cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6807197
title: The role of SAGA coactivator complex in snRNA transcription

description: The general snRNA gene transcription apparatus has been extensively studied. However, the role of coactivators in this process is far from being clearly understood. Here, we have demonstrated that the <i>Drosophila</i> SAGA complex interacts with the PBP complex, the key component of the snRNA gene transcription apparatus, and is present at the promoter regions of the snRNA genes transcribed by both the RNA polymerase II and RNA polymerase III (U6 snRNA). We show that SAGA interacts with the Brf1 transcription factor, which is a part of the RNA polymerase III transcription apparatus and is present at promoters of a number of Pol III-transcribed genes. Mutations inactivating several SAGA subunit genes resulted in reduced snRNA levels in adult flies, indicating that SAGA is indeed the transcriptional coactivator for the snRNA genes. The transcription of the Pol II and Pol III-transcribed U genes was reduced by mutations in all tested SAGA complex subunits. Therefore, the transcription of the Pol II and Pol III-transcribed U genes was reduced by the mutations in the deubiquitinase module, as well as in the acetyltransferase module of the SAGA, indicating that the whole complex is essential for their transcription. Therefore, the SAGA complex activates snRNA genes suggesting its wide involvement in the regulation of gene transcription, and consequently, in the maintenance of cellular homeostasis.
DOI: 10.6084/m9.figshare.6807197.v2
title: The role of SAGA coactivator complex in snRNA transcription

description: The general snRNA gene transcription apparatus has been extensively studied. However, the role of coactivators in this process is far from being clearly understood. Here, we have demonstrated that the <i>Drosophila</i> SAGA complex interacts with the PBP complex, the key component of the snRNA gene transcription apparatus, and is present at the promoter regions of the snRNA genes transcribed by both the RNA polymerase II and RNA polymerase III (U6 snRNA). We show that SAGA interacts with the Brf1 transcription factor, which is a part of the RNA polymerase III transcription apparatus and is present at promoters of a number of Pol III-transcribed genes. Mutations inactivating several SAGA subunit genes resulted in reduced snRNA levels in adult flies, indicating that SAGA is indeed the transcriptional coactivator for the snRNA genes. The transcription of the Pol II and Pol III-transcribed U genes was reduced by mutations in all tested SAGA complex subunits. Therefore, the transcription of the Pol II and Pol III-transcribed U genes was reduced by the mutations in the deubiquitinase module, as well as in the acetyltransferase module of the SAGA, indicating that the whole complex is essential for their transcription. Therefore, the SAGA complex activates snRNA genes suggesting its wide involvement in the regulation of gene transcription, and consequently, in the maintenance of cellular homeostasis.
DOI: 10.6084/m9.figshare.6807197.v3
title: The role of SAGA coactivator complex in snRNA transcription

description: The general snRNA gene transcription apparatus has been extensively studied. However, the role of coactivators in this process is far from being clearly understood. Here, we have demonstrated that the <i>Drosophila</i> SAGA complex interacts with the PBP complex, the key component of the snRNA gene transcription apparatus, and is present at the promoter regions of the snRNA genes transcribed by both the RNA polymerase II and RNA polymerase III (U6 snRNA). We show that SAGA interacts with the Brf1 transcription factor, which is a part of the RNA polymerase III transcription apparatus and is present at promoters of a number of Pol III-transcribed genes. Mutations inactivating several SAGA subunit genes resulted in reduced snRNA levels in adult flies, indicating that SAGA is indeed the transcriptional coactivator for the snRNA genes. The transcription of the Pol II and Pol III-transcribed U genes was reduced by mutations in all tested SAGA complex subunits. Therefore, the transcription of the Pol II and Pol III-transcribed U genes was reduced by the mutations in the deubiquitinase module, as well as in the acetyltransferase module of the SAGA, indicating that the whole complex is essential for their transcription. Therefore, the SAGA complex activates snRNA genes suggesting its wide involvement in the regulation of gene transcription, and consequently, in the maintenance of cellular homeostasis.
DOI: 10.25921/rvcq-0b40
title: EM710 Water Column Sonar Data Collected During NF1501
DOI: 10.6084/m9.figshare.23154827.v4
title: mammalianFacialChromatinData

description: BigWig files from H3K27ac ChIP-seq and ATAC-seq datasets from the craniofacial regions of the human and mouse embryos. Human samples were generated using genome version Hg38.
DOI: 10.6084/m9.figshare.23154827.v5
title: mammalianFacialChromatinData

description: BigWig files from H3K27ac ChIP-seq and ATAC-seq datasets from the craniofacial regions of the human and mouse embryos. Human samples were generated using genome version Hg38.
DOI: 10.6084/m9.figshare.23154827
title: mammalianFacialChromatinData

description: BigWig files from H3K27ac ChIP-seq and ATAC-seq datasets from the craniofacial regions of the human and mouse embryos. Human samples were generated using genome version Hg38.
DOI: 10.6084/m9.figshare.23154827.v7
title: mammalianFacialChromatinData

