Figure 6.
Allele-specific regulation of TLX3 by enhancer hijacking. (A) Violin plot with median and quartiles showing CpG methylation at the TLX3 promoter in t(5;14)-negative Jurkat and t(5;14)-positive (UT242, UT308, and DND-41) cells. (B) Schematic of single nucleotide polymorphism (SNP) rs138378198 identified by WGS in UT242, located 318 bp upstream of the TLX3 transcription start site. The reference (Ref) C and alternative (Alt) G allele sequences are indicated, allowing for allelic interrogation of DNA methylation and gene expression. (C) Schematic of SNP rs918472 identified by WGS in patient UT308 and DND-41 at the 3’UTR of TLX3. The reference (Ref) G and alternative (Alt) A allele sequences are indicated, allowing for interrogation of allele-specific TLX3 expression. (D) Bar plot representation of composite CpG methylation calculated from bisulfite sequencing reads mapped to Ref or Alt allele. (E) Genome browser track with nucleotide alignment coverage scores of bisulfite sequencing data in UT242. The nucleotide sequences within the 56 bp region of the TLX3 promoter are shown with SNP rs138378198 indicated as red diamonds. Chromosomal coordinates correspond to hg19 genome assembly. Nucleotide sequence color represents IGV genome browser viewer track color scheme. A, green; C, blue; G, brown; and T, red. Dashed boxes indicate CpG dinucleotides. Gray coverage bars underlying a given nucleotide denote correct alignment matches. The presence and relative proportion of coloration within these bars indicate which mismatched nucleotide is detected for a given position and the depth of sequencing reads carrying the mismatch, respectively. For bisulfite sequencing, an unmethylated C (blue) converted to T (red) is represented as red coloration underlying C bases, whereas methylated C are not converted. (F) Genome browser track with nucleotide alignment coverage scores and underlying raw reads of RNA-seq data in UT242. The nucleotide sequences within a 38 bp region of the TLX3 promoter are shown with SNP rs138378198 indicated as a red diamond. Chromosomal coordinates correspond to hg19 genome assembly. (G) Bar plot representation of the proportion of UT242 RNA-seq reads aligning to Ref or Alt allele. (H) Bar plot representation of the proportion of UT308 RNA-seq reads aligning to Ref or Alt allele. (I) Genome browser track with nucleotide alignment coverage scores and underlying raw reads of RNA-seq data in UT308. The nucleotide sequences within a 40 bp region of the TLX3 3’UTR are shown with SNP rs918472 indicated as a red diamond. Chromosomal coordinates correspond to hg19 genome assembly. (J) Bar plot representation of the proportion of DND-41 RNA-seq reads aligning to Ref or Alt allele. (K) Genome browser track with nucleotide alignment coverage scores and underlying raw reads of RNA-seq data in DND-41. The nucleotide sequences within a 40 bp region of the TLX3 3’UTR are shown with SNP rs918472 indicated as a red diamond.

Allele-specific regulation of TLX3 by enhancer hijacking. (A) Violin plot with median and quartiles showing CpG methylation at the TLX3 promoter in t(5;14)-negative Jurkat and t(5;14)-positive (UT242, UT308, and DND-41) cells. (B) Schematic of single nucleotide polymorphism (SNP) rs138378198 identified by WGS in UT242, located 318 bp upstream of the TLX3 transcription start site. The reference (Ref) C and alternative (Alt) G allele sequences are indicated, allowing for allelic interrogation of DNA methylation and gene expression. (C) Schematic of SNP rs918472 identified by WGS in patient UT308 and DND-41 at the 3’UTR of TLX3. The reference (Ref) G and alternative (Alt) A allele sequences are indicated, allowing for interrogation of allele-specific TLX3 expression. (D) Bar plot representation of composite CpG methylation calculated from bisulfite sequencing reads mapped to Ref or Alt allele. (E) Genome browser track with nucleotide alignment coverage scores of bisulfite sequencing data in UT242. The nucleotide sequences within the 56 bp region of the TLX3 promoter are shown with SNP rs138378198 indicated as red diamonds. Chromosomal coordinates correspond to hg19 genome assembly. Nucleotide sequence color represents IGV genome browser viewer track color scheme. A, green; C, blue; G, brown; and T, red. Dashed boxes indicate CpG dinucleotides. Gray coverage bars underlying a given nucleotide denote correct alignment matches. The presence and relative proportion of coloration within these bars indicate which mismatched nucleotide is detected for a given position and the depth of sequencing reads carrying the mismatch, respectively. For bisulfite sequencing, an unmethylated C (blue) converted to T (red) is represented as red coloration underlying C bases, whereas methylated C are not converted. (F) Genome browser track with nucleotide alignment coverage scores and underlying raw reads of RNA-seq data in UT242. The nucleotide sequences within a 38 bp region of the TLX3 promoter are shown with SNP rs138378198 indicated as a red diamond. Chromosomal coordinates correspond to hg19 genome assembly. (G) Bar plot representation of the proportion of UT242 RNA-seq reads aligning to Ref or Alt allele. (H) Bar plot representation of the proportion of UT308 RNA-seq reads aligning to Ref or Alt allele. (I) Genome browser track with nucleotide alignment coverage scores and underlying raw reads of RNA-seq data in UT308. The nucleotide sequences within a 40 bp region of the TLX3 3’UTR are shown with SNP rs918472 indicated as a red diamond. Chromosomal coordinates correspond to hg19 genome assembly. (J) Bar plot representation of the proportion of DND-41 RNA-seq reads aligning to Ref or Alt allele. (K) Genome browser track with nucleotide alignment coverage scores and underlying raw reads of RNA-seq data in DND-41. The nucleotide sequences within a 40 bp region of the TLX3 3’UTR are shown with SNP rs918472 indicated as a red diamond.

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