5. Most XCI genes in the X-chromosome with Xq28 duplication of
the two females were not transcriptionally expressed
XCI statuses of X-linked genes were defined as escape, variable escape,
and inactive. XCI genes, such as MECP2 and IRAK1 , were
only expressed in the active X (Xa) chromosome. Escape XCI genes,
located mostly in the pseudoautosomal region, were expressed both in Xa
chromosomes and the inactive X (Xi) chromosome. Variable escape XCI
genes were determined to be variable XCI statuses (Tukiainen et al.,
2017).
We listed all SNPs information on the X-chromosome detected by both RNA
sequencing and WES. For I2 and II2, in the non-pseudoautosomal region,
where most SNPs of XCI genes in the X-chromosome with Xq28 duplication
were no transcription, and there was a lower overall transcription for
variable and escaping XCI genes (Supp. Table S4).
6. MECP2 and IRAK1 on the Xq28-duplicated alleles
of the two females were not transcriptionally expressed by RNA
sequencing
Then we focused on the Xq28-duplicated region (Supp. Table S5). All SNP
expressions of XCI genes (MECP2, IRAK1, TMEM187, TKTL1 ) in II2
and I2 were in a homozygous condition, indicating complete skewed XCI in
II2 and I2. In the Xq28-duplicated region, there are several informative
SNPs, which can definite parental origin, such as MECP2(chrX:154030040), IRAK1 (chrX:154013378, chrX:154018741,
chrX:154019032), TMEM187 (chrX:153982271, chrX:153982294,
chrX:153982503, chrX:153982797) (Figure 4 and Supp. Table S5). DNA and
cDNA genotypes of MECP2 (chrX:154030040) were also detected by
PCR-sanger sequencing (Figure 3B). It showed that the alleles inheriting
from the mother I2, which is with Xq28 duplication, were not
transcriptionally expressed. Likewise, in the variable XCI genesHCFC1 , NAA10 and the escaping XCI gene RENBP , the
duplicated alleles inherited from the mother I2 were in lower
expression. As informative SNPs of XCI genes presented in Figure 4 and
Supp. Table S5, we found that the XCI genes MECP2 andIRAK1 on the Xq28-duplicated alleles of II2 and I2 were in
silencing transcription.