Nuclear pore protein TPR associates with lamin B1 and affects nuclear lamina organization and nuclear pore distribution

Fišerová, Jindřiška; Maninová, Miloslava; Sieger, Tomáš; Uhlířová, Jana; Šebestová, Lenka; Efenberková, Michaela; Čapek, Martin; Fišer, Karel; Hozák, Pavel

doi:10.1007/s00018-019-03037-0

Cited by 18 publications

(17 citation statements)

References 52 publications

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“…6 G). In contrast, and consistent with our HCA, Cbx2 −/− fibroblasts exhibit a significant reduction in both the size and density of Lamin B1 filaments as detected by a Skeleton algorithm specifically designed for quantitative analysis of segmented, binary images of nuclear lamina filaments (Fišerová et al, 2019), confirming the presence of significantly shorter (P < 0.01) Lamin B1 branches (skeletons) in Cbx2 −/− nuclei (Fig. 6 G).…”

Section: B)supporting

confidence: 86%

“…To test whether premature senescence in Cbx2 −/− cells is also associated with abnormal structure and function of the nuclear lamina, we used high content confocal microscopy in conjunction with SR-SIM to quantify and structurally analyze Lamin B1 expression (Fišerová et al, 2019). HCA revealed a significant reduction (P < 0.001) in Lamin B1 fluorescence intensity in Cbx2 −/− nuclei compared with wild-type controls (Fig.…”

Section: B)mentioning

confidence: 99%

“…Data were analyzed using MetaXpress software (Molecular Devices, LLC) following detection of nuclei using DAPI fluorescence and measurement of nuclear surface areas and mean fluorescence intensity using the 488-nm filter. Skeleton analysis was conducted using the Skeletonize3D plugin of ImageJ software (National Institutes of Health) to perform skeletonization of binary images (8-bit) of Lamin B1 immunofluorescence staining as previously described (Fišerová et al, 2019). Briefly, following tagging of all pixels in a skeleton image, all junctions, triple and quadruple points, and branches were counted, and the mean branch length was measured.…”

Section: Integrative Analysismentioning

confidence: 99%

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Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements

Baumann

Zhang

Fuente

2020

Journal of Cell Biology

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The polycomb group protein CBX2 is an important epigenetic reader involved in cell proliferation and differentiation. While CBX2 overexpression occurs in a wide range of human tumors, targeted deletion results in homeotic transformation, proliferative defects, and premature senescence. However, its cellular function(s) and whether it plays a role in maintenance of genome stability remain to be determined. Here, we demonstrate that loss of CBX2 in mouse fibroblasts induces abnormal large-scale chromatin structure and chromosome instability. Integrative transcriptome analysis and ATAC-seq revealed a significant dysregulation of transcripts involved in DNA repair, chromocenter formation, and tumorigenesis in addition to changes in chromatin accessibility of genes involved in lateral sclerosis, basal transcription factors, and folate metabolism. Notably, Cbx2−/− cells exhibit prominent decondensation of satellite DNA sequences at metaphase and increased sister chromatid recombination events leading to rampant chromosome instability. The presence of extensive centromere and telomere defects suggests a prominent role for CBX2 in heterochromatin homeostasis and the regulation of nuclear architecture.

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Section: B)supporting

confidence: 86%

Section: B)mentioning

confidence: 99%

Section: Integrative Analysismentioning

confidence: 99%

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Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements

Baumann

Zhang

Fuente

2020

Journal of Cell Biology

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“…TPR is a nucleoporin located in the nuclear basket structure of the NPC and could act as a negative regulator of NPC number (McCloskey et al, 2018). In contrast two other studies found that siRNA reduction of TPR reduced NPC number (Funasaka et al, 2012; Fišerová et al, 2019). In our experiments, we also observed a small, but statistically significant increase in NPC numbers after TPR knockdown in WT cells.…”

