cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6886568.v1
title: Myosin VI in the nucleus of neurosecretory PC12 cells: Stimulation-dependent nuclear translocation and interaction with nuclear proteins<sup>*</sup>

description: Myosin VI (MVI) is a unique actin-based motor protein moving towards the minus end of actin filaments, in the opposite direction than other known myosins. Besides well described functions of MVI in endocytosis and maintenance of Golgi apparatus, there are few reports showing its involvement in transcription. We previously demonstrated that in neurosecretory PC12 cells MVI was present in the cytoplasm and nucleus, and its depletion caused substantial inhibition of cell migration and proliferation. Here, we show an increase in nuclear localization of MVI upon cell stimulation, and identification of potential nuclear localization (NLS) and nuclear export (NES) signals within MVI heavy chain. These signals seem to be functional as the MVI nuclear presence was affected by the inhibitors of nuclear import (ivermectin) and export (leptomycin B). In nuclei of stimulated cells, MVI colocalized with active RNA polymerase II, BrUTP-containing transcription sites and transcription factor SP1 as well as SC35 and PML proteins, markers of nuclear speckles and PML bodies, respectively. Mass spectrometry analysis of samples of a GST-pull-down assay with the MVI tail domain as a “bait” identified several new potential MVI binding partners. Among them are proteins involved in transcription and post-transcriptional processes. We confirmed interaction of MVI with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and nucleolin, proteins involved in pre-mRNA binding and transport, and nucleolar function, respectively. Our data provide an insight into mechanisms of involvement of MVI in nuclear processes <i>via</i> interaction with nuclear proteins and support a notion for important role(s) for MVI in gene expression.
DOI: 10.7910/dvn/debtui/slejjm
title: 1-29.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886565.v2
title: Progerin phosphorylation in interphase is lower and less mechanosensitive than lamin-A,C in iPS-derived mesenchymal stem cells

description: Interphase phosphorylation of lamin-A,C depends dynamically on a cell's microenvironment, including the stiffness of extracellular matrix. However, phosphorylation dynamics is poorly understood for diseased forms such as progerin, a permanently farnesylated mutant of <i>LMNA</i> that accelerates aging of stiff and mechanically stressed tissues. Here, fine-excision alignment mass spectrometry (FEA-MS) is developed to quantify progerin and its phosphorylation levels in patient iPS cells differentiated to mesenchymal stem cells (MSCs). The stoichiometry of total A-type lamins (including progerin) versus B-type lamins measured for Progeria iPS-MSCs prove similar to that of normal MSCs, with total A-type lamins more abundant than B-type lamins. However, progerin behaves more like farnesylated B-type lamins in mechanically-induced segregation from nuclear blebs. Phosphorylation of progerin at multiple sites in iPS-MSCs cultured on rigid plastic is also lower than that of normal lamin-A and C. Reduction of nuclear tension upon i) cell rounding/detachment from plastic, ii) culture on soft gels, and iii) inhibition of actomyosin stress increases phosphorylation and degradation of lamin-C &gt; lamin-A &gt; progerin. Such mechano-sensitivity diminishes, however, with passage as progerin and DNA damage accumulate. Lastly, transcription-regulating retinoids exert equal effects on both diseased and normal A-type lamins, suggesting a differential mechano-responsiveness might best explain the stiff tissue defects in Progeria.
DOI: 10.6084/m9.figshare.6886562
title: Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols

description: Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range <i>cis</i>- and <i>trans-</i>chromosomal contacts.
DOI: 10.6084/m9.figshare.6886562.v1
title: Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols

description: Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range <i>cis</i>- and <i>trans-</i>chromosomal contacts.
DOI: 10.7910/dvn/debtui/dvfla0
title: 1-20.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886565.v1
title: Progerin phosphorylation in interphase is lower and less mechanosensitive than lamin-A,C in iPS-derived mesenchymal stem cells

