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Series GSE115633 Query DataSets for GSE115633
Status Public on Aug 14, 2018
Title Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells [Hi-C]
Organism Homo sapiens
Experiment type Other
Summary Background. Mammalian cells are flexible and can rapidly change shape when they contract, adhere, or migrate. Their 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 constricted space, where the nuclear shape must change in order to fit through. This happens many times in the life cycle of a neutrophil, which must protect its chromatin from damage and disruption associated with migration.

Results. Total RNA-sequencing identified that neutrophil migration 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 cytoskeleton remodelling. Hi-C was used to capture the genome organisation in control and migrated cells. Chromatin did not switch between the active (A) and inactive (B) compartments after migration. However, global depletion of mid- to long-range contacts was observed following active migration through the 5 µm pores. Chromatin contacts that decreased in frequency were enriched in inactive chromatin.

Conclusion. Mid- to long-range contacts are preferentially lost within inactive chromatin, thus 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 human health and disease.
 
Overall design Hi-C sequencing of neutrophil-like cells migrated through large (14µm) or small (5µm) pores, with an unmigrated control population.
 
Contributor(s) Jacobson EC, O'Sullivan JM
Citation(s) 30477489
doi: https://0-doi-org.brum.beds.ac.uk/10.1101/339085
Submission date Jun 11, 2018
Last update date Mar 20, 2019
Contact name Justin M. O'Sullivan
E-mail(s) justin.osullivan@auckland.ac.nz
Organization name University of Auckland
Department Liggins Institute
Street address 85 Park Road, Grafton
City Auckland
ZIP/Postal code 1023
Country New Zealand
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (9)
GSM3185669 ctrl_1_HiC
GSM3185670 ctrl_2_HiC
GSM3185671 ctrl_3_HiC
This SubSeries is part of SuperSeries:
GSE115634 RNA-seq and Hi-C sequencing of neutrophil-like cells migrated through large or small pores
Relations
BioProject PRJNA475595
SRA SRP150259

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE115633_100kb_14mig.PC1.bed.gz 367.6 Kb (ftp)(http) BED
GSE115633_100kb_5mig_ds.PC1.bed.gz 367.6 Kb (ftp)(http) BED
GSE115633_100kb_ctrlmig_ds.PC1.bed.gz 367.4 Kb (ftp)(http) BED
GSE115633_14mig.binSignal.txt.gz 1.0 Mb (ftp)(http) TXT
GSE115633_14mig_domains.txt.gz 38.3 Kb (ftp)(http) TXT
GSE115633_14mig_v_5mig_100_40_ds_ints.txt.gz 3.8 Mb (ftp)(http) TXT
GSE115633_14migv_ctrl_100_40_ints.txt.gz 24.1 Mb (ftp)(http) TXT
GSE115633_5mig_ds.binSignal.txt.gz 1.0 Mb (ftp)(http) TXT
GSE115633_5mig_ds_domains.txt.gz 35.9 Kb (ftp)(http) TXT
GSE115633_5mig_v_14mig_100_40_ds_ints.txt.gz 3.1 Mb (ftp)(http) TXT
GSE115633_5migv_ctrl_100_40_ints.txt.gz 28.1 Mb (ftp)(http) TXT
GSE115633_ctrl_v_14mig_100_40_ints.txt.gz 36.7 Mb (ftp)(http) TXT
GSE115633_ctrl_v_5mig_100_40_ints.txt.gz 37.4 Mb (ftp)(http) TXT
GSE115633_ctrlmig_ds.binSignal.txt.gz 1.0 Mb (ftp)(http) TXT
GSE115633_ctrlmig_ds_domains.txt.gz 37.9 Kb (ftp)(http) TXT
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Processed data are available on Series record

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