Journal: Nature Communications

Article Title: Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

doi: 10.1038/s41467-023-35911-8

Figure Lengend Snippet: Detection of structural variants using liCHi-C data for B-cell precursor acute lymphoblastic leukemia (B-ALL) sample 3 generated using a six-cutter restriction enzyme (HindIII) ( A ) and a four-cutter restriction enzyme (MboI) ( B ). Gray matrices represent the ratio between B-ALL and CLP contact matrices at 1 Mb resolution across the genome. Black arrows indicate the location of copy number losses. C Absolute frequency of interaction according to the genomic distance between interacting regions for liCHi-C libraries generated with MboI (blue) and HindIII (green) digestion, respectively. The median and highest absolute frequency of interactions are represented by solid and dashed lines, respectively. D DDX41 gene promoter-centered interaction landscape (arcs) generated with HindIII (top) and MboI (bottom), respectively. Green shade depicts the DDX41 gene promoter, while yellow shades depict putative enhancer regions for it. Arrows symbolize gene placement and orientation along the genomic window.

Article Snippet: After incubation at 37 °C and 950 rpm for 30 min, 37.5 µl 10% Triton X-100 (AppliChem cat. #A4975,0100) were laid on the wall of the tube, mixed by inversion and incubated at 37 °C and 950 rpm for 30 min. Chromatin within the nuclei was overnight digested at 37 °C and 950 rpm after adding 7.5 µl of HindIII restriction enzyme at 100U/µl or 37.5 µl of MboI restriction enzyme at 25U/µl (New England Biolabs cat. #R0104T or #R0147M).

Techniques: Generated