description: BigWig files from H3K27ac ChIP-seq and ATAC-seq datasets from the craniofacial regions of the human and mouse embryos. Human samples were generated using genome version Hg38.
DOI: 10.6084/m9.figshare.23154827.v6
title: mammalianFacialChromatinData

description: BigWig files from H3K27ac ChIP-seq and ATAC-seq datasets from the craniofacial regions of the human and mouse embryos. Human samples were generated using genome version Hg38.
DOI: 10.25773/1f84-7304
title: Elizabeth River Basin Environmental Justice Indicators
DOI: 10.5519/qd.sx7cwrlo
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.8786210
title: Clathrin heavy chain phosphorylated at T606 plays a role in proper cell division

description: Clathrin regulates mitotic progression, in addition to membrane trafficking. However, the detailed regulatory mechanisms of clathrin during mitosis remain elusive. Here, we demonstrate novel regulation of clathrin during mitotic phase of the cell cycle. Clathrin heavy chain (CHC) was phosphorylated at T606 by its association partner cyclin G-associated kinase (GAK). This phosphorylation was required for proper cell proliferation and tumor growth of cells implanted into nude mice. Immunofluorescence analysis showed that the localization of CHC-pT606 signals changed during mitosis. CHC-pT606 signals localized in the nucleus and at the centrosome during interphase, whereas CHC signals were mostly cytoplasmic. Co-immunoprecipitation suggested that CHC formed a complex with GAK and polo-like kinase 1 (PLK1). Depletion of GAK using siRNA induced metaphase arrest and aberrant localization of CHC-pT606, which abolished Kiz-pT379 (as a phosphorylation target of PLK1) signals on chromatin at metaphase. Taken together, we propose that the GAK_CHC-pT606_PLK1_Kiz-pT379 axis plays a role in proliferation of cancer cells.
DOI: 10.6084/m9.figshare.8786210.v1
title: Clathrin heavy chain phosphorylated at T606 plays a role in proper cell division

description: Clathrin regulates mitotic progression, in addition to membrane trafficking. However, the detailed regulatory mechanisms of clathrin during mitosis remain elusive. Here, we demonstrate novel regulation of clathrin during mitotic phase of the cell cycle. Clathrin heavy chain (CHC) was phosphorylated at T606 by its association partner cyclin G-associated kinase (GAK). This phosphorylation was required for proper cell proliferation and tumor growth of cells implanted into nude mice. Immunofluorescence analysis showed that the localization of CHC-pT606 signals changed during mitosis. CHC-pT606 signals localized in the nucleus and at the centrosome during interphase, whereas CHC signals were mostly cytoplasmic. Co-immunoprecipitation suggested that CHC formed a complex with GAK and polo-like kinase 1 (PLK1). Depletion of GAK using siRNA induced metaphase arrest and aberrant localization of CHC-pT606, which abolished Kiz-pT379 (as a phosphorylation target of PLK1) signals on chromatin at metaphase. Taken together, we propose that the GAK_CHC-pT606_PLK1_Kiz-pT379 axis plays a role in proliferation of cancer cells.
DOI: 10.6084/m9.figshare.5895559.v2
title: DNA polymerase <b>η</b> mutational signatures are found in a variety of different types of cancer

description: DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.
DOI: 10.6084/m9.figshare.5867913
title: Induced pluripotent stem cells derived from human amnion in chemically defined conditions

description: Fetal stem cells are a unique type of adult stem cells that have been suggested to be broadly multipotent with some features of pluripotency. Their clinical potential has been documented but their upgrade to full pluripotency could open up a wide range of cell-based therapies particularly suited for pediatric tissue engineering, longitudinal studies or disease modeling. Here we describe episomal reprogramming of mesenchymal stem cells from the human amnion to pluripotency (AM-iPSC) in chemically defined conditions. The AM-iPSC expressed markers of embryonic stem cells, readily formed teratomas with tissues of all three germ layers present and had a normal karyotype after around 40 passages in culture. We employed novel computational methods to determine the degree of pluripotency from microarray and RNA sequencing data in these novel lines alongside an iPSC and ESC control and found that all lines were deemed pluripotent, however, with variable scores. Differential expression analysis then identified several groups of genes that potentially regulate this variability in lines within the boundaries of pluripotency, including metallothionein proteins. By further studying this variability, characteristics relevant to cell-based therapies, like differentiation propensity, could be uncovered and predicted in the pluripotent stage.
DOI: 10.6084/m9.figshare.5867913.v1
title: Induced pluripotent stem cells derived from human amnion in chemically defined conditions

