CRISPR between the genes: how to experiment with enhancers and epigenomics | Hacker News Reader

CRISPR between the genes: how to experiment with enhancers and epigenomics

genomics.quiltdata.com

16 pointsakarve9 comments

Hi. In this post we discuss CRISPR as a kind of "GPS for the genome" that allows scientists to explore protein, RNA, and DNA interactions in intergenic regions. This is a cutting edge application of CRISPR. We ran through all of the human genome to find more than 2 million guide RNAs "between the genes" and made the data publicly available. Send us your questions and comments. If you're looking for a background in running CRISPR experiments, check out our first post https://news.ycombinator.com/item?id=10973394

If you don't want to turn-off a finicky set of science geeks please flip the stock image at the top of your web-page. It screams that you don't know the normal handedness of DNA [1], (and calls to suspicion what other basic structural genetic facts you-all might be unaware of)

[1] http://users.fred.net/tds/leftdna/

thanks for catching that. we swapped out the stock image for a shot of the author's lab. perhaps not as pretty, but certainly not as misleading :)

this is not the first time i have been bitten by stock photography. i'm concluding that it's worth the effort to shoot originals whenever possible.

Graphically well done. I don't know about "misleading", but that certainly appears more authentic. As to any "shoot originals" of DNA strands we have to satisfy ourselves with crystallographic or NMR models, (nuclei and electrons being somewhat shy beasts as far as photography is concerned). One only has to depict it helixing to the right as it recedes from the viewer to be free of annoying quibbles (from me [wink])

yeah, i'm not planning to "shoot originals" of DNA any time soon. just article headers at the macro-molecular scale :)

after your comment i carefully examined every detail of the picture (not just the handedness) and, as a chemist, was annoyed by enough details (especially the hydrogen bonds) to nix the whole thing.

To do some very basic research in math, the absolute minimum one should know is the basics of number theory, group theory and real analysis. By analogy, what's the absolute minimum knowledge for someone who wants to enter the field(as far as CRISPR goes) to at least be able to read papers and maybe do some labwork? Thanks.

I'd strongly recommend starting with the non-profit Addgene's guide to CRISPR (https://www.addgene.org/crispr/guide/). A great place to start and accompanying blog posts keep up to date. Also a great place to get the DNA building blocks, libraries, etc.

i'd start with the basics of cell biology, gene expression, and Cas-9 (wikipedia would work), then go right into "High throughput functional genomics using CRISPR–Cas9" and work backwards from the paper to fill in the gaps in your knowledge. the paper is dense. nevertheless it gives you the grand big picture of CRISPR. this way you don't spend months learning genomics theory, some of which is already outdated.

http://www.nature.com/nrg/journal/v16/n5/full/nrg3899.html

for a quick high-level view of Cas-9, there's doudna's talk https://www.youtube.com/watch?v=SuAxDVBt7kQ

"Molecular Biology For Computer Scientists" is a decent place to start (pdf): http://www.cs.princeton.edu/~mona/IntroMaterials/hunter-bio-...

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