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I've been reading this paper entitled "A high-resolution map of the three-dimensional chromatin interactome in human cells", about interactome in 3D chromatin.

We next applied the above algorithm to the 518,032 anchor regions in the human genome, with each containing one or a few HindIII restriction fragments (fragments shorter than 2 kilobases (kb) are merged) (Fig. 2a), and uncovered a total of 1,116,312 chromatin interactions with a false discovery rate (FDR) of 0.1

Simple questions: what are these anchor regions in the human genome?

How could I group them into types/categories?

Thanks

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Good question. Anchor regions are regions that connect to the nuclear matrix. More specifically, in eukaryotic organisms, chromatin is anchored to the nuclear matrix by short DNA sequences of about 100-2,000 bp called matrix attachment regions or MAR. To answer the second part of your question, there are many categories (and opinions about those categories) of anchor regions. The most comprehensive way of categorizing these regions however I believe is by whether they are constitutively (always) or transiently (sometimes) bound to the nuclear structure.

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  • $\begingroup$ Thanks @rhill45 Where could I find the categories that you mentioned? Could you give me a list or a link to a paper? $\endgroup$ Oct 14 '14 at 14:43
  • $\begingroup$ From the reading I've done, I think they have been very well catalogued and are still being identified. Here's a 2008 review on MARS.genomebiology.com/content/pdf/gb-2008-9-1-201.pdf $\endgroup$
    – rhill45
    Oct 14 '14 at 16:39

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