Section: Discussioncontrasting

confidence: 60%

Computational analysis of lamin isoform interactions with nuclear pore complexes

Kittisopikul

Shimi

Tatli

et al. 2020

Preprint

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Nuclear lamin isoforms assemble into fibrous meshworks within the nuclear lamina 16 (NL) where they are associated with nuclear pore complexes (NPCs). Although the lamins and 17NPCs are major components of the nuclear envelope (NE), little is known about their structural 18 relationships. We used 3D structured illumination microscopy (3D-SIM) and sub-pixel image 19 analysis to show that NPCs are closely associated with lamin fibers in mouse embryonic 20 fibroblasts (MEFs). When lamin A/C (LA/C) or lamin B1 (LB1) are removed by gene knockout, the 21 NPCs retained their association and redistributed with the resulting enlarged lamin meshworks. 22 Cryo-ET revealed that more LA/C than LB1 fibers contacted the nucleoplasmic ring of NPCs. 23 Knockdown of the outer ring nucleoporin ELYS induced NPC clusters that excluded LA/C fibers. 24 Knockdown of the basket nucleoporin TPR reduced the size of LA/C, LB1, and LB2 meshworks 25 while retaining their close association with NPCs. NUP153 knockdown reduced LA/C and B2 26 meshwork size in wild type (WT) MEFs and caused NPC clustering in nuclei lacking LB1. Therefore, 27 lamins and nucleoporins act together to maintain the organization and distribution of lamin 28 meshworks and NPCs. 29 30 teins, the nuclear lamins, and nuclear pore complexes (NPCs) (Aebi et al., 1986; Fisher et al., 1986; 33 Goldman et al., 1986; McKeon et al., 1986). The four lamin isoforms LA, LC, LB1, and LB2 are mainly 34 associated with the inner nuclear membrane where they assemble into discrete meshworks of 35 fibers composing the nuclear lamina (NL). The NPCs penetrate the NE forming transport passage-36 ways delineated by the fusion of the inner and outer nuclear membranes, thereby allowing for 37 bidirectional transport across the NE. They are composed of multiple copies of 30 proteins known 38 1 of 27Manuscript to be submitted to eLife as nucleoporins (Beck and Hurt, 2016). Both the nuclear lamins and NPC structures are closely 39 associated with chromatin at the nuclear periphery (Guelen et al., 2008; Peric-Hupkes et al., 2010; 40 Ibarra and Hetzer, 2015). 41 The lamins are classified as A-type (LA, LC) and B-type (LB1, LB2). LA and LC are derived from 42 the Lmna gene by alternative splicing (Lin and Worman, 1993), whereas LB1 and LB2 are encoded 43 81 ity of the four lamin fiber meshworks and NPCs located within a thin layer at the nuclear surface. 82The results of our analyses demonstrate that NPCs are closely associated with lamin fibers. At 83 higher resolution cryo-ET confirms that both LA/C and LB1 filaments interact closely with the NPCs 84 at the nucleoplasmic ring. Targeted disruption of nucleoporins and lamin isoforms demonstrates 85 the interdependence of the spatial distributions of lamin fibers and NPCs. 86 2 of 27 Manuscript to be submitted to eLife WT WT Lmnb1 -/-Lmna -/-LA LB1 LB1 LA LB2 LC NPC NPC NPC NPC NPC NPC A B Figure 1. Co-Distribution of Lamin Fibers and NPCs. Colabeling of lamins and nuclear pore complexes in wt and lamin KO MEF nuclei using indire...

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“…The TPR depletion was more prominent in MTs, where the TPR FI reached ~10% (shTPR1) or 40% (shTPR2) at NP and only ~10% (shTPR1) or 30% (shTPR2) in nucleoplasm compared to WT MTs ( Figure 1 a,e–g). The overall nuclear pore density was, however, not affected by TPR depletion ( Figure S1e ), in accordance with the published data [ 41 ]. In conclusion, our data suggest that in TPR-depleted cells, the number of TPR molecules per NPC is reduced rather than total number of NPCs.…”

Section: Resultssupporting

confidence: 92%

Nucleoporin TPR Affects C2C12 Myogenic Differentiation via Regulation of Myh4 Expression

Uhlířová

Šebestová

Fišer

et al. 2021

Cells

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The nuclear pore complex (NPC) has emerged as a hub for the transcriptional regulation of a subset of genes, and this type of regulation plays an important role during differentiation. Nucleoporin TPR forms the nuclear basket of the NPC and is crucial for the enrichment of open chromatin around NPCs. TPR has been implicated in the regulation of transcription; however, the role of TPR in gene expression and cell differentiation has not been described. Here we show that depletion of TPR results in an aberrant morphology of murine proliferating C2C12 myoblasts (MBs) and differentiated C2C12 myotubes (MTs). The ChIP-Seq data revealed that TPR binds to genes linked to muscle formation and function, such as myosin heavy chain (Myh4), myocyte enhancer factor 2C (Mef2C) and a majority of olfactory receptor (Olfr) genes. We further show that TPR, possibly via lysine-specific demethylase 1 (LSD1), promotes the expression of Myh4 and Olfr376, but not Mef2C. This provides a novel insight into the mechanism of myogenesis; however, more evidence is needed to fully elucidate the mechanism by which TPR affects specific myogenic genes.

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Nuclear pore protein TPR associates with lamin B1 and affects nuclear lamina organization and nuclear pore distribution

Cited by 18 publications

References 52 publications

Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements

Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements

Computational analysis of lamin isoform interactions with nuclear pore complexes

Nucleoporin TPR Affects C2C12 Myogenic Differentiation via Regulation of Myh4 Expression

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