Jon Lim
Jon Lim's scratchpad
Our five genes of interest:
HLCS
HMGN1
DYRK1A
BRWD1
RUNX1
Vocabulary/Background for 'Trisomy 21 alters DNA Methylation in Parent-of-Origin-Dependent and Independent manners'
Goals
1. Find a high-certainty method of ascertaining parent-of-origin of HSA21
2. Explore parent-of-origin effects on gene expression
3. Evaluate parent-of-origin effects on methylation of RUNX1 (HSA21) and TMEM131 (HSA2), known to be differentially regulated in Trisomy 21.
INTRO
Since Down Syndrome mainly caused by maternal nondisjunction during oogenesis, cases of paternal inheritance are rare, difficult to study. Trying to determine what the parent-of-origin effect is.
Genomic imprinting - inherited gene silencing, mediated by DNa or histone methylation
Not sure why the authors bring up uniparental disomy (both copies of a chromosome from one parent)...shares some similarity with DS, but more likely to suffer from recessive disorders / total gene silencing than a dosage effect. Is this the androgenetic mole used as a control later?
Authors argue that imprinting may cause parent-of-origin-dependent effects of nondisjoined HSA21
CpG - possible methylation site
STR - short tandem repeats
RESULTS
First, notice methylation profile of CGIs. CGIs 2, 3, 5 are differentially methylated in male and female gametes.
Fig. 2 - exp. validation: no methylation for WRB CGI-1 and 3 when looking at HhaI(+) readout.contrast with wRB CGI-2, which was previously reported to be methylated in blood cells.
Pg 10: Looking at healthy disomic subjects, the snp neighboring CGI-2 gives the known parental identity of the chromosome. Authors found that maternal HSA21 was consistently methylated at CGI-2, and paternal HSA21 unmethylated. This matches with the known differential methylation in the gametes (imprinting?).
Fig. 3 - Looking at typical nuclear trios, the neighboring SNP gives parent-of-origin of the chromosome. The developed assay shows conclusively that methylation is 1:1 with parent-of-origin. HhaI digests unmethylated DNA, leaving behind maternal allele. McrBC digests methylated DNA, leaving behind paternal allele. Conclusion: imprinting on maternal chromosomes.
Fig. 6A-B Unlike at the WRB CGI-2 DMR, RUNX1 and TMEME131 methylation changes in Trisomy 21 probands were NOT PARENT-DEPENDENT.
Pgs 14-16: no evidence that the WRB DMR imprinting effects changes in gene expression (evidenced by biallelic mRNA reads for all neighboring SNPs that had available data.
