Epigenetic dynamics – free

By Grant Jacobs 15/03/2013

Those with interests in epigenetics and genome structure may want to check out Nature Structural and Molecular Biology’s focus on epigenetic dynamics. (This gives me an opportunity to briefly sound off on a favourite topic…)

One fascinating development over the past few years has been explorations of the three-dimensional nature of genomes, how they are arranged within the nucleus of our cells, how the spatial organisation of genomes might affect how genes are used, interactions between parts of our genomes and far, far too many other questions…

I guess you could say you know an interesting area of science by the questions it raises.

Yeast genome model. From Duan et al, Nature, 2010.
Yeast genome model. From Duan et al, Nature, 2010.

As a student, I studied proteins that bind DNA and the protein-DNA interactions they make. I’m still interested in that—old interests don’t die that easily in science—but these things now fall within a wide range of aspects.

Although a relatively short list of reviews, the focus on epigenetic dynamics covers an interesting range of topics that illustrate how studying gene regulation have moved from simple beginnings of the immediate promoter and protein binding sites in DNA of the 1980s (or so) to the rich complexity of DNA and histone modifications, nucleosome (re-)positioning, protein complexes, chromatin loops, chromosomal domains, regulatory RNAs and more.*

Particularly appealing is that all of the articles are free for anyone to read.**

(Original from Luger lab, sourced from Biomedical Beat.)
(Original from Luger lab, sourced from Biomedical Beat.)

Speaking for myself, it’s great to see a more ‘spatial’ thinking about genomes emerge in molecular biology over the past few years. One of the appealing things about 3-D genome structure work (to me) is that it shifts whole genomes into computational structural biology rather than the more ‘linear’ approach typical of the current genome projects.***


* This list is no way near complete. The new developments keep coming, too. Recent papers report circular RNAs that have a role in gene regulation, for example.

** I currently work as a consultant. One consequence is that access to the research literature can be a hassle – it’s nice to be able to just jump in. There are other collections of reviews on epigenetics, chromatin and genome structure available.

*** I’ve written a book chapter on computational methods associated with computational modelling of the structure of gene regions or whole genomes.

Other articles on Code for life:

(The last few are more technical; the earlier ones are for a wider audience.)

Animating our DNA

The scale of cellular life and compacting chromosomes

Epigenetics – introductory explanations

Epigenetics and 3-D gene structure

Find transcription factor motifs in genomes better: add histone acetylation data

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