description: Interphase phosphorylation of lamin-A,C depends dynamically on a cell's microenvironment, including the stiffness of extracellular matrix. However, phosphorylation dynamics is poorly understood for diseased forms such as progerin, a permanently farnesylated mutant of <i>LMNA</i> that accelerates aging of stiff and mechanically stressed tissues. Here, fine-excision alignment mass spectrometry (FEA-MS) is developed to quantify progerin and its phosphorylation levels in patient iPS cells differentiated to mesenchymal stem cells (MSCs). The stoichiometry of total A-type lamins (including progerin) versus B-type lamins measured for Progeria iPS-MSCs prove similar to that of normal MSCs, with total A-type lamins more abundant than B-type lamins. However, progerin behaves more like farnesylated B-type lamins in mechanically-induced segregation from nuclear blebs. Phosphorylation of progerin at multiple sites in iPS-MSCs cultured on rigid plastic is also lower than that of normal lamin-A and C. Reduction of nuclear tension upon i) cell rounding/detachment from plastic, ii) culture on soft gels, and iii) inhibition of actomyosin stress increases phosphorylation and degradation of lamin-C &gt; lamin-A &gt; progerin. Such mechano-sensitivity diminishes, however, with passage as progerin and DNA damage accumulate. Lastly, transcription-regulating retinoids exert equal effects on both diseased and normal A-type lamins, suggesting a differential mechano-responsiveness might best explain the stiff tissue defects in Progeria.
DOI: 10.7910/dvn/debtui/m3yfqw
title: 1-2.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886559
title: O-GlcNAcylation of boundary element associated factor (BEAF 32) in <i>Drosophila melanogaster</i> correlates with active histone marks at the promoters of its target genes

description: Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in <i>Drosophila</i>. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated. We mapped O-GlcNAc site at T91 of BEAF 32 and showed that it is linked to the deposition of active histone (H3K4me3) marks at transcription start site (TSS) of associated genes. Its role as a boundary associated factor, however, does not depend on this modification. Our study shows that by virtue of O-GlcNAcylation, BEAF 32 is linked to epigenetic mechanisms that activate a subset of associated genes.
DOI: 10.7910/dvn/debtui/gitwuc
title: 1-4.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886559.v2
title: O-GlcNAcylation of boundary element associated factor (BEAF 32) in <i>Drosophila melanogaster</i> correlates with active histone marks at the promoters of its target genes

description: Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in <i>Drosophila</i>. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated. We mapped O-GlcNAc site at T91 of BEAF 32 and showed that it is linked to the deposition of active histone (H3K4me3) marks at transcription start site (TSS) of associated genes. Its role as a boundary associated factor, however, does not depend on this modification. Our study shows that by virtue of O-GlcNAcylation, BEAF 32 is linked to epigenetic mechanisms that activate a subset of associated genes.
DOI: 10.6084/m9.figshare.6886553
title: Differential staining of peripheral nuclear chromatin with Acridine orange implies an A-form epichromatin conformation of the DNA

description: The chromatin observed by conventional electron microscopy under the nuclear envelope constitutes a single layer of dense 30–35 nm granules, while ∼30 nm fibrils laterally attached to them, form large patches of lamin-associated domains (LADs). This particular surface “epichromatin” can be discerned by specific (H2A+H2B+DNA) conformational antibody at the inner nuclear envelope and around mitotic chromosomes. In order to differentiate the DNA conformation of the peripheral chromatin we applied an Acridine orange (AO) DNA structural test involving RNAse treatment and the addition of AO after acid pre-treatment. MCF-7 cells treated in this way revealed yellow/red patches of LADs attached to a thin green nuclear rim and with mitotic chromosomes outlined in green, topologically corresponding to epichromatin epitope staining by immunofluorescence. Differentially from LADs, the epichromatin was unable to provide metachromatic staining by AO, unless thermally denatured at 94<sup>o</sup>C. DNA enrichment in GC stretches has been recently reported for immunoprecipitated ∼ 1Kb epichromatin domains. Together these data suggest that certain epichromatin segments assume the relatively hydrophobic DNA A-conformation at the nuclear envelope and surface of mitotic chromosomes, preventing AO side dimerisation. We hypothesize that epichromatin domains form nucleosome superbeads. Hydrophobic interactions stack these superbeads and align them at the nuclear envelope, while repulsing the hydrophilic LADs. The hydrophobicity of epichromatin explains its location at the surface of mitotic chromosomes and its function in mediating chromosome attachment to the restituting nuclear envelope during telophase.
DOI: 10.7910/dvn/debtui/uefieu
title: 1-26.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886553.v1
title: Differential staining of peripheral nuclear chromatin with Acridine orange implies an A-form epichromatin conformation of the DNA

