scholarly journals The versatility of Ascorbate Peroxidase-aided mapping uncovers insights of the nuclear lamina interactions and function

2020 ◽  
Author(s):  
Joseph R. Tran ◽  
Danielle I. Paulson ◽  
James J. Moresco ◽  
Stephen A. Adam ◽  
John R. Yates ◽  
...  
Keyword(s):  
Protein Trafficking ◽  
Nuclear Lamina ◽  
Sequence Motif ◽  
Proximity Ligation ◽  
Lamin B1 ◽  
Histone Lysine ◽  
And Function ◽  
Systematic Identification ◽  
Rna And Dna

AbstractThe nuclear lamina (NL) is a proteinaceous network found beneath the inner nuclear membrane. The NL is linked to a number of dynamic cellular activities including chromatin organization, transcription and RNA/protein trafficking through nuclear pores. Our understanding of the NL has been hindered in part by the general insolubility and low extractability of proteins from this region. This has spurred the development of proximity ligation methods that label proteins and/or DNA near the NL for systematic identification (Bar et al., 2018; Chen et al., 2018b; Guelen et al., 2008; Roux et al., 2012). To simplify labeling and improve temporal resolution, we fused APEX2 (Hung et al., 2014; Lam et al., 2015) to the nuclear lamina protein lamin-B1 to map proteins, RNA and DNA associated with the NL. We show that APEX2 labeling of the NL is robust and requires as little as 20 seconds. In addition to identifying the NL proteome, this method revealed NL-proximal RNA species that were largely spliced. These NL-proximal RNAs show a bias toward long 3’ UTRs, suggesting an RNA-regulatory role of the NL. This is further supported by the finding of a bias toward longer 3’ UTRs in genes deregulated in lamin-null cells. Interestingly, these RNAs share a sequence motif in their 3’ UTRs. Finally, we demonstrate that the APEX2 method can reliably map lamina-associated domains (LADs) at different stages of the cell cycle, revealing a variability of short LADs regions enriched for histone lysine 27 trimethylation (H3K27me3). Thus the APEX2 method report here is a useful addition to the molecular toolbox for the study of the NL and permits the identification of proteome, transcriptome, and genome elements associated with this nuclear substructure.

scholarly journals An APEX2 proximity ligation method for mapping interactions with the nuclear lamina

2020 ◽  
Vol 220 (1) ◽  
Author(s):  
Joseph R. Tran ◽  
Danielle I. Paulson ◽  
James J. Moresco ◽  
Stephen A. Adam ◽  
John R. Yates ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Nuclear Membrane ◽  
Regulatory Protein ◽  
Nuclear Lamina ◽  
Inner Nuclear Membrane ◽  
Proximity Ligation ◽  
Lamin B1 ◽  
Ligation Method ◽  
Rna And Dna

The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3′ UTR bias, a finding consistent with an observed bias toward longer 3′ UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3′ UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.

Extracellular vesicle interplay in cardiovascular pathophysiology

2021 ◽  
Author(s):  
Sherin Saheera ◽  
Vivek P Jani ◽  
Kenneth W Witwer ◽  
Shelby Kutty
Keyword(s):  
Plasma Membrane ◽  
Cardiovascular System ◽  
Lipid Bilayer ◽  
Cellular Responses ◽  
Extracellular Vesicle ◽  
Cargo Proteins ◽  
And Function ◽  
Intercellular Communications ◽  
Rna And Dna

Extracellular vesicles (EVs) are nanosized lipid bilayer-delimited particles released from cells that mediate intercellular communications and play a pivotal role in various physiological and pathological processes. Subtypes of EVs may include plasma-membrane ectosomes or microvesicles and endosomal-origin exosomes, although functional distinctions remain unclear. EVs carry cargo proteins, nucleic acids (RNA and DNA), lipids, and metabolites. By presenting or transferring this cargo to recipient cells, EVs can trigger cellular responses. Here, we summarize what is known about EV biogenesis, composition, and function, with an emphasis on the role of EVs in cardiovascular system. Additionally, we provide an update on the function of EVs in cardiovascular pathophysiology, further highlighting their potential for diagnostic and therapeutic applications.

scholarly journals Lamin B1 and lamin B2 are long-lived proteins with distinct functions in retinal development

2016 ◽  
Vol 27 (12) ◽  
pp. 1928-1937 ◽  
Author(s):  
David Razafsky ◽  
Candace Ward ◽  
Chloe Potter ◽  
Wanqiu Zhu ◽  
Yunlu Xue ◽  
...  
Keyword(s):  
Nuclear Lamina ◽  
Building Blocks ◽  
Postnatal Life ◽  
Cone Photoreceptors ◽  
Obvious Effect ◽  
Lamin B1 ◽  
Embryonic Neurogenesis ◽  
And Function ◽  
Embryonic Retina ◽  
Rod And Cone Photoreceptors