description: Fetal stem cells are a unique type of adult stem cells that have been suggested to be broadly multipotent with some features of pluripotency. Their clinical potential has been documented but their upgrade to full pluripotency could open up a wide range of cell-based therapies particularly suited for pediatric tissue engineering, longitudinal studies or disease modeling. Here we describe episomal reprogramming of mesenchymal stem cells from the human amnion to pluripotency (AM-iPSC) in chemically defined conditions. The AM-iPSC expressed markers of embryonic stem cells, readily formed teratomas with tissues of all three germ layers present and had a normal karyotype after around 40 passages in culture. We employed novel computational methods to determine the degree of pluripotency from microarray and RNA sequencing data in these novel lines alongside an iPSC and ESC control and found that all lines were deemed pluripotent, however, with variable scores. Differential expression analysis then identified several groups of genes that potentially regulate this variability in lines within the boundaries of pluripotency, including metallothionein proteins. By further studying this variability, characteristics relevant to cell-based therapies, like differentiation propensity, could be uncovered and predicted in the pluripotent stage.
DOI: 10.6084/m9.figshare.5895559
title: DNA polymerase <b>η</b> mutational signatures are found in a variety of different types of cancer

description: DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.
DOI: 10.6084/m9.figshare.5895559.v1
title: DNA polymerase <b>η</b> mutational signatures are found in a variety of different types of cancer

description: DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.
DOI: 10.22002/5f3zb-9xm59
title: River floc data extracted from a river suspended sediment concentration-depth profile data compilation

description: The file "riverfloc_datacompilation.csv" contains the data in csv format. The file "metadata.txt" contains the metadata describing the data in the csv file.
This version corrects an error in which the ionic strength and relative charge density (variables 48 and 50) were underestimated by a factor of 1000.
description: Related Publication:
A Mechanistic Model for Mud Flocculation in Freshwater Rivers

Justin Nghiem Caltech

Woodward W. Fischer Caltech

Gen K. Li Caltech

Michael P. Lamb Caltech
eng
DOI: 10.5517/ccdc.csd.cc2bmf6m
title: CCDC 2163620: Experimental Crystal Structure Determination

description: Related Article: Elahe Keshavarzian, Zahra Asadi, Vaclav Eigner, Michal Dusek, Banafsheh Rastegari|2023|J.Mol.Liq.|380|121701|doi:10.1016/j.molliq.2023.121701
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2649k7
title: CCDC 2029928: Experimental Crystal Structure Determination

description: Related Article: Z.O. Battaglia, J.T. Kersten, E.M. Nicol, P. Whitworth, K.A. Wheeler, C.L. Hall, J. Potticary, V. Hamilton, S.R. Hall, G.D. D'Ambruoso, M. Matsumoto, S.D. Warren, M.E. Cremeens|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|217|doi:10.1107/S2053229623003704
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc264b7y
title: CCDC 2029949: Experimental Crystal Structure Determination

description: Related Article: Z.O. Battaglia, J.T. Kersten, E.M. Nicol, P. Whitworth, K.A. Wheeler, C.L. Hall, J. Potticary, V. Hamilton, S.R. Hall, G.D. D'Ambruoso, M. Matsumoto, S.D. Warren, M.E. Cremeens|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|217|doi:10.1107/S2053229623003704
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ftgrh
title: CCDC 2258807: Experimental Crystal Structure Determination

description: Related Article: D.E. Vicentes, R. Rodríguez, J. Cobo, C. Glidewell|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|227|doi:10.1107/S2053229623003728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ftgsj
title: CCDC 2258808: Experimental Crystal Structure Determination

description: Related Article: D.E. Vicentes, R. Rodríguez, J. Cobo, C. Glidewell|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|227|doi:10.1107/S2053229623003728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ftgtk
title: CCDC 2258809: Experimental Crystal Structure Determination

description: Related Article: D.E. Vicentes, R. Rodríguez, J. Cobo, C. Glidewell|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|227|doi:10.1107/S2053229623003728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ftgvl
title: CCDC 2258810: Experimental Crystal Structure Determination

description: Related Article: D.E. Vicentes, R. Rodríguez, J. Cobo, C. Glidewell|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|227|doi:10.1107/S2053229623003728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ftgwm
title: CCDC 2258811: Experimental Crystal Structure Determination

description: Related Article: D.E. Vicentes, R. Rodríguez, J. Cobo, C. Glidewell|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|227|doi:10.1107/S2053229623003728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dzndg
title: CCDC 2233996: Experimental Crystal Structure Determination

description: Related Article: G. Murtaza, M. Khan, S. Farooq, M.I. Choudhary, S. Yousuf|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|237|doi:10.1107/S2053229623003753
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ftgxn
title: CCDC 2258812: Experimental Crystal Structure Determination

description: Related Article: D.E. Vicentes, R. Rodríguez, J. Cobo, C. Glidewell|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|227|doi:10.1107/S2053229623003728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dzncf
title: CCDC 2233995: Experimental Crystal Structure Determination

description: Related Article: G. Murtaza, M. Khan, S. Farooq, M.I. Choudhary, S. Yousuf|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|237|doi:10.1107/S2053229623003753
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dzqqv
title: CCDC 2234068: Experimental Crystal Structure Determination

description: Related Article: G. Murtaza, M. Khan, S. Farooq, M.I. Choudhary, S. Yousuf|2023|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|79|237|doi:10.1107/S2053229623003753
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.