cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4046601.v1
title: Human Atg8-cardiolipin interactions in mitophagy: Specific properties of LC3, GABARAPL2 and GABARAP

description: The phospholipid cardiolipin (CL) has been proposed to play a role in selective mitochondrial autophagy, or mitophagy. CL externalization to the outer mitochondrial membrane would act as a signal for the human Atg8 ortholog subfamily, MAP1LC3 (LC3). The latter would mediate both mitochondrial recognition and autophagosome formation, ultimately leading to removal of damaged mitochondria. We have applied quantitative biophysical techniques to the study of CL interaction with various Atg8 human orthologs, namely LC3B, GABARAPL2 and GABARAP. We have found that LC3B interacts preferentially with CL over other di-anionic lipids, that CL-LC3B binding occurs with positive cooperativity, and that the CL-LC3B interaction relies only partially on electrostatic forces. CL-induced increased membrane fluidity appears also as an important factor helping LC3B to bind CL. The LC3B C terminus remains exposed to the hydrophilic environment after protein binding to CL-enriched membranes. In intact U87MG human glioblastoma cells rotenone-induced autophagy leads to LC3B translocation to mitochondria and subsequent delivery of mitochondria to lysosomes. We have also observed that GABARAP, but not GABARAPL2, interacts with CL <i>in vitro</i>. However neither GABARAP nor GABARAPL2 were translocated to mitochondria in rotenone-treated U87MG cells. Thus the various human Atg8 orthologs might play specific roles in different autophagic processes.
DOI: 10.7910/dvn/v1rjpf/2qmadc
title: blc20160524_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zbzvvj
title: blc20160819_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mlatq2
title: blc20161119_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046580
title: The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

description: Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease.
DOI: 10.7910/dvn/v1rjpf/pbgadf
title: blc20160708_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046580.v2
title: The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

description: Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease.
DOI: 10.7910/dvn/v1rjpf/9gmua8
title: blc20160220_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046580.v1
title: The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

description: Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease.
DOI: 10.6084/m9.figshare.4046574
title: Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

description: Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.
DOI: 10.7910/dvn/v1rjpf/vljzya
title: blc20160709_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046568
title: Dataset for 'Towards photopharmacological antimicrobial chemotherapy using photoswitchable amidohydrolase inhibitors'

description: Dataset to accompany article titled ''Towards photopharmacological antimicrobial chemotherapy using photoswitchable amidohydrolase inhibitors', published in ACS Infectious Diseases, 2016, DOI:10.1021/acsinfecdis.6b00148<br><br>Data included:<br>Characterisation of intermediates and final compounds (IR, NMR, MS)<br>UV/vis spectra<br>IC<sub>50 </sub>data<br>Computational docking<br>
DOI: 10.7910/dvn/v1rjpf/dxlkbe
title: blc20160628_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046568.v1
title: Dataset for 'Towards photopharmacological antimicrobial chemotherapy using photoswitchable amidohydrolase inhibitors'

description: Dataset to accompany article titled ''Towards photopharmacological antimicrobial chemotherapy using photoswitchable amidohydrolase inhibitors', published in ACS Infectious Diseases, 2016, DOI:10.1021/acsinfecdis.6b00148<br><br>Data included:<br>Characterisation of intermediates and final compounds (IR, NMR, MS)<br>UV/vis spectra<br>IC<sub>50 </sub>data<br>Computational docking<br>
DOI: 10.6084/m9.figshare.4046574.v2
title: Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

description: Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.
DOI: 10.7910/dvn/v1rjpf/1qpdje
title: blc20160521_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046574.v1
title: Transcription of highly repetitive tandemly organized DNA in amphibians and birds: a historical overview and modern concepts

description: Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.
DOI: 10.7910/dvn/v1rjpf/d6ivry
title: blc20160427_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/8p9cjb
title: blc20160620_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/klvcog
title: blc20160827_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9wsdxg
title: blc20160101_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uovrug
title: blc20160309_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qy2mch
title: blc20160814_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/0ri7re
title: blc20161216_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/tgufkf
title: blc20160707_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/uhoqgz
title: blc20161126_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4046520
title: Ibarra-Zatarain et al., 2016 Senegalese sole stress coping style data.xlsx

description: <br>Senegalese sole stress coping style data.
DOI: 10.7910/dvn/v1rjpf/rllhq8
title: blc20161222_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4043880
title: Data associated with Williams et al. 2016 (DOI : 10.1007/s10533-016-0264-y)

description: Lake chemistry and phytoplankton data associated with Williams et al. 2016. Biogeochemistry (<b>DOI : </b>10.1007/s10533-016-0264-y)
DOI: 10.6084/m9.figshare.4043880.v1
title: Data associated with Williams et al. 2016 (DOI : 10.1007/s10533-016-0264-y)

description: Lake chemistry and phytoplankton data associated with Williams et al. 2016. Biogeochemistry (<b>DOI : </b>10.1007/s10533-016-0264-y)
DOI: 10.7910/dvn/v1rjpf/yaramv
title: blc20161114_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4043835
title: ESM Table S1 dataset to the article "Scratch that itch: revisiting links between self-directed behaviour and parasitological, social and environmental factors in a free-ranging primate"

description: Supplementary material from "Scratch that itch: revisiting links between self-directed behaviour and parasitological, social and environmental factors in a free-ranging primate"
DOI: 10.7910/dvn/v1rjpf/tgq2c3
title: blc20161106_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4043835.v1
title: ESM Table S1 dataset to the article "Scratch that itch: revisiting links between self-directed behaviour and parasitological, social and environmental factors in a free-ranging primate"

description: Supplementary material from "Scratch that itch: revisiting links between self-directed behaviour and parasitological, social and environmental factors in a free-ranging primate"
DOI: 10.7910/dvn/v1rjpf/6sy9zw
title: blc20160307_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/ffjmqz
title: blc20161120_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/eyvksv
title: blc20160607_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/ww6jfq
title: blc20160311_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/oocs5x
title: blc20161214_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/c3cwqu
title: blc20160416_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/doyqxh
title: blc20160610_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/fpfqaj
title: blc20160718_03.txt.gz

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DOI: 10.6084/m9.figshare.4043610
title: RSPAC-890.zip

description: a description
DOI: 10.6084/m9.figshare.4043700
title: mUbiSiDa - Database of mammalian protein ubiquitination site

description: mUbiSiDa, mammalian Ubiquitination Site Database, is a comprehensive database of ubiquitination sites in mammals. It is freely available for non-commercial use. This database collects only ubiquitination sites with experimental evidences, and can be a valuable resource for the study of ubiquitination in mammals, especially in human.
DOI: 10.7910/dvn/v1rjpf/4po4q8
title: blc20161211_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4043610.v1
title: RSPAC-890.zip

description: a description
DOI: 10.7910/dvn/v1rjpf/pknm7o
title: blc20160731_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/yocemo
title: blc20161221_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/bnsc8c
title: blc20160624_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/irdxun
title: blc20161121_03.txt.gz

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DOI: 10.7910/dvn/v1rjpf/8kk0mx
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DOI: 10.7910/dvn/v1rjpf/bfd16d
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DOI: 10.7910/dvn/v1rjpf/1zfhxp
title: blc20160914_03.txt.gz

description: :unav