description: The chromatin observed by conventional electron microscopy under the nuclear envelope constitutes a single layer of dense 30–35 nm granules, while ∼30 nm fibrils laterally attached to them, form large patches of lamin-associated domains (LADs). This particular surface “epichromatin” can be discerned by specific (H2A+H2B+DNA) conformational antibody at the inner nuclear envelope and around mitotic chromosomes. In order to differentiate the DNA conformation of the peripheral chromatin we applied an Acridine orange (AO) DNA structural test involving RNAse treatment and the addition of AO after acid pre-treatment. MCF-7 cells treated in this way revealed yellow/red patches of LADs attached to a thin green nuclear rim and with mitotic chromosomes outlined in green, topologically corresponding to epichromatin epitope staining by immunofluorescence. Differentially from LADs, the epichromatin was unable to provide metachromatic staining by AO, unless thermally denatured at 94<sup>o</sup>C. DNA enrichment in GC stretches has been recently reported for immunoprecipitated ∼ 1Kb epichromatin domains. Together these data suggest that certain epichromatin segments assume the relatively hydrophobic DNA A-conformation at the nuclear envelope and surface of mitotic chromosomes, preventing AO side dimerisation. We hypothesize that epichromatin domains form nucleosome superbeads. Hydrophobic interactions stack these superbeads and align them at the nuclear envelope, while repulsing the hydrophilic LADs. The hydrophobicity of epichromatin explains its location at the surface of mitotic chromosomes and its function in mediating chromosome attachment to the restituting nuclear envelope during telophase.
DOI: 10.6084/m9.figshare.6886559.v1
title: O-GlcNAcylation of boundary element associated factor (BEAF 32) in <i>Drosophila melanogaster</i> correlates with active histone marks at the promoters of its target genes

description: Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in <i>Drosophila</i>. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated. We mapped O-GlcNAc site at T91 of BEAF 32 and showed that it is linked to the deposition of active histone (H3K4me3) marks at transcription start site (TSS) of associated genes. Its role as a boundary associated factor, however, does not depend on this modification. Our study shows that by virtue of O-GlcNAcylation, BEAF 32 is linked to epigenetic mechanisms that activate a subset of associated genes.
DOI: 10.7910/dvn/debtui/k0pusw
title: 1-31.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886550
title: Elevated TGF β2 serum levels in Emery-Dreifuss Muscular Dystrophy: Implications for myocyte and tenocyte differentiation and fibrogenic processes

description: Among rare diseases caused by mutations in <i>LMNA</i> gene, Emery-Dreifuss Muscular Dystrophy type 2 and Limb-Girdle muscular Dystrophy 1B are characterized by muscle weakness and wasting, joint contractures, cardiomyopathy with conduction system disorders. Circulating biomarkers for these pathologies have not been identified. Here, we analyzed the secretome of a cohort of patients affected by these muscular laminopathies in the attempt to identify a common signature. Multiplex cytokine assay showed that transforming growth factor beta 2 (TGF β2) and interleukin 17 serum levels are consistently elevated in the vast majority of examined patients, while interleukin 6 and basic fibroblast growth factor are altered in subgroups of patients. Levels of TGF β2 are also increased in fibroblast and myoblast cultures established from patient biopsies as well as in serum from mice bearing the H222P <i>Lmna</i> mutation causing Emery-Dreifuss Muscular Dystrophy in humans. Both patient serum and fibroblast conditioned media activated a TGF β2-dependent fibrogenic program in normal human myoblasts and tenocytes and inhibited myoblast differentiation. Consistent with these results, a TGF β2 neutralizing antibody avoided fibrogenic marker activation and myogenesis impairment. Cell intrinsic TGF β2-dependent mechanisms were also determined in laminopathic cells, where TGF β2 activated AKT/mTOR phosphorylation. These data show that TGF β2 contributes to the pathogenesis of Emery-Dreifuss Muscular Dystrophy type 2 and Limb-Girdle muscular Dystrophy 1B and can be considered a potential biomarker of those diseases. Further, the evidence of TGF β2 pathogenetic effects in tenocytes provides the first mechanistic insight into occurrence of joint contractures in muscular laminopathies.
DOI: 10.7910/dvn/debtui/x1k7cf
title: 1-45.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886550.v2
title: Elevated TGF β2 serum levels in Emery-Dreifuss Muscular Dystrophy: Implications for myocyte and tenocyte differentiation and fibrogenic processes

