What Are These Regions Called Again - Reference Gaps On Chr13, Chr14, Chr15, Chr21, Chr22

Question

[richardc.gsc]

Hi all, On Chromosome 13, 14, 15, 21, 22 of the human genome there are large gaps in the reference sequence at the beginning of the p-arm. There is a name for these large reference-less regions. Its always a little tricky to google something you can't remember the name of.

What are these regions called?

Answer 1

[Devon Ryan]

There's a gap track on the UCSC genome browser that will label the gaps with a useful descriptor. In general, the p-arms of acrocentric chromosomes (the ones you mentioned) contain highly repetitive sequences and are constitutively heterochromatic (i.e., highly compacted).

[Dan D]

Yeah, it's not euchromatic like I had originally thought. In the mid-2000s there was a lot of discussion in the literature about filling in the euchromatic gaps, but after reading this paper: http://www.stanford.edu/class/cs273a/papers.spr07/02/finishedHGCritique.pdf I see that the remaining large gaps are heterochromatic. The linked paper addresses the OPs areas of interest on the 5th page under the Acrocentric DNA heading.

Answer 2

[Dan D]

Euchromatic gap, perhaps?