Supplementary Figure 2: Analysis of PAR-TERRA transcripts.
a. PAR transcripts resemble TERRA RNA in Northern blotting analysis. Top panel: Map of sub-BAC probes. Northern blot analysis of PAR-TERRA in ES cells using TERRA-specific or PAR-specific oligo probes (27k, 29k, 34k and 47k).
b. Read statistics for TERRA-capture RNA-seq. After TERRA capture, cDNA libraries were generated using either random primers or telomeric-repeat primers. These tables are related to Figure 2f.
c. Overwhelming majority of (TTAGGG)n-containing RNAs originate from sex chromosomes. Mapped fragment (frag.) counts for TERRA-capture RNA-seq experiments for various chromosomes. The X and Y are grouped together because (i) X and Y PARs are nearly identical, (ii) the highly repetitive nature of the PARs makes sequence assembly nearly impossible at the present time, and (iii) more PAR sequences have been assembled on the Y than on the X. See Panel d below.
d. Mapped fragment counts for TERRA-capture RNA-seq experiments for various chromosomes. “+ strand” indicates the forward (Watson) strand. “– strand “ indicates the reverse (Crick) strand. The X and Y reads are separated. See also Panel c above. However, it should be noted that these allelic calls on the X and Y PARs are not fully reliable because (i) X and Y PARs are nearly identical, (ii) the highly repetitive nature of the PARs makes sequence assembly nearly impossible at the present time, and (iii) more PAR sequences have been assembled on the Y than on the X. Thus, the Y-PAR has more mapped reads, but this should be regarded as a technical artifact. RNA FISH signal densitometry suggests the X and Y produce similar amounts of PAR-TERRA in vivo, as XX and XY ES cells have similarly intense PAR-TERRA foci.
e. PAR DNA contains long telomeric repeats. Diagrams of PAR BAC clones: RP24-500I4 and RP24-338D22, consist of PAR consensus sequence, GACA simple repeats and telomeric repeats.
f. PAR transcripts continue to transcribe into telomeric repeats. The Tophat alignment of TERRA-capture RNA-seq show that PAR-TERRA transcripts are aligned to the junction of GACA and telomeric repeats in PAR BAC DNA (RP24-500I4).
