Bird protections frustrate Duxbury beachgoers at every tern - The Boston Globe

Duxbury is among the places in Massachusetts battling over beach access, as restrictions to protect nesting shorebirds have worked, and created more restrictions.

bostonglobe.com

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

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...

cell.com

2026 STAT Madness

2026 bracket Welcome to STAT Madness, a bracket-style contest to find the best innovation in science and medicine. Explore groundbreaking innovations from

direc.to

Seeing into Hi-C: How our scientific connectivity revealed the close connections in our DNA to be a work of art

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

pubs.aip.org

CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cells

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

doi.org

biorxiv.org

4D Nucleome Consortium produces detailed models of the 3D genome over time in cells

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.

direc.to

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm

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...

rdcu.be

Unexpected allies: DNA packaging aids gene expression | Cornell Chronicle

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.

bit.ly

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - 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 the cytoplasm.

nature.com

An integrated view of the structure and function of the human 4D nucleome - Nature

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...

nature.com

Escape from X inactivation is directly modulated by Xist noncoding RNA

Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...

rdcu.be

Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 via LINE1 regulatory elements - EMBO Reports

Mouse embryonic stem cells (mESCs), in addition to differentiating into the three germ layers, can reverse typical developmental trajectories, as exemplified by their ability to de-differentiate into ...

link.springer.com