Table 1.
Genetic loci with similarities to Snrpn–Ube3a for which DNA FISH probes were created for chromatin decondensation analyses in adult mouse whole brain sections
| Gene locus | Imprinted | snoRNAsa | ncRNA | Brain expressionb | Transcript size (kb) | DNA FISH probe (kb) | Decondensed chromatin |
|---|---|---|---|---|---|---|---|
| Snrpn–Ube3a | Yes | 80 | Yes | High | 1111 | 888c | Yes |
| Igf2/H19 | Yes | None | Yes | High/low | 8.7/2.7 | 244 | No |
| Dlx5/Dlx6 | Yes | None | No | Med/med | 4.5/4.0 | 203 | No |
| Igf2r | Yes | None | Yes | Med | 8.7 | 204 | No |
| Ndn/Magel2/Mkrn3 | Yes | None | No | High/med/med | 1.7/2.2/2.5 | 169 | No |
| Gtl2 | Yes | 9 | Yes | High | 208 | 244 | Yes |
| Htr2c | No | 1 | Yes | High | 235 | 190 | No |
| Tsix | No | None | Yes | Med | 53 | 224 | No |
| Dmdd | No | None | No | Med–highe | 2256 | 245 | No |
aBased on UCSC Genome Browser Mouse 2007 assembly alignment of homologous human snoRNAs at these loci and current published numbers (13,14,28).
bBased on UCSC Genome Browser heat maps from GNF1M Mouse Chip for all except Snrpn–Ube3a (based on previously published results (17) and Allen Brain Atlas).
cBAC DNA FISH probes (ranging from 127 to 191 kb each) individually showed chromatin decondensation over this region, the combined BAC DNA FISH probe covered the PWS-IC through Ube3a (complete length of the transcript varies by publication).
dDmd was the only single gene locus examined for which the BAC DNA FISH probe did not cover the majority of the transcript.
eWhile Dmd shows only medium expression in brain overall (by UCSC genome browser heat map), it has high expression in adult mouse Purkinje neurons (Allen Brain Atlas) where it was examined for chromatin decondensation.