Extended Data Fig. 5: TT-seq and chromatin analysis in WT and Msl2-KO NPCs.
(a) Allelic analysis of TT-seq (Transient transcriptome sequencing) results of female 9sCa WT and Msl2-KO NPCs. Left: Log2[FC] of allelic nascent gene expression comparing Msl2-KO clones 1 and 2 to WT. Right: Subtraction of the RNA synthesis rate for Msl2-KO clones 1 and 2 from WT. The first two columns refer to changes observed for allele 1 and the last columns for allele 2. The rows are ordered based on the categories as illustrated in Fig. 1d. Scales show Z score normalized log2[FC]. (b) Overall changes in chromatin features at downregulated genes scored by allelic DE analysis in male CaBl/BlCa and female 9sCa Msl2-WT and KO NPCs separated by allele 1 (left) and allele 2 (right). Numbers of allelic DE genes per cell line are indicated. Bar plots summarize the number of ATAC-seq and histone modification ChIP-seq peaks showing either decreased (purple) or increased signal (yellow) in Msl2-KO versus WT NPCs (see Methods). (c) ATAC-seq and histone modification ChIP-seq metagene profiles for genes of the bi-to-monoA2 category in female 9sCa WT (grey) and 2 Msl2-KO (KO1 and KO2; pink) NPC clones subdivided into three log2[FC] quantiles. Data is shown for allele 1 only. Log2[FC] of ChIP-seq levels (IP/Input) are depicted with shadows representing the standard error. (d-g) ATAC-seq and histone modification ChIP-seq metagene profiles (TSS +/− 2 kb) for bi-to-monoA1 genes in male BlCa (d) and female 9sCa NPCs (e) and bi-to-monoA2 genes in CaBl (f) and female 9sca NPCs (g). Signals are displayed for allele1 (top), allele2 (middle) and the signal obtained from standard (non-allele-specific) analysis (bottom). Log2[FC] of ChIP-seq levels (IP/Input) are depicted with shadows representing the standard error. (h) RNA-seq, ATAC-seq and H3K27me3/H4K36me3 ChIP-seq tracks for the bi-to-monoA2 genes Mecp2 (left) and Zfp607a (right) in female 9sCa WT and Msl2-KO NPCs. Log2[FC] ChIP-seq levels (IP/Input) are shown. (i-k) ATAC-seq and histone modification ChIP-seq metagene profiles for bi-to-bi-down genes in male CaBl (i), BlCa (j) and female 9sCa (k) WT and Msl2-KO NPCs. Signals are displayed for allele 1 (top), allele 2 (middle) and the signal obtained from standard (non-allele-specific) analysis (bottom). Log2[FC] of ChIP-seq levels (IP/Input) are depicted with shadows representing the standard error.
