bulk cut t ag (EpiCypher)

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(A) Top, illustration of the part of the brain used for all experiments, labeled “non-visual brain”. Bottom, number of biological replicates of brains profiled using RNA-seq, Micro-C, ATAC-seq, <t>or</t> <t>CUT&Tag</t> for H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3, H3K27me3, H2AK119ub, or for IgG control. (B) Micro-C contact maps for the whole-genome scale (left) and for portions of scaffold 15 ( Hsal 9.0) at increasing resolutions (res). The matrices are shown as KR-normalized, balanced contact frequencies. (C) Size in millions of base pairs for the longest 25 scaffolds (red colors) in comparison to all other scaffolds (white) in assembly version v1.0 , v8.6 , and v9.0 (this study). (D) Number of scaffolds in assembly version v1.0 , v8.6 , and v9.0 (current version). (E) ATAC, H3K27ac, H3K4me1, and H3K27me3 signal at enhancers (center ± 5 kb). Enhancers were classified into active, bivalent, primed, and poised based on their accessibility and histone marks in worker brains. The y axis represents raw counts per million (CPM) for ATAC, or scaled, IgG-normalized CPM (for CUT&Tag, see methods). (F) Comparison of assignments of enhancers to target genes using Micro-C and with proximity assignment method. Numbers of active, bivalent, primed, and poised enhancers (as defined by their chromatin state in worker brains) for which gene target assignment using Micro-C and proximity coincided (“match with proximal”), matched to multiple promoters including the proximal promoter, or matched to distal promoters. The number of biological replicates for all analyses is shown in panel (A).

Bulk Cut T Ag, supplied by EpiCypher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Journal: bioRxiv

Article Title: Socially regulated genes are spatially hyperconnected to enhancers in the ant brain

doi: 10.64898/2026.04.08.717219

Figure Lengend Snippet: (A) Top, illustration of the part of the brain used for all experiments, labeled “non-visual brain”. Bottom, number of biological replicates of brains profiled using RNA-seq, Micro-C, ATAC-seq, or CUT&Tag for H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3, H3K27me3, H2AK119ub, or for IgG control. (B) Micro-C contact maps for the whole-genome scale (left) and for portions of scaffold 15 ( Hsal 9.0) at increasing resolutions (res). The matrices are shown as KR-normalized, balanced contact frequencies. (C) Size in millions of base pairs for the longest 25 scaffolds (red colors) in comparison to all other scaffolds (white) in assembly version v1.0 , v8.6 , and v9.0 (this study). (D) Number of scaffolds in assembly version v1.0 , v8.6 , and v9.0 (current version). (E) ATAC, H3K27ac, H3K4me1, and H3K27me3 signal at enhancers (center ± 5 kb). Enhancers were classified into active, bivalent, primed, and poised based on their accessibility and histone marks in worker brains. The y axis represents raw counts per million (CPM) for ATAC, or scaled, IgG-normalized CPM (for CUT&Tag, see methods). (F) Comparison of assignments of enhancers to target genes using Micro-C and with proximity assignment method. Numbers of active, bivalent, primed, and poised enhancers (as defined by their chromatin state in worker brains) for which gene target assignment using Micro-C and proximity coincided (“match with proximal”), matched to multiple promoters including the proximal promoter, or matched to distal promoters. The number of biological replicates for all analyses is shown in panel (A).

Article Snippet: Antibodies used for bulk CUT&Tag were as listed and diluted according to manufacturer’s recommendations: H3K27me3 (rabbit, Epicypher, 13-0055), H3K27me3 rabbit, Cell Signaling, C36B11), H3K4me3 (rabbit, Epicypher, 13-0041), H3K4me3 (rabbit, Abcam, ab213224), H3K4me1 (rabbit, Abcam, ab8895), H3K27ac (rabbit, Abcam, ab4729), H3K9me3 (rabbit, Abcam, ab8898), H2AK119ub1, (rabbit, Cell Signaling, D27C4), H3K36me3, (rabbit, Abcam, Ab9050), Rabbit IgG (secondary antibody, guinea pig, antibodies-online, ABIN101961), IgG (negative control, rabbit, Epicypher, 13-0042).

Techniques: Labeling, RNA Sequencing, Control, Comparison

(A) Micro-C and chromatin enrichment across a 1 Mb region on scaffold 49. Chromatin interactions are visualized as balanced, Knight-Ruiz (KR)-normalized contact frequencies. TAD boundaries at different resolutions were identified by insulation score. RNA-seq, ATAC-seq and CUT&Tag signal for H3K4me3, H3K27ac, H3K4me1, H3K27me3 are shown in CPM along with annotated genes. (B) Percentage of TAD boundaries overlapping with promoter (± 1 kb from the TSS), exonic, intronic, and intergenic regions. (C) ATAC-seq (CPM) and CUT&Tag signal (H3K4me3, H3K27ac, H3K4me1, H3K27me3, H2AK119ub, and H3K9me3, normalized with scaled IgG) enrichment at all TAD boundaries. (D) Motif enrichment at TAD boundaries overlapping with promoter, genic, or intergenic regions in Harpegnathos or Drosophila , identified by SEA-based analysis using shuffled sequences preserving dinucleotide frequencies as the background.

