Journal: bioRxiv

Article Title: Sox8 and Sox9 regulate differentiation and nuclear positioning of retinal Müller glia

doi: 10.64898/2026.01.12.698638

Figure Lengend Snippet: (A) Schematic of the CUT&RUN experimental pipeline. (B) Overlap of P2 Sox8/9 peaks and P2 RPC DARs. (C) GO enrichment of P2 Sox8/9 peaks and P2 RPC DARs. (D) Distribution of Sox8/9 binding loci in distinct gene regions at P2 and P17 compared to H3K27ac and H3K4me3 controls . (E) Distribution of Sox8/9 binding loci relative to transcription start site (TSS) at P2 and P17 compared to H3K27ac and H3K4me3 controls . (F) Number of Sox8/9 CUT&RUN peaks that overlap with enriched/differentially accessible regions in either P2 RPCs, P17 Control MGs, or P17 Sox8/9 cKO MGs. (G) Percentage of Sox8/9 CUT&RUN peaks that overlap with enriched/differentially accessible regions in either P2 RPCs or P17 Control MGs. (H) GO enrichment of overlapping Sox8/9 DKO DEG, DAR, and P17 Sox8/9 peaks.

Article Snippet: Cold CUT&RUN wash buffer was prepared according to manufacturer’s guidance (EpiCypher, 14-1048) and was used as substitute for the final nuclei wash and resuspension.

Techniques: Binding Assay, Control

Journal: bioRxiv

Article Title: HIF-1α coordinates adrenal steroidogenesis through direct transcriptional control and regulation of miRNA biogenesis

doi: 10.64898/2026.02.24.707817

Figure Lengend Snippet: A) Schematic representation of the CUT&Tag protocol. Under standard culture conditions (21% O□), Y-1 cells express undetectable levels of HIF-1α protein. For the CUT&Tag procedure, the cells were either left untreated as a control or treated with DMOG for 24 hours to stabilize HIF-1α. This treatment leads to nuclear accumulation of HIF-1α and its binding to target genes. The nuclei were then isolated, lightly fixed with formaldehyde, and bound to concanavalin A-coated beads. The HIF-1α-bound chromatin regions were labeled on the beads using a primary anti-HIF-1α antibody, a secondary antibody, and protein A-Tn5 adapters. The tagged DNA fragments were then released, PCR-amplified, and subjected to Illumina next-generation sequencing. B) The genomic distribution of enriched (left) and depleted (right) HIF-1α-bound sequences in DMOG-treated versus control cells (see also Additional file 2). C) Top 15 KEGG pathways enriched among HIF-1α-bound genes. Bar length indicates the pathway enrichment ratio, and colors represent FDR (see also Additional file 3). D) Motif enrichment analysis of HIF-1α-bound sequences revealed conserved binding motifs for HIF-1/2α and 30 additional transcription factors (p < 0.01, Benjamini < 0.1) that are grouped into six major families (see Additional file 4).

Article Snippet: The beads were then washed with 0.5 ml of CUT&Tag wash buffer and the pA-Tn5 adapter complex (Epicypher, #15-1117) in 300 wash buffer (20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor EDTA-Free tablets; Merck, #11836170001) was added at 1:20.

Techniques: Control, Binding Assay, Isolation, Labeling, Amplification, Next-Generation Sequencing

Journal: bioRxiv

Article Title: HIF-1α coordinates adrenal steroidogenesis through direct transcriptional control and regulation of miRNA biogenesis

doi: 10.64898/2026.02.24.707817

Figure Lengend Snippet:

Article Snippet: The beads were then washed with 0.5 ml of CUT&Tag wash buffer and the pA-Tn5 adapter complex (Epicypher, #15-1117) in 300 wash buffer (20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor EDTA-Free tablets; Merck, #11836170001) was added at 1:20.

Techniques:

Journal: bioRxiv

Article Title: HIF-1α coordinates adrenal steroidogenesis through direct transcriptional control and regulation of miRNA biogenesis

doi: 10.64898/2026.02.24.707817

Figure Lengend Snippet: A) Schematic depiction of the miRNA processing pathway. The pathway components identified in the HIF-1α CUT&Tag assay are depicted with protein names highlighted in red. Among the genes bound by HIF-1α are both members of the nuclear microprocessor complex ( Drosha and Dgcr8 ) as well as a number of RISC components ( Ago1-4 , Snd1 , Mtdh , Tarbp1 and Tnrc6a/b ). B) Identified miRNA biogenesis and function genes with the assigned location of the putative HIF-1α binding region and a number of canonical HIF-1α binding sites detected within each region.

Article Snippet: The beads were then washed with 0.5 ml of CUT&Tag wash buffer and the pA-Tn5 adapter complex (Epicypher, #15-1117) in 300 wash buffer (20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor EDTA-Free tablets; Merck, #11836170001) was added at 1:20.

Techniques: Binding Assay

Journal: STAR Protocols

Article Title: Protocol to study the genomic profile of histone lactylation with CUT&RUN assay in tumor-associated macrophages

doi: 10.1016/j.xpro.2025.103766

Figure Lengend Snippet: Wash buffer

Article Snippet: 10X Wash Buffer (Cell Signaling #31415) , 10 μL.

Techniques: Protease Inhibitor

Journal: STAR Protocols

Article Title: Protocol to study the genomic profile of histone lactylation with CUT&RUN assay in tumor-associated macrophages

doi: 10.1016/j.xpro.2025.103766

Figure Lengend Snippet: Digitonin buffer

Article Snippet: 10X Wash Buffer (Cell Signaling #31415) , 10 μL.

Techniques: Protease Inhibitor