Jan Soroczynski
@jsoro.bsky.social
At CTCF boundaries, walk polarity is asymmetric between flanking nucleosomes—biased toward the loop interior. Consistent with directional cohesin extrusion, resolved at nucleosome scale. CADwalks span sub-nucleosomal to chromosomal scales in a single assay.
15/
15/
January 21, 2026 at 7:32 PM
At CTCF boundaries, walk polarity is asymmetric between flanking nucleosomes—biased toward the loop interior. Consistent with directional cohesin extrusion, resolved at nucleosome scale. CADwalks span sub-nucleosomal to chromosomal scales in a single assay.
15/
15/
Analyzing fragment order in CADwalks, we find shuttling at long range – consecutive steps that venture out and back. Fragments making distal contacts are enriched for active regulatory chromatin. We also probe local fiber folding and nucleosomal footprints.
14/
14/
January 21, 2026 at 7:32 PM
Analyzing fragment order in CADwalks, we find shuttling at long range – consecutive steps that venture out and back. Fragments making distal contacts are enriched for active regulatory chromatin. We also probe local fiber folding and nucleosomal footprints.
14/
14/
This unlocks CADwalks: consecutive ligations between nucleosomal and sub-nucleosomal fragments, sequenced as intact concatemers. Each walk from a single nucleus. Reduced base-composition bias, no end repair.
13/
13/
January 21, 2026 at 7:32 PM
This unlocks CADwalks: consecutive ligations between nucleosomal and sub-nucleosomal fragments, sequenced as intact concatemers. Each walk from a single nucleus. Reduced base-composition bias, no end repair.
13/
13/
Because CAD-cleaved ends are natively ligatable, we can skip end repair and biotin entirely. Direct CAD-C does this and still yields high-quality maps. Native CAD ends ligate directly to each other.
12/
12/
January 21, 2026 at 7:32 PM
Because CAD-cleaved ends are natively ligatable, we can skip end repair and biotin entirely. Direct CAD-C does this and still yields high-quality maps. Native CAD ends ligate directly to each other.
12/
12/
We call this ligation-gating. Capturing a loop requires both anchors in proximity AND both ligatable at once. CAD's ligation-competent ends raise this joint probability –consistent with both the loop sensitivity and the short-range enrichment. See Supplementary Note.
11/
11/
January 21, 2026 at 7:32 PM
We call this ligation-gating. Capturing a loop requires both anchors in proximity AND both ligatable at once. CAD's ligation-competent ends raise this joint probability –consistent with both the loop sensitivity and the short-range enrichment. See Supplementary Note.
11/
11/
But here's the puzzle: 1D ligation-junction coverage at loop anchors looks nearly identical between CAD-C and Micro-C. So why more loops? It's not about cutting more at accessible sites. It's about both anchors being simultaneously ligatable in the same cross-linked complex.
10/
10/
January 21, 2026 at 7:32 PM
But here's the puzzle: 1D ligation-junction coverage at loop anchors looks nearly identical between CAD-C and Micro-C. So why more loops? It's not about cutting more at accessible sites. It's about both anchors being simultaneously ligatable in the same cross-linked complex.
10/
10/
CAD-C recapitulates compartments, TADs, & loops – w/ same or improved contrast. CAD-C-detected loops skew toward active chromatin; we see more TSS-anchored loops than Micro-C or Hi-C. CAD-C detects promoter loops to CRISPRi-validated enhancers that Micro-C misses at matched depth.
9/
9/
January 21, 2026 at 7:32 PM
CAD-C recapitulates compartments, TADs, & loops – w/ same or improved contrast. CAD-C-detected loops skew toward active chromatin; we see more TSS-anchored loops than Micro-C or Hi-C. CAD-C detects promoter loops to CRISPRi-validated enhancers that Micro-C misses at matched depth.
9/
9/
We tested CAD-C in three human cell lines at saturating CAD concentrations. All worked on first try. Ligation efficiency was high, producing long concatemers.
8/
8/
January 21, 2026 at 7:32 PM
We tested CAD-C in three human cell lines at saturating CAD concentrations. All worked on first try. Ligation efficiency was high, producing long concatemers.
8/
8/
We optimized the CAD:ICAD construct for purification from E. coli and orthogonal activation by TEV protease. Result: consistent genome coverage across a 125-fold CAD concentration range.
7/
7/
January 21, 2026 at 7:32 PM
We optimized the CAD:ICAD construct for purification from E. coli and orthogonal activation by TEV protease. Result: consistent genome coverage across a 125-fold CAD concentration range.
7/
7/
Enter CAD (DFF40), a metazoan apoptotic nuclease. It has what we needed: reduced base-composition bias vs MNase, strict endonuclease (no chew-back), and ligation-ready ends (blunt 5'-P/3'-OH). CAD is naturally held inactive by its chaperone-inhibitor ICAD.
6/
6/
January 21, 2026 at 7:32 PM
Enter CAD (DFF40), a metazoan apoptotic nuclease. It has what we needed: reduced base-composition bias vs MNase, strict endonuclease (no chew-back), and ligation-ready ends (blunt 5'-P/3'-OH). CAD is naturally held inactive by its chaperone-inhibitor ICAD.
6/
6/