Journal: bioRxiv

Article Title: Socially regulated genes are spatially hyperconnected to enhancers in the ant brain

doi: 10.64898/2026.04.08.717219

Figure Lengend Snippet: (A) Micro-C and chromatin enrichment across a 1 Mb region on scaffold 49. Chromatin interactions are visualized as balanced, Knight-Ruiz (KR)-normalized contact frequencies. TAD boundaries at different resolutions were identified by insulation score. RNA-seq, ATAC-seq and CUT&Tag signal for H3K4me3, H3K27ac, H3K4me1, H3K27me3 are shown in CPM along with annotated genes. (B) Percentage of TAD boundaries overlapping with promoter (± 1 kb from the TSS), exonic, intronic, and intergenic regions. (C) ATAC-seq (CPM) and CUT&Tag signal (H3K4me3, H3K27ac, H3K4me1, H3K27me3, H2AK119ub, and H3K9me3, normalized with scaled IgG) enrichment at all TAD boundaries. (D) Motif enrichment at TAD boundaries overlapping with promoter, genic, or intergenic regions in Harpegnathos or Drosophila , identified by SEA-based analysis using shuffled sequences preserving dinucleotide frequencies as the background.

Techniques: Insulation, RNA Sequencing, Preserving

(A) K-means clustering of 4,608 TADs into 6 classes, annotated based on their chromatin enrichment. Each row represents a TAD. (B) Percentage of the genome covered by each TAD class. (C) Size distribution of each TAD class. (D) Percentage of chromatin loops classified as promoter–promoter (P–P), enhancer–promoter (E–P), promoter–gene body (P–GB), enhancer–gene body (E–GB), gene body–gene body (GB–GB), or “undefined”, indicating that at least one of the two anchors maps to an intergenic region devoid of enhancers. (E) Distribution of anchor distance in kb for each class of chromatin loop. (F) Motif enrichment at all loop anchors against a shuffled background (left column), at all promoters with loops against promoters without loops (middle column), or promoters with loops and marked by H3K4me3 against promoters with loops but devoid of H3K4me3 (right column). Preferential tissue expression is indicated on the left (see also Fig. S5C). (G) Distribution of genome-wide normalized interaction frequency against distance. Red dots show identified meta-loops; light and dark gray curves show 1st–99th or 25th–75th percentile ranges of all contact pairs, respectively; black line shows the median. (H) An example meta-domain formed by two TADs comprising Eip98C (horizontal) and Eip78C (vertical) connected by three meta-loops, anchored at sites indicated by red blocks at the margins of the interaction matrix. The Micro-C contact frequencies, KR-normalized and balanced are shown in the center matrix; insulation score, ATAC-seq, and CUT&Tag signal for H3K4me3, H3K27me3, H3K27ac are plotted along the margins for the two loci.

Journal: bioRxiv

Article Title: Socially regulated genes are spatially hyperconnected to enhancers in the ant brain

doi: 10.64898/2026.04.08.717219

Figure Lengend Snippet: (A) K-means clustering of 4,608 TADs into 6 classes, annotated based on their chromatin enrichment. Each row represents a TAD. (B) Percentage of the genome covered by each TAD class. (C) Size distribution of each TAD class. (D) Percentage of chromatin loops classified as promoter–promoter (P–P), enhancer–promoter (E–P), promoter–gene body (P–GB), enhancer–gene body (E–GB), gene body–gene body (GB–GB), or “undefined”, indicating that at least one of the two anchors maps to an intergenic region devoid of enhancers. (E) Distribution of anchor distance in kb for each class of chromatin loop. (F) Motif enrichment at all loop anchors against a shuffled background (left column), at all promoters with loops against promoters without loops (middle column), or promoters with loops and marked by H3K4me3 against promoters with loops but devoid of H3K4me3 (right column). Preferential tissue expression is indicated on the left (see also Fig. S5C). (G) Distribution of genome-wide normalized interaction frequency against distance. Red dots show identified meta-loops; light and dark gray curves show 1st–99th or 25th–75th percentile ranges of all contact pairs, respectively; black line shows the median. (H) An example meta-domain formed by two TADs comprising Eip98C (horizontal) and Eip78C (vertical) connected by three meta-loops, anchored at sites indicated by red blocks at the margins of the interaction matrix. The Micro-C contact frequencies, KR-normalized and balanced are shown in the center matrix; insulation score, ATAC-seq, and CUT&Tag signal for H3K4me3, H3K27me3, H3K27ac are plotted along the margins for the two loci.

Techniques: Expressing, Genome Wide, Insulation

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