Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells

Abstract

BackgroundMammalian cells are flexible and can rapidly change shape when they contract, adhere, or migrate. The nucleus must be stiff enough to withstand cytoskeletal forces, but flexible enough to remodel as the cell changes shape. This is particularly important for cells migrating through confined spaces, where the nuclear shape must change in order to fit through a constriction. This occurs many times in the life cycle of a neutrophil, which must protect its chromatin from damage and disruption associated with migration. Here we characterized the effects of constricted migration in neutrophil-like cells.ResultsTotal RNA sequencing identified that migration of neutrophil-like cells through 5- or 14-μm pores was associated with changes in the transcript levels of inflammation and chemotaxis-related genes when compared to unmigrated cells. Differentially expressed transcripts specific to migration with constriction were enriched for groups of genes associated with cytoskeletal remodeling.Hi-C was used to capture the genome organization in control and migrated cells. Limited switching was observed between the active (A) and inactive (B) compartments after migration. However, global depletion of short-range contacts was observed following migration with constriction compared to migration without constriction. Regions with disrupted contacts, TADs, and compartments were enriched for inactive chromatin.ConclusionShort-range genome organization is preferentially altered in inactive chromatin, possibly protecting transcriptionally active contacts from the disruptive effects of migration with constriction. This is consistent with current hypotheses implicating heterochromatin as the mechanoresponsive form of chromatin. Further investigation concerning the contribution of heterochromatin to stiffness, flexibility, and protection of nuclear function will be important for understanding cell migration in relation to human health and disease.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0608-2) contains supplementary material, which is available to authorized users.

Constricted migration is associated with stable 3D genome structure differences in cancer cell

“…Bottom-5 cells exhibit a loss in the strongest B-B interactions and an overall increase in interactions between the strongest B and strongest A compartments. This phenomenon has been previously reported in neutrophils after passage through small pores, suggesting it may be a general feature of confined migration genomic structural changes (Jacobson et al, 2018). This change in interaction frequency correlates with changes in gene expression.…”

“…This suggests that confined migration itself can induce some of the changes we observe. As passage through a constriction physically moves the chromosomal regions in the nucleus, certain interactions, such as the strongest B-B interactions in our data, may be pulled apart as suggested by chromatin stretching previously described (Irianto et al, 2017b) and loss of B-B interaction strength with confined migration observed in neutrophils (Jacobson et al, 2018). Meanwhile, loci previously more distant are given an opportunity to associate and may form new aggregates through phase separation.…”

“…Previous work has shown that 3D chromosome organization changes correlate with the progression of cancer (Taberlay et al, 2016, Barutcu et al, 2015 and that both the formation and downstream effect of chromosomal translocations in cancer progression is influenced by 3D genome structure (Zhang et al, 2012, Hnisz et al, 2016. In addition, some changes have been noted in the 3D genome structures of neutrophils that have undergone constricted migration (Jacobson et al, 2018). Taken together, previous evidence suggests that chromosome structure may influence a cancer cell's ability to undergo confined migration, that changes in chromosome structure could be caused by nuclear deformation, and that such chromosome structure changes could influence gene regulation and cancer cell phenotype.…”

TNF-α differentially regulates cell cycle genes in promyelocytic and granulocytic HL-60/S4 cells

“…In order to investigate transcriptional responses to TNF-α, the promyelocytic cell line HL-60/S4 was differentiated into a granulocytic form by treatment with ATRA for 96 hours, as described previously [36]. Both undifferentiated (promyelocytic) and differentiated (granulocytic) cells were treated with 16ng/mL TNF-α in calcium supplemented media for two hours.…”

“…As required, cells were differentiated into a granulocytic phenotype with 1 µM all trans retinoic acid (ATRA) dissolved in ethanol (Sigma Aldrich) for four days as previously described ( [30,36,72]). Cells were centrifuged (200xg, 5 min, room temp.)…”