description: Among rare diseases caused by mutations in <i>LMNA</i> gene, Emery-Dreifuss Muscular Dystrophy type 2 and Limb-Girdle muscular Dystrophy 1B are characterized by muscle weakness and wasting, joint contractures, cardiomyopathy with conduction system disorders. Circulating biomarkers for these pathologies have not been identified. Here, we analyzed the secretome of a cohort of patients affected by these muscular laminopathies in the attempt to identify a common signature. Multiplex cytokine assay showed that transforming growth factor beta 2 (TGF β2) and interleukin 17 serum levels are consistently elevated in the vast majority of examined patients, while interleukin 6 and basic fibroblast growth factor are altered in subgroups of patients. Levels of TGF β2 are also increased in fibroblast and myoblast cultures established from patient biopsies as well as in serum from mice bearing the H222P <i>Lmna</i> mutation causing Emery-Dreifuss Muscular Dystrophy in humans. Both patient serum and fibroblast conditioned media activated a TGF β2-dependent fibrogenic program in normal human myoblasts and tenocytes and inhibited myoblast differentiation. Consistent with these results, a TGF β2 neutralizing antibody avoided fibrogenic marker activation and myogenesis impairment. Cell intrinsic TGF β2-dependent mechanisms were also determined in laminopathic cells, where TGF β2 activated AKT/mTOR phosphorylation. These data show that TGF β2 contributes to the pathogenesis of Emery-Dreifuss Muscular Dystrophy type 2 and Limb-Girdle muscular Dystrophy 1B and can be considered a potential biomarker of those diseases. Further, the evidence of TGF β2 pathogenetic effects in tenocytes provides the first mechanistic insight into occurrence of joint contractures in muscular laminopathies.
DOI: 10.7910/dvn/debtui/3n33hv
title: 1-24.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/wkodif
title: 1-50.25V

description: sigma=1.25Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/xssbt1
title: 1-35.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/y9a2f5
title: 1-29.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/zobbdc
title: 1-10.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/vnpula
title: 1-25.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886532
title: <i>In silico</i> design of a novel chimeric <i>shigella</i> IpaB fused to C terminal of <i>clostridium perfringens</i> enterotoxin as a vaccine candidate

description: This study aimed to design a novel chimeric protein <i>in silico</i> to serve as a serotype-independent vaccine candidate against <i>Shigella</i>. The chimera contains amino acid residues 240–460 of <i>Shigella</i> invasion plasmid antigen B (IpaB) and the C-terminus of <i>Clostridium perfringens</i> enterotoxin (C-CPE). Amino acid sequences of 537 peptide linkers were obtained from two protein linker databases. 3D structures of IpaB-CPE<sub>290–319</sub>, IpaB-CPE<sub>184–319</sub>, IpaB-CPE<sub>194–319</sub> and 537 newly designed IpaB-linker-CPE<sub>290–319</sub> constructs with varying linker regions were predicted. These predicted 3D structures were merged with the 3D structures of native IpaB<sub>240–460</sub>, CPE<sub>194–319</sub>, CPE<sub>184–319</sub> and CPE<sub>290–319</sub> to select the structure most similar to native IpaB and C-CPE. Several <i>in silico</i> tools were used to determine the suitability of the selected IpaB-C-CPE structure as a vaccine candidate. None of the 537 linkers was capable of preserving the native structure of CPE<sub>290–319</sub> within the IpaB-linker-CPE<sub>290–319</sub> structure. <i>In silico</i> analysis determined that the IpaB-CPE<sub>194–319</sub> 3D structure was the most similar to the 3D structure of the respective native CPE domain and that it was a stable chimeric protein exposing multiple B-cell epitopes. IpaB-CPE<sub>194–319</sub> was designed for its capability to bind to human intestinal epithelial and M cells and to accumulate on these cells. The predicted B-cell epitopes are likely to be capable of inducing a mucosal antibody response in the human intestine against <i>Shigella</i> IpaB. This study also showed that the higher binding affinities of CPE<sub>184–319</sub> and CPE<sub>194–319</sub> to claudin molecules than those of CPE<sub>290–319</sub> is the result of preserving the 3D structures of CPE<sub>184–319</sub> and CPE<sub>194–319</sub> when they are linked to the C-termini of other proteins.