Migration Through A Small Pore Disrupts Inactive Chromatin Organization In Neutrophil-Like Cells

Authors

Elsie C. Jacobson
Jo K. Perry
David S. Long
Ada L. Olins, University of New EnglandFollow
Donald E. Olins, University of New EnglandFollow
Bryon E. Wright
Mark H. Vickers
Justin M. O'Sullivan

Document Type

Article

Publication Date

11-26-2018

Abstract

Background: Mammalian 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. Results: Total 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. Conclusion: Short-range genome organization is preferentially altered in inactive chromatin, possibly protecting

Comments

Originally published:
Jacobson, E. C., Perry, J. K., Long, D. S., Olins, A. L., Olins, D. E., Wright, B. E., . . . Justin, M. O. (2018). Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells. BMC Biology, 16 doi:http://dx.doi.org.une.idm.oclc.org/10.1186/s12915-018-0608-2

Copyright © 2018 The Authors. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”).

Supplementary file descriptions:
Supplementary file 1:
Figures S1–S6. 1. HL60 cells differentiated into neutrophil-like cells and migrated through two pore sizes. 2. SEM of porous membranes. 3. RNA-seq summary plots, and comparison of migration with differentiation. 4. Topological domain changes after migration through two pore sizes. 5. Compartment status of increased frequency contacts between migration with and without constriction. 6. Genome-wide distribution of disrupted contacts, compartments, and TADs. (PDF 3721 kb)
Originally available: https://static-content.springer.com/esm/art%3A10.1186%2Fs12915-018-0608-2/MediaObjects/12915_2018_608_MOESM1_ESM.pdf

Supplementary file 2:
Table S1. Significantly differentially expressed genes. All genes with significantly differential gene expression (FDR < 0.05) between either 5-μm pores compared to control, 14-μm pores compared to control, or 5-μm pores compared to 14-μm pores. Sets refer to those described on page 4 (Transcriptional changes after migration and remodeling are distinct). HUGO gene names, Ensembl gene names and IDs are provided as identifiers. Columns suffixed with ‘_5’ represent results from 5-μm pore compared to control. Columns suffixed with ‘_14’ represent results from 14-μm pore compared to control. Columns suffixed with ‘_5v14’ represent results from 5-μm pore compared to 14-μm pore. The ‘padj’ shows the FDR adjusted p value. (XLSX 258 kb)
Originally available: https://static-content.springer.com/esm/art%3A10.1186%2Fs12915-018-0608-2/MediaObjects/12915_2018_608_MOESM2_ESM.xlsx

Supplementary file 3:
Table S2-S5, S7-S9. 2. Gene ontology enrichment (Biological process) of Fig. 2b. 3. Gene ontology enrichment (Biological process) of Fig. 2c. 4. Gene ontology enrichment (Biological process) of Fig. 2d. 5. Gene ontology enrichment (Molecular function) of Fig. 2d. 7. RNA-seq QC. 8. HiCUP QC. 9. Hi-C replicate correlations. (DOCX 40 kb)
Originally available: https://static-content.springer.com/esm/art%3A10.1186%2Fs12915-018-0608-2/MediaObjects/12915_2018_608_MOESM3_ESM.docx

Supplementary file 4:
Table S6. PC1 values and correlation between the interaction patterns of 100-kb bins. Each 100-kb bin has both a PC1 value indicating compartment status, and an interaction pattern with every other bin in the chromosome. When bins have a low correlation (R < 0.6) and an opposite PC1 value, this is considered a disruption to the compartment status of this region. Calculated using the runHiCpca.pl and getHiCcorrDiff.pl scripts in HOMER. Regions with missing values, and chromosomes with PC1 values indicating chromosome arm, are excluded from this table. (XLSX 2741 kb)
Originally available: https://static-content.springer.com/esm/art%3A10.1186%2Fs12915-018-0608-2/MediaObjects/12915_2018_608_MOESM4_ESM.xlsx

Recommended Citation

Jacobson, Elsie C.; Perry, Jo K.; Long, David S.; Olins, Ada L.; Olins, Donald E.; Wright, Bryon E.; Vickers, Mark H.; and O'Sullivan, Justin M., "Migration Through A Small Pore Disrupts Inactive Chromatin Organization In Neutrophil-Like Cells" (2018). Pharmaceutical Sciences Faculty Publications. 15.
https://dune.une.edu/pharmsci_facpubs/15