Journal: bioRxiv

Article Title: Mega-frequency mutagenesis: generation of non-random precise mutations with extremely high frequency upon adaptation of cancer cells to drugs and stress

doi: 10.64898/2026.02.20.707073

Figure Lengend Snippet: Development of recurrent mutations after drug treatments. A. The number of mutations in three parallel subclones following development of resistance to Dox. The number of mutations common to all three subclones (red), common to two out of three subclones (green) and mutations unique for each subclone (blue). B. A scheme showing that generation of mutations common between clones cannot occur during the propagation of the parental clone. See explanation in the text. C.Example of the lack of enrichment of mutations in open chromatin. Open chromatin assessed by ATACseq is shown in the lane with blue peaks, positions of mutations are shown in the lane with red bars. Data analysis in this experiment is shown in Table S2. C. Overlap of mutations between GDR and Lorlatinib. D. Overlap of mutations between osimertinib and Doxorubicin. E. Overlap of mutations between two independent lorlatinib-treated samples and one crizotinib-treated sample. F. Computer simulation of random generation of osimertinib-induced mutations. Observed number of common mutations is shown as red line. Random sampling of mutations and their overlap (100,000 pairs) is shown as blue lines. G. Overlap of mutations between osimertinib day 21 (0SM-3T) and osimertinib subclone 1 samples (OSM-1CL). H. Overlap of mutations between osimertinib day 21 (0SM-3T) and osimertinib mutations common between three subclones (OSM-TRPL).

Article Snippet: Samples for ATAC sequencing (ATACseq) were prepared using Zymo-Seq ATAC Library Kit (Cat#D5458) following the manufacturer protocol.

Techniques: Clone Assay, Sampling

Journal: bioRxiv

Article Title: Histone H3K9 Methyltransferases Regulate Cortical Growth by Coordinating Heterochromatin Formation and Neural Progenitor Dynamics

doi: 10.64898/2026.01.23.701405

Figure Lengend Snippet: (A) IDR analysis of H3K9me3 ChIP-seq peaks in E14.5 control cortices comparing two replicates. Black dots indicate 51,053 reproducible peaks, and red dots represent non-reproducible peaks. (B) IDR analysis of H3K9me3 ChIP-seq peaks in two TKO replicates. Only 1,200 reproducible peaks were detected, consistent with H3K9me3 depletion in the TKO cortex. (C) Differential accessibility analysis in E14.5 control versus TKO cortices. The MA plot highlights 455 ATAC-seq peaks with increased accessibility and 117 peaks with decreased accessibility in TKO cortices (FDR < 0.05). (D) Genomic annotation of peaks with increased accessibility in TKO cortices shows enrichment in intergenic and intronic sequences. (E) Differential enrichment of H3K27ac ChIP-seq signals between E14.5 control and TKO cortices. A total of 168 regions showed increased H3K27ac, whereas 63 regions showed decreased H3K27ac in TKO cortices (FDR < 0.05). (F) Most regions with increased H3K27ac in TKO cortices were localized to promoters.

Article Snippet: ATAC-seq libraries were generated using the Zymo-Seq ATAC Library Kit (Zymo, D5458) according to the manufacturer’s instructions.

Techniques: ChIP-sequencing, Control

Journal: bioRxiv

Article Title: Histone H3K9 Methyltransferases Regulate Cortical Growth by Coordinating Heterochromatin Formation and Neural Progenitor Dynamics

doi: 10.64898/2026.01.23.701405

Figure Lengend Snippet: (A) Heatmaps showing H3K9me3-enriched genomic regions in E14.5 control cortices and their depletion in TKO cortices. (B) Pie chart depicting the genomic distribution of H3K9me3 in E14.5 cortical cells, with the majority of signal localized to intergenic and intronic regions. (C) DNA motif enrichment analysis within H3K9me3 ChIP-seq peaks from E14.5 control cortex. The top six enriched TF motifs are shown. (D) Heatmaps displaying H3K27ac, H3K9me3, and ATAC-seq signals in E14.5 control cortex. H3K9me3 predominantly decorated genomic regions characterized by low H3K27ac and low chromatin accessibility. (E) Heatmaps of ATAC-seq, H3K27ac, and H3K9me3 signals at a subset of chromatin regions in E14.5 control (Ctl) and TKO cortices. Regions that gained accessibility in TKO cortices were marked by H3K9me3 in controls, and some acquired moderate levels of H3K27ac. Regions that lost accessibility in TKO cortices were not associated with H3K9me3 loss. (F) Heatmaps showing ATAC-seq signal at E17.5 over chromatin regions that gained or lost accessibility at E14.5, as defined in (E). Regions that increased accessibility at E14.5 remained open at E17.5 in the TKO cortex.

Article Snippet: ATAC-seq libraries were generated using the Zymo-Seq ATAC Library Kit (Zymo, D5458) according to the manufacturer’s instructions.

Techniques: Control, ChIP-sequencing

Journal: bioRxiv

Article Title: Histone H3K9 Methyltransferases Regulate Cortical Growth by Coordinating Heterochromatin Formation and Neural Progenitor Dynamics

doi: 10.64898/2026.01.23.701405

Figure Lengend Snippet: (A) Fraction of repeat element classes marked by H3K9me3 in the E14.5 control cortex that gained chromatin accessibility in the TKO cortex. (B) Bulk RNA-seq analysis revealed activation of repeat elements in the TKO cortex. The heatmap shows color-coded classification of dysregulated repeat element (RE) families (see main text for details). (C) Schematic illustrating TE activation and its association with upregulation of proximal genes in the TKO cortex. (D) BETA analysis demonstrated a significant association between TE activation and upregulation of proximal genes, whereas no significant association was observed for downregulated genes. The plot displays p-values and cumulative fractions of upregulated and downregulated genes relative to the background. (E) Genome browser tracks showing an H3K9me3-marked region upstream of Ccny that gained accessibility at E14.5 and E17.5 in the TKO cortex (dashed rectangle). This region contained a TE (IAPLTR2b), indicated by the arrow. RNA-seq tracks show concurrent upregulation of both IAPLTR2b and Ccny in the TKO cortex. (F) Genome browser tracks showing loss of H3K9me3 and increased accessibility within an intronic region of Pced1b (dashed rectangle). The arrow indicates the region with increased accessibility that partially overlapped with a simple repeat ([TCC]n) and a TE (SINE PB1D10) (Repeat Elements track). Loss of a broad H3K9me3 domain within the Pced1b intronic sequences was accompanied by robust transcriptional activation (RNA-seq tracks) of several TEs (Repeat Elements track) and Pced1b in the TKO cortex. (G) DNA motif enrichment analysis of loci that lost H3K9me3 and gained accessibility in the TKO cortex. Motifs for several KLF regulators were significantly enriched within these regions. (H) ATAC-seq footprinting analysis using the regions with increased chromatin accessibility in the TKO cortex as input. Enhanced footprint depth (shown between dashed lines) was observed for KLF10 and KLF11, indicating increased TF occupancy upon chromatin decompaction. The number of loci exhibiting increased KLF10 and KLF11 footprints is indicated. The regions flanking the footprints showed globally increased accessibility in the TKO cortex.

Article Snippet: ATAC-seq libraries were generated using the Zymo-Seq ATAC Library Kit (Zymo, D5458) according to the manufacturer’s instructions.

Techniques: Control, RNA Sequencing, Activation Assay, Footprinting