Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative mechanistic basis for the gene...

Scientific data can be beautiful. An example where the data itself have a particularly striking appearance even before any scientific meaning has been ascribed

Chromosome conformation capture (3C)-derived methods have become an indispensable tool in the study of gene regulation. The three-dimensional contacts they are able to assay depend strongly on the properties of the enzyme used to fragment chromatin prior to proximity-driven ligation. Micrococcal nuclease (MNase), used in Micro-C, increases resolution at the expense of low ligation efficiency and the need for extensive enzyme titration. To overcome these limitations, we engineered a highly active, TEV protease-activatable caspase-activated DNase (CAD) to enable an efficient, low-sequence-bias, and high-resolution proximity ligation assay we call CAD-C. CAD-C was successful on the first attempt for each human cell line tested and the resulting datasets capture loops, TADs, compartments, and stripes similarly to Micro-C. However, compared to Micro-C and Hi-C, CAD-C shows enhanced sensitivity for promoter-enhancer loops. Leveraging the ligation-competent DNA ends produced by CAD cleavage, we show that CAD-C is compatible with a highly streamlined, repair-free protocol and produces multi-step CADwalks, consecutive ligations between nucleosomal or sub-nucleosomal fragments. With these walks, we probe local chromatin fiber folding contacts, nucleosomal and sub-nucleosomal footprints, and long-range nuclear organization regimes in human cell lines. CAD-C is an efficient, robust chromatin structure assay that can span sub-nucleosomal to chromosomal length scales in a single experiment. ### Competing Interest Statement V.I.R. and J.S. are inventors on a related patent application covering CAD-C (PCT application filed 2024). NIH Common Fund, https://ror.org/001d55x84, 1DP2GM150021 Irma T. Hirschl Trust, https://ror.org/01yaqvf46, Career Scientist Award Rita Allen Foundation, https://ror.org/0515k5w36, Scholar Award Stavros Niarchos Foundation, https://ror.org/0210rze73, Institute for Global Infectious Disease Research at Rockefeller University Grant Robertson Technology Development Fund at Rockefeller University Boehringer Ingelheim (Germany), https://ror.org/00q32j219, PhD Fellowship to JS U.S. National Science Foundation, https://ror.org/021nxhr62, GRFP to LAW International Human Frontier Science Program Organization, https://ror.org/02ebx7v45, Postdoctoral Cross-Disciplinary Fellowship to AO Natural Sciences and Engineering Research Council of Canada, Postgraduate fellowship to HC, Postgraduate fellowship to JLY

The 4D Nucleome Consortium has extensively mapped and analyzed the 3-D folding of the human genome in human embryonic stem cells and immortalized fibroblasts over time.

Nature Cell Biology - Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through...

Researchers discovered that DNA packaging structures called nucleosomes, which have been traditionally seen as roadblocks for gene expression, actually help reduce torsional stress in DNA strands and facilitate genetic information decoding.

Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.

The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...

We have investigated changes in chromosome conformation, nuclear organization, and transcription during differentiation and maturation of control and mutant motor neurons harboring hexanucleotide expa...

We used Hi-C, imaging, proteomics, and polymer modeling to define rules of engagement for SMC (structural maintenance of chromosomes) complexes as cells refold interphase chromatin into rod-shaped mit...

UMass Chan Medical School scientists detail simple rules for folding the genome during mitosis

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…

The dictum “Everything should be made as simple as possible, but no simpler” poses a problem for biology. How simply can it be told without doing damage to its complex nature? The answer might be foun...

A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields

The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and line...

Transcription factors (TFs) may activate or repress gene expression through an interplay of different mechanisms, including RNA polymerase (RNAP) recruitment, exclusion, and initiation. TFs often have...