Lamin B1 and lamin B2 are essential building blocks of the nuclear lamina, a filamentous meshwork lining the nucleoplasmic side of the inner nuclear membrane. Deficiencies in lamin B1 and lamin B2 impair neurodevelopment, but distinct functions for the two proteins in the development and homeostasis of the CNS have been elusive. Here we show that embryonic depletion of lamin B1 in retinal progenitors and postmitotic neurons affects nuclear integrity, leads to the collapse of the laminB2 meshwork, impairs neuronal survival, and markedly reduces the cellularity of adult retinas. In stark contrast, a deficiency of lamin B2 in the embryonic retina has no obvious effect on lamin B1 localization or nuclear integrity in embryonic retinas, suggesting that lamin B1, but not lamin B2, is strictly required for nucleokinesis during embryonic neurogenesis. However, the absence of lamin B2 prevents proper lamination of adult retinal neurons, impairs synaptogenesis, and reduces cone photoreceptor survival. We also show that lamin B1 and lamin B2 are extremely long-lived proteins in rod and cone photoreceptors. OF interest, a complete absence of both proteins during postnatal life has little or no effect on the survival and function of cone photoreceptors.

scholarly journals Concentration-dependent lamin assembly and its roles in the localization of other nuclear proteins

2014 ◽  
Vol 25 (8) ◽  
pp. 1287-1297 ◽  
Author(s):  
Yuxuan Guo ◽  
Youngjo Kim ◽  
Takeshi Shimi ◽  
Robert D. Goldman ◽  
Yixian Zheng
Keyword(s):  
Nuclear Lamina ◽  
Nuclear Pore ◽  
Lamin A ◽  
Nuclear Pore Complexes ◽  
Developmental Defects ◽  
Protein Levels ◽  
Lamin B1 ◽  
Mouse Cells ◽  
Pore Complexes ◽  
And Function

The nuclear lamina (NL) consists of lamin polymers and proteins that bind to the polymers. Disruption of NL proteins such as lamin and emerin leads to developmental defects and human diseases. However, the expression of multiple lamins, including lamin-A/C, lamin-B1, and lamin-B2, in mammals has made it difficult to study the assembly and function of the NL. Consequently, it has been unclear whether different lamins depend on one another for proper NL assembly and which NL functions are shared by all lamins or are specific to one lamin. Using mouse cells deleted of all or different combinations of lamins, we demonstrate that the assembly of each lamin into the NL depends primarily on the lamin concentration present in the nucleus. When expressed at sufficiently high levels, each lamin alone can assemble into an evenly organized NL, which is in turn sufficient to ensure the even distribution of the nuclear pore complexes. By contrast, only lamin-A can ensure the localization of emerin within the NL. Thus, when investigating the role of the NL in development and disease, it is critical to determine the protein levels of relevant lamins and the intricate shared or specific lamin functions in the tissue of interest.

scholarly journals Colocalization of intranuclear lamin foci with RNA splicing factors

1999 ◽  
Vol 112 (24) ◽  
pp. 4651-4661 ◽  
Author(s):  
G. Jagatheesan ◽  
S. Thanumalayan ◽  
B. Muralikrishna ◽  
N. Rangaraj ◽  
A.A. Karande ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Rna Splicing ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Splicing Factors ◽  
Lamin A ◽  
Lamin B1 ◽  
Differential Reactivity ◽  
Fibrous Network

The lamins form a fibrous network underlying the inner nuclear membrane termed the nuclear lamina. In order to gain insights into the role of lamins in nuclear organization, we have characterized a monoclonal antibody (LA-2H10) raised against recombinant rat lamin A that labels nuclei in a speckled pattern in all cells of unsynchronized populations of HeLa and rat F-111 fibroblast cells, unlike the typical nuclear periphery staining by another monoclonal antibody to lamin A, LA-2B3. In immunolocalization studies the lamin A speckles or foci were found to colocalize with the RNA splicing factors SC-35 and U5-116 kD, but not with p80 coilin found in coiled bodies. Lamin B1 was also associated with these foci. These foci dispersed when cells entered mitosis and reformed during anaphase. The differential reactivity of LA-2H10 and LA-2B3 was retained after nuclei were extracted with detergents, nucleases and salt to disrupt interactions of lamins with chromatin and other nuclear proteins. Using deletion fragments of recombinant lamin A, the epitope recognized by LA-2H10 was located between amino acids 171 and 246. Our findings are consistent with a structural role for lamins in supporting nuclear compartments containing proteins involved in RNA splicing.

