The Nucleus’ Secret to Shapeshifting

Whether at the start of a sinus infection or a fresh open wound, neutrophils are the first line of defense in an immune attack.¹ In order to rush to the scene to kill infectious microbes, they have a time-saving trick up their sleeves. They transfigure their nuclei into a variety of shapes, including an eye-catching, poly-segmented kind, which allow them to swiftly squeeze through tight spaces between cells en route to the infected site.² However, researchers were unsure what factors drive this nuclear metamorphosis. 

Reporting in Nature, scientists induced nuclei to change shape, matching the morphologies cells take on to slip through tight gaps in tissues.³ They found that depleting a key cellular protein implicated in chromatin modification facilitated nuclear shapeshifting. Their findings add one piece to the puzzle of how neutrophil nuclei adopt their bizarre figures.

Neutrophils derive from precursor cells that have normal spherical nuclei. Cornelis Murre, a molecular biologist at the University of California, San Diego and study coauthor, sought out the factors responsible for this shift in nuclear morphology.

Murre and his colleagues hypothesized that proteins controlling the folding and packaging of DNA in the nucleus might also influence the overall architecture of the organelle. When they compared protein expression between neutrophils and their progenitors, one protein caught their attention: loop-extrusion loading factor nipped-B-like protein (NIPBL). This factor, which scientists previously found regulates chromatin organization, dropped in abundance as progenitors transformed into neutrophils, suggesting nuclear remodeling might kick off in its absence.⁴

To determine if the reduction in NIPBL levels underpinned the shift in structure, Murre and his colleagues depleted NIPBL by triggering its breakdown in progenitor cells. “In three days, they became neutrophils,” Murre said. Their nuclei transformed into a flurry of shapes, including a poly-segmented form that closely resembled those observed in control neutrophils. “They are not random morphologies. They mimic what happens in the bone marrow,” Murre added.

With a molecular switch for nuclear shapeshifting in hand, the research team explored how NIPBL controls the organelle’s shape. Previously, other researchers showed that this protein folds DNA into loops, like a shoelace not yet tied into a knot.⁴ Murre hypothesized that when neutrophil precursors drop their NIPBL levels, large changes in DNA looping ensue, potentially triggering a cascade of events that warps the nucleus’ shape.

To explore the extent to which NIPBL’s loss affects the abundance of DNA loops, they mapped out these loops in precursor cells using a technique called high-throughput chromosome conformation capture (Hi-C) before and after NIPBL depletion.⁵ Chromatin segments found at loop junctions are in such close proximity that they can become chemically fused together during Hi-C. By sequencing the fused segments, Murre and his team pinpointed where loops formed in the genome.

When the team depleted NIPBL in precursor cells, 9,000 loops at specific locations in the genome disappeared, and 4,000 new loops formed at other sites, revealing that NIPBL’s absence precipitated widescale changes in chromatin organization. 

Although they detected thousands of loops influenced by NIPBL, Ming Hu, a computational biologist at the Cleveland Clinic and study coauthor, thinks that some fell under the radar. “Hi-C has limited sensitivity to capture long-range loops, so we’re exploring other experimental technologies to try to increase the sensitivity,” he said. 

The study offers a glimpse into how neutrophil nuclei adopt their bizarre shapes, but the researchers still need to piece together how a reduction in NIPBL triggers the process, including what role the DNA loops might play.

“This [study] will open further investigations into the importance of three-dimensional chromatin organization in driving cellular functions and fate,” said Jan Lammerding, a biomedical engineer at Cornell University who was not involved with the work.

One hypothesis is that the DNA loops could determine which genes are switched on in the cell. Inside a nucleus, chromosomes jumble together like a game of Twister. This can bring regulatory elements, such as enhancers, from one chromosome into contact with genes from another chromosome, creating complex gene-regulatory networks.⁶ Large scale changes to DNA loops might rewire these networks, switching on genes that distort the nucleus’ shape. Alternatively, NIPBL could trigger the metamorphosis independent of its role in orchestrating DNA looping via some other pathway. 

Neutrophils aren’t unique for their bizarre nuclei, and Murre said that these findings could pave the way for research into how other innate immune cells, like basophils, eosinophils, and mast cells, transfigure their nuclei.⁷

References

1. Burn GL, et al. The neutrophil. Immunity. 2021;54(7):1377-1391.
2. Rowat AC, et al. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. JBC. 2013;288(12):8610-8618.
3. Patta I, et al. Nuclear morphology is shaped by loop-extrusion programs. Nature. 2024;627(8002):196-203.
4. Alonso-Gil D, Losada A. NIPBL and cohesin: new take on a classic tale. Trends Cell Biol. 2023;33(10):860-871.
5. Hauth A, et al. Deciphering high-resolution 3D chromatin organization via capture Hi-C. JoVE. 2022;(188):64166.
6. McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet. 2021;108(2):269-283.
7. Rigoni A, et al. Mast cells, basophils and eosinophils: From allergy to cancer. Semin Immunol. 2018;35:29-34.