JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Khan, Aziz; Fornés, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragón, Jaime A; Lee, Robin van der; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada Rajabhau; Tan, Ge; Baranašić, Damir; Arenillas, David J.; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoît; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony

doi:10.1093/nar/gkx1188

Cited by 603 publications

(637 citation statements)

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“…We then carried out an analysis of the VNTR locus for genomic features and expression data interrogating large consortium datasets. The VNTR overlaps two eQTLs identified in the version 6 of the To look for potential regulatory networks, we carried out a binding site analysis using Jaspar (Khan et al, 2018) and identified myeloid zinc finger 1 (MZF1; Morris, Hromas, & Rauscher, 1994) as the transcription factor with the highest probability of binding the VNTR ( Figure 6). MZF1 is a zinc finger protein with an established role in hemopoiesis.…”

Section: Genomic Analysis Of Vntr Locusmentioning

confidence: 99%

A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

Bertuzzi

Tang²,

Calligaris

et al. 2020

Human Mutation

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Minisatellites, also called variable number of tandem repeats (VNTRs), are a class of repetitive elements that may affect gene expression at multiple levels and have been correlated to disease. Their identification and role as expression quantitative trait loci (eQTL) have been limited by their absence in comparative genomic hybridization and single nucleotide polymorphisms arrays. By taking advantage of cap analysis of gene expression (CAGE), we describe a new example of a minisatellite hosting a transcription start site (TSS) which expression is dependent on the repeat number. It is located in the third intron of the gene nitrogen permease regulator like protein 3 (NPRL3). NPRL3 is a component of the GAP activity toward rags 1 protein complex that inhibits mammalian target of rapamycin complex 1 (mTORC1) activity and it is found mutated in familial focal cortical dysplasia and familial focal epilepsy. CAGE tags represent an alternative TSS identifying TAGNPRL3 messenger RNAs (mRNAs). TAGNPRL3 is expressed in red blood cells both at mRNA and protein levels, it interacts with its protein partner NPRL2 and its overexpression inhibits cell proliferation. This study provides an example of a minisatellite that is both a TSS and an eQTL as well as identifies a new VNTR that may modify mTORC1 activity.

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Section: Genomic Analysis Of Vntr Locusmentioning

confidence: 99%

A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

Bertuzzi

Tang²,

Calligaris

et al. 2020

Human Mutation

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“…For analysis of the putative BbMcm1-binding site, the promoter regions (~1.5 kb upstream of each start codon) of selected genes were retrieved and analysed using the JASPAR 2018 database (Khan et al, 2018). For yeast one-hybrid tests, the DNA-binding sequence of Bbmcm1 was amplified from the complementary DNA (cDNA) with primers DB-F and DB-R (Supporting Information Table S1) and cloned into the NdeI and EcoRI sites of vector pGADT7 AD and fused a Gal4 activation domain (AD) under the control of the constitutively active ADH promoter to generate plasmid pGADT7-Bbmcm1 DB.…”

Section: Bioinformatics Analysis and Yeast One-hybrid Testsmentioning

confidence: 99%

MADS‐box transcription factor Mcm1 controls cell cycle, fungal development, cell integrity and virulence in the filamentous insect pathogenic fungus Beauveria bassiana

Zhao

Yang

et al. 2019

Environmental Microbiology

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Summary MADS‐box transcription factor Mcm1 plays crucial roles in regulating mating processes and pathogenesis in some fungi. However, its roles are varied in fungal species, and its function remains unclear in entomopathogenic fungi. Here, Mcm1 orthologue, Bbmcm1, was characterized in a filamentous entomopathogenic fungus, Beauveria bassiana. Disruption of Bbmcm1 resulted in a distinct reduction in growth with abnormal conidiogenesis, and a significant decrease in conidial viability with abnormal germination. ΔBbmcm1 displayed impaired cell integrity, with distorted cell wall structure and altered cell wall component. Abnormal cell cycle was detected in ΔBbmcm1 with longer G2/M phase but shorter G1/G0 and S phases in unicellular blastospores, and sparser septa in multicellular hyphae, which might be responsible for defects in development and differentiation due to the regulation of cell cycle‐involved genes, as well as the corresponding cellular events‐associated genes. Dramatically decreased virulence was examined in ΔBbmcm1, with impaired ability to escape haemocyte encapsulation, which was consistent with markedly reduced cuticle‐degrading enzyme production by repressing their coding genes, and downregulated fungal effector protein‐coding genes, suggesting a novel role of Mcm1 in interaction with host insect. These data indicate that Mcm1 is a crucial regulator of development, cell integrity, cell cycle and virulence in insect fungal pathogens.

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“…Resulting gene lists of interesting modules were extracted and uploaded to DAVID for gene ontology analysis with the aforementioned parameters. TFs from each module were extracted with information curated by JASPAR (33). Gene coexpression networks were prepared with Cytoscape (34) representing the top 20 hub genes of each module or TFs in each module with their top 3 connected genes.…”

Section: Computational Analysismentioning

confidence: 99%

High‐depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis

2018

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Mesenchymal stem/stromal cells (MSCs) provide an attractive cell source for cartilage repair and cell therapy; however, the underlying molecular pathways that drive chondrogenesis of these populations of adult stem cells remain poorly understood. We generated a rich data set of high-throughput RNA sequencing of human MSCs throughout chondrogenesis at 6 different time points. Our data consisted of 18 libraries with 3 individual donors as biologic replicates, with each library possessing a sequencing depth of 100 million reads. Computational analyses with differential gene expression, gene ontology, and weighted gene correlation network analysis identified dynamic changes in multiple biologic pathways and, most importantly, a chondrogenic gene subset, whose functional characterization promises to further harness the potential of MSCs for cartilage tissue engineering. Furthermore, we created a graphic user interface encyclopedia built with the goal of producing an open resource of transcriptomic regulation for additional data mining and pathway analysis of the process of MSC chondrogenesis.-Huynh, N. P. T., Zhang, B., Guilak, F. High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis.

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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Cited by 603 publications

References 0 publications

A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

MADS‐box transcription factor Mcm1 controls cell cycle, fungal development, cell integrity and virulence in the filamentous insect pathogenic fungus Beauveria bassiana

High‐depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis

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