scholarly journals Cell signaling pathways in autosomal-dominant leukodystrophy (ADLD): the intriguing role of the astrocytes

2020 ◽  
Author(s):  
Stefano Ratti ◽  
Isabella Rusciano ◽  
Sara Mongiorgi ◽  
Eric Owusu Obeng ◽  
Alessandra Cappellini ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Molecular Mechanisms ◽  
Autosomal Dominant ◽  
Neurodegenerative Disorder ◽  
Nuclear Lamina ◽  
Cellular Models ◽  
Lamin B1 ◽  
Nuclear Alterations ◽  
First Time

Abstract Autosomal-dominant leukodystrophy (ADLD) is a rare fatal neurodegenerative disorder with overexpression of the nuclear lamina component, Lamin B1 due to LMNB1 gene duplication or deletions upstream of the gene. The molecular mechanisms responsible for driving the onset and development of this pathology are not clear yet. Vacuolar demyelination seems to be one of the most significant histopathological observations of ADLD. Considering the role of oligodendrocytes, astrocytes, and leukemia inhibitory factor (LIF)-activated signaling pathways in the myelination processes, this work aims to analyze the specific alterations in different cell populations from patients with LMNB1 duplications and engineered cellular models overexpressing Lamin B1 protein. Our results point out, for the first time, that astrocytes may be pivotal in the evolution of the disease. Indeed, cells from ADLD patients and astrocytes overexpressing LMNB1 show severe ultrastructural nuclear alterations, not present in oligodendrocytes overexpressing LMNB1. Moreover, the accumulation of Lamin B1 in astrocytes induces a reduction in LIF and in LIF-Receptor (LIF-R) levels with a consequential decrease in LIF secretion. Therefore, in both our cellular models, Jak/Stat3 and PI3K/Akt axes, downstream of LIF/LIF-R, are downregulated. Significantly, the administration of exogenous LIF can partially reverse the toxic effects induced by Lamin B1 accumulation with differences between astrocytes and oligodendrocytes, highlighting that LMNB1 overexpression drastically affects astrocytic function reducing their fundamental support to oligodendrocytes in the myelination process. In addition, inflammation has also been investigated, showing an increased activation in ADLD patients’ cells.

scholarly journals The role of lamin B1 for the maintenance of nuclear structure and function

Nucleus ◽  
2015 ◽  
Vol 6 (1) ◽  
pp. 8-14 ◽  
Author(s):  
Jordi Camps ◽  
Michael R Erdos ◽  
Thomas Ried
Keyword(s):  
Nuclear Structure ◽  
Structure And Function ◽  
Lamin B1 ◽  
And Function

scholarly journals Cell type-specific role of lamin-B1 and its inflammation-driven reduction in organ building and aging

2018 ◽  
Author(s):  
Sibiao Yue ◽  
Xiaobin Zheng ◽  
Yixian Zheng
Keyword(s):  
Structural Proteins ◽  
Thymic Epithelial Cells ◽  
Cell Type ◽  
Organ Building ◽  
Lamin B1 ◽  
Architectural Proteins ◽  
Cell Type Specific ◽  
Developmental Role ◽  
And Function

SummaryCellular architectural proteins often participate in organ development and maintenance. Although functional decay of some of these proteins during aging is known, the cell-type specific developmental role and the cause and consequence of their subsequent decay remain to be established especially in mammals. By studying lamins, the nuclear structural proteins, we demonstrate that lamin-B1 functions specifically in the thymic epithelial cells (TECs) for proper thymus organogenesis. An upregulation of proinflammatory cytokines in the intra-thymic myeloid immune cells during aging accompanies a gradual reduction of adult TEC lamins-B1. These cytokines cause adult TEC senescence and lamin-B1 reduction. We identify 17 adult TEC subsets and show that TEC lamin-B1 maintains the composition of these TECs. Lamin-B1 supports the expression of TEC genes needed for maintaining adult thymic architecture and function. Thus, structural proteins involved in organ building and maintenance can undergo inflammation-driven decay which can in turn contribute to age-associated organ degeneration.

scholarly journals Identification of lamin B–regulated chromatin regions based on chromatin landscapes

2015 ◽  
Vol 26 (14) ◽  
pp. 2685-2697 ◽  
Author(s):  
Xiaobin Zheng ◽  
Youngjo Kim ◽  
Yixian Zheng
Keyword(s):  
Embryonic Stem ◽  
Nuclear Lamina ◽  
Chromatin Interaction ◽  
Dependent Manner ◽  
Structural Components ◽  
Genomic Features ◽  
Lamin B ◽  
Lamin B1 ◽  
Repressive Chromatin

Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL–chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin–NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin–chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation.

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