Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins

Stephens, Andrew D.; Liu, Patrick Z.; Banigan, Edward J.; Almassalha, Luay M.; Backman, Vadim; Adam, Stephen A.; Goldman, Robert D.; Marko, John F.

doi:10.1091/mbc.e17-06-0410

Cited by 274 publications

(433 citation statements)

References 61 publications

(146 reference statements)

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“…Our results show that the nuclei of Bottom-5 cells deform more than Top-5 cells when embedded in a collagen matrix or even when spontaneously migrating on a 2D surface. Previous research has shown that nucleus stiffness can be altered by increasing or decreasing the overall expression of Lamin A/C or by changing overall levels of heterochromatin (Lammerding et al, 2006, Stephens et al, 2017, Stephens et al, 2018. But, the apparent change in nucleus pliability observed in the current study cannot be explained by changes in overall Lamin A/C content or heterochromatin levels: Lamin A/C and H3K9me3 levels were constant as measured by both immunostaining and western blot.…”

Section: Discussioncontrasting

confidence: 73%

“…Genes within less-accessible heterochromatin tend to be inactive while those localized to more accessible euchromatin tend to be active or poised for quick transcriptional activation (Gaspar-Maia et al, 2011, van Steensel andBelmont, 2017). Chromatin state has also been shown to influence nuclear physical properties: increased levels of heterochromatin increase nuclear stiffness while increased euchromatin levels decrease stiffness and increase nuclear deformability (Stephens et al, 2017, Stephens et al, 2018. Such global changes in chromatin state can also influence confined migration; for example, increasing euchromatin or decreasing heterochromatin inhibits mouse melanoma cell migration (Gerlitz and Bustin, 2010).…”

Section: Introductionmentioning

confidence: 99%

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

Golloshi

Freeman

Das

et al. 2019

Preprint

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To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation and DNA repair, here we investigate how confined migration affects or is affected by 3D genome structure. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone 10 rounds of constricted migration. These cells display a stable increase in migration efficiency, elongated morphology, and an abnormal distribution of Lamin A/C and heterochromatin. Using Hi-C, we observe changes in chromosome spatial compartmentalization specific to constricted cells and related alterations in expression of genes associated with migration and metastasis. These cells also show increased nuclear deformations when cultured in a 3D collagen matrix and altered behavior when co-cultured with fibroblasts in organoids. Our observations reveal a relationship between chromosome structure changes, metastatic gene signatures, and the abnormal nuclear appearance of aggressive melanoma.

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Section: Discussioncontrasting

confidence: 73%

Section: Introductionmentioning

confidence: 99%

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

Golloshi

Freeman

Das

et al. 2019

Preprint

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“…To test their relative contribution for the nuclear asymmetry, we analyzed Dynein distribution on the NE following depletion of Lamin A by RNAi or 315 after treatment with ICRF-193, a Topoisomerase II (TopoII) inhibitor, or Valproic acid (VPA), a histone deacetylase inhibitor (HDAC). Treatment with either TopoII or HDAC inhibitors should interfere with chromatin structure, decreasing overall nuclear stiffness [35]. Interestingly, inhibition of either TopoII or HDACs induced a loss of Dynein specifically on the NE (Fig.…”

Section: Chromatin Condensation Is Required For Centrosome Positioningmentioning

confidence: 95%

“…Radial displacement maps were produced as the radial shift of each point in the membrane with respect to the reference (median) membrane contour. Nuclear irregularity index was calculated as described previously [35].…”

Section: Quantitative Analysis Of Centrosomes Cell Membrane and Nuclmentioning

confidence: 99%

Mechanosensitive nuclear asymmetries define a bipolar spindle scaffold to ensure mitotic fidelity

Nunes¹,

Dantas²,

Castro³

et al. 2019

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Results: 55 Centrosomes position on the shortest nuclear axis at nuclear envelope breakdownTo characterize mitotic spindle assembly at high spatiotemporal resolution, we performed 4D imaging in HeLa cells. We observed that when cells are seeded on a substrate that does not activate integrin signaling (poly-L-lysine; PLL), centrosomes separate independently of NEB ( Fig. S1A), as reported previously [2, 25]. However, 60 when seeded on integrin-activating fibronectin (FBN), ~82% of the cells separate their centrosomes to opposite sides of the nucleus before NEB. Moreover, cells that have an increased spreading area at NEB show longer inter-centrosome distances ( Fig. S1B), suggesting that centrosome separation prior to NEB is a function of the adhesion area.To normalize cell area and shape in 2D, we seeded cells on defined FBN micropatterns 65 and monitored centrosome dynamics, cell membrane and nuclear shape ( Fig. 1A), which were subsequently reconstructed using specifically developed computational algorithms ( Fig. S2). Centrosome dynamics relative to the micropattern was defined by two angles theta and phi, reflecting movements in xy (azimuth) and xz (inclination), respectively (Fig. 1B). These vary between 0 o (aligned with the long axis of the pattern) and 90 o 70 (perpendicular to the pattern). We anticipated that separated centrosomes should align with the long axis of the micropattern, due to the distribution of retraction fibers imposed by extracellular matrix organization [17,20]. However, during mitotic entry, centrosomes deviated from the underlying micropattern, as observed by the high variability of theta and phi (Fig. 1B). This was accompanied by a rotation of the nucleus relative to the long 75 axis of the pattern, as well as a decrease in cell area (Fig. 1C). Due to the shape asymmetry of the line micropattern, we could calculate cell membrane eccentricity, which varies between 1 (completely elongated cell) and 0 (spherical cell). As cell progressed towards NEB, membrane eccentricity decrease (Fig. 1D) due to a retraction of the long cell axis (Fig. 1E, 0 o ) and a simultaneous increase in cell width, perpendicularly to the 80 pattern ( Fig. 1E, F; 90 o ; *** p<0.001). Interestingly, during the rounding process, the

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“…At the cellular level, the accumulation of progerin induces progressive alterations of nuclear shape and cellular senescence 27 . Notably, inhibition of PcG functions can trigger "nuclear blebbing", an alteration of the nuclear shape typically observed in Lamin A deficient cells 28 , suggesting that chromatin architecture and nuclear shape strictly depend on each other. Consistently, LADs organization and PcG-dependent H3K27me3 mark are altered in HGPS 29,30 .…”

mentioning

confidence: 99%

Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis

Sebestyén

Marullo

Lucini

et al. 2019

Preprint

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Hutchinson-Gilford progeria syndrome (HGPS) is characterized by the progressive accumulation of progerin, an aberrant form of Lamin A. This leads to chromatin structure disruption, in particular by interfering with Lamina Associated Domains. Although several cellular and molecular alterations have been characterized, it is still unclear how chromatin structural changes translate into premature senescence in HGPS. Moreover, early events in chromatin remodeling have not been detected so far. We developed a new high-throughput sequencing-based method, named SAMMY-seq, for genome-wide characterization of heterochromatin accessibility changes. Using SAMMY-seq, we detected early stage alterations of chromatin structure in HGPS primary fibroblasts. Of note, these structural changes do not disrupt the distribution of H3K9me3 but are associated with site-specific H3K27me3 variations and transcriptional dysregulation of Polycomb target genes. Our results show that SAMMY-seq represents a novel and sensitive tool to characterize heterochromatin alterations. Moreover, we found that the assembly of lamin associated domains is strictly connected to the correct Polycomb repression, rapidly lost in early HGPS pathogenesis.

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Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins

Cited by 274 publications

References 61 publications

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

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

Mechanosensitive nuclear asymmetries define a bipolar spindle scaffold to ensure mitotic fidelity

Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis

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