parts to choose from allowing […]

Plant Receptor Re-engineered to Hear “Drought!” From a New Signal

February 12, 2015

Don’t get me wrong, plants have a lot of things going for them. However, as Groot’s fellow Galaxy Guardians can attest, vocabulary isn’t one of them. It can be hard to communicate with plants, even once you figure out their language. Take the plant abscisic acid (ABA) receptor, PYR1, for example. PYR1 communicates via ABA, […]

Expressed Long Non-coding RNAs Snitch on Tissue-specific Enhancers

February 11, 2015

Predicting tissue-specific enhancers is a tricky business. While histone marks such as H3K4me1 and binding of p300 are good enhancer predictors, pointing out which enhancers are tissue-specific is more of a challenge. That is, of course, unless you have PreSTIGE – an algorithm developed by the Scacheri lab that identifies tissue-specific enhancers by combining H3K4me1 […]

Stem Cells Take the Sting out of Radiotherapy

February 11, 2015

Radiotherapy is an important and effective tool in the war against cancer, but its use for treating brain tumors brings with it unwanted side effects that can cause long term suffering to the patient. Radiation induces the depletion of oligodendrocyte progenitor cells (OPCs) which leads to the loss of the protective myelin sheath that covers […]

Culture Shock: The Transition to Transformed Cell Alters the Methylome

February 10, 2015

Whether it’s making the monumental move to high school, switching jobs or experiencing the culture shock from moving countries, adjusting to a new environment isn’t always easy. Often we have to make concessions and tradeoffs, the extent of which is very much dependent on the type of environment we find ourselves in. It turns out […]

Turn on Your Genes with a Helping Hand from CRISPR-Cas9

February 10, 2015

We all know that the genome editing superhero CRISPR-Cas9 is a master of modifying the genome, but a recent paper from Zhang lab shows that it is more than just a one-trick pony. This latest research boosts the previously developed CRISPR-Cas9 transcriptional activators both in terms of the level of gene induction and in the […]

Cell Organelles Trip the Light Fantastic with Optogenetics

February 10, 2015

The future is looking bright for optogenetics – a technique which uses light to control cellular processes. Following on from a previous illuminating study covered here at Epigenie (Shedding Light on Stem Cell Therapy for Parkinson’s with Optogenetics), another group of researchers have utilized optogenetics in a novel manner – the light-mediated control of sub-cellular […]

SynBioLGDB: A Gateway for Logical Biology

February 9, 2015

Electrical engineering is a strong contender for the central analogy of synthetic biology. Synthetic biologists often think of electrical circuits when designing gene networks, and logic gates are central to the metaphor. Biological logic gates can be difficult to design from scratch, however, and they can’t just be bought at Radio Shack, even before it […]

Review: Crosslinking-Immunoprecipitation (CLIP) Methods

February 8, 2015

RNA-protein interactions are key to understanding human health and disease. Crosslinking-immunoprecipitation (CLIP) and related technologies are powerful tools for characterizing these interactions. Since their introduction in 2008 (Licatalosi et al., 2008), CLIP-based approaches have been applied to prominent RNA research fields such as HIV and cancer. Recently, Sebla Kutluay and colleagues used CLIP to characterize […]