Journal: bioRxiv

Article Title: Fasting primes small intestinal regeneration after damage via a microbiome–metabolite-chromatin axis

doi: 10.64898/2026.03.06.710208

Figure Lengend Snippet: a. Schematic of whole-crypt isolation for CUT&Tag and bulk RNA seq analyses. b. Enrichment plot for H3K27ac peaks in Fed (-Tetra), Fed(+Tetra), Fast (-Tetra) and Fast (+Tetra). c. Upset plots showing overlap of CUT&Tag seq H3K27ac peaks among FED (-Tetra), Fed (+Tetra), Fast (-Tetra) and Fast (+Tetra). The CUT&Tag seq peaks unique to Fast (-Tetra) were analyzed separately. d. Top 10 MSigDB GSEA pathways based on H3K27ac proximal promoter peaks overlapping with publicily available HiChIP and inhouse ChIP seq data in Fast (-Tetra) condition. e. Genome browser view of CUT&Tag tracks for H3K27ac-enriched regions in SI crypts at the p53 pathway-responsive genes Vdr, Fos and Nupr1 under FAST (-Tetra) conditions. f. ChIP-qPCR analysis of H3K27ac enrichment at Vdr, Fos , and Nupr1 -specific peaks in Fed (-Tetra), Fed (+Tetra), Fast (-Tetra) and Fast (+Tetra) samples. g. Motif enrichment analysis for enhancers unique to Fast (-Tetra) group using HOMER.

Article Snippet: CUT&Tag assays were conducted using the CUTANA CUT&Tag kit (EpiCypher) according to manufacturer’s instructions.

Techniques: Isolation, RNA Sequencing, HiChIP, ChIP-sequencing, ChIP-qPCR

Journal: bioRxiv

Article Title: Fasting primes small intestinal regeneration after damage via a microbiome–metabolite-chromatin axis

doi: 10.64898/2026.03.06.710208

Figure Lengend Snippet: a. Experimental design. Mice were fed ad libitum or fasted for 24 h, followed by total abdominal irradiation (11.5 Gy). Small intestinal crypt cells were collected at 0 h, 24 hpi, 48 hpi, or 72 hpi (post-irradiation) and subjected to single-cell ATAC sequencing (scATAC-seq). b. UMAP projection of aggregated scATAC-seq data colored by sample, showing condition-specific shifts in chromatin accessibility. c. UMAP colored by cluster identity, identifying major intestinal epithelial populations. d. Bubble plot showing chromatin accessibility of stem and revival marker loci (Clu, Olfm4) across conditions. Cluster 6 corresponds to the Clu+Olfm4+ persister stem cell population. e. Bubble plot showing chromatin accessibility (log2FC) of stem cell, revival, and injury-associated gene loci in Cluster 3 (C3) and Cluster 6 (C6). f. Percentage of Clu+Olfm4+ cells (Cluster 6) across all samples, demonstrating increased representation during fasting. g. Integration of CUT&Tag H3K27ac data with RNA-seq for the activated genes in Fed (-Tetra), Fed (+Tetra), Fast (-Tetra) and Fast (+Tetra) samples. All genes displayed are differentially expressed (p ≤ 0.05, log2FC ≥ 2 or ≤ –2). n = 2 mice per group. h. Bar graph showing the number of shared accessible regions between scATAC-seq and H3K27ac CUT&Tag datasets. “Common” refers to overlapping enhancer-like peaks. i. HOMER motif enrichment analysis showing -log10 p-values for transcription factor motifs associated with intestinal progenitor identity and injury response (IR) protection, alongside their corresponding gene expression levels from bulk RNA-seq in fed and fasted conditions and at 0-, 24-, 48-, and 72-hours post irradiation (hpi). j. Graphical representation of data shown in panel i for fed and 24 fasted mice. Y axis represents binned -log10 p-values of transcription factor motif activity. k. Graphical representation of data show in panel i for fed and fasted mice. mice at 0-, 24-, 48-, and 72-hours post irradiation (hpi). Y axis represents binned -log10 p-values of transcription factor motif activity.

Article Snippet: CUT&Tag assays were conducted using the CUTANA CUT&Tag kit (EpiCypher) according to manufacturer’s instructions.

Techniques: Irradiation, Single Cell, Sequencing, Marker, RNA Sequencing, Gene Expression, Activity Assay

Journal: bioRxiv

Article Title: Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type

doi: 10.64898/2026.02.26.708296

Figure Lengend Snippet: a , Schematic for experiment design. Heart resection injuries were performed in tcf21:nucEGFP; ptx3a:mScartlet animals. Ventricles were collected at 3 dpa together with those of uninjured siblings (Ctrl). Ventricles were dissociated, and EGFP + or EGFP + mScarlet + epicardial cells were isolated by FACS for the CUT&TAG assay. b , A browser track of the genomic region comprising gene scxa showing the transcripts, chromatin accessibility profiles, and CUT&TAG marks of H3K4me1 in the epicardium across replicates from Ctrl, 3 dpa, and 7 dpa samples. The whole-ventricle H3K27Ac profile of the uninjured (Ctrl) and regenerating (Reg) hearts is shown. Gray boxes indicate putative enhancer regions with increased accessibility and enhancer markers during regeneration. c , Putative HIF1A binding sites in the 4 enhancer (Enh) regions shown in (b). d , Whole-mount images showing scxa :mCherry expressions without (Ctrl, left) or with PHZ treatment (middle). The framed region is enlarged to show detail on the top right with the coronary vessel marker fli1a :EGFP shown in red in the overlayed image (bottom right). Scale bar, 100 μm. e , Quantification of ventricular coverage of scxa :mCherry signals as shown in (d). Student’s t -test. f , Whole-mount images showing scxa :mCherry expressions without (Ctrl, left) or with PHZ treatment (right). The framed region is enlarged to show detail on the bottom right Scale bar, 100 μm. g , Quantification of ventricular coverage of scxa :mCherry signals as shown in (f). Student’s t -test. h, Whole-mount images showing scxa :mCherry expressions with vehicle (Ctrl, left) or DMOG (right) treatment at 8 wpf after a 2-week treatment. The framed regions are enlarged in the bottom right for details. Scale bar, 100 mm. i, Quantification of ventricular coverage of scxa :mCherry signals at 8 wpf. Student’s t -test.

Article Snippet: Nuclei preparation and CUT&TAG library preparation using rabbit anti-H3K4me1 antibody (Abcam, ab8895) were performed using the EpiCypher CUTANATM CUT&Tag Kit following the manual.

Techniques: Isolation, Binding Assay, Marker