Genome-wide transcriptome analysis of NIPBL hematopoeitic progenitors and megakaryocytes
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ABSTRACT:
PROVIDER: PRJNA490377 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7819996_1.fastq.gz | Fastqsanger.gz | |||
| SRR7819996_2.fastq.gz | Fastqsanger.gz | |||
| SRR7819997_1.fastq.gz | Fastqsanger.gz | |||
| SRR7819997_2.fastq.gz | Fastqsanger.gz | |||
| SRR7819998_1.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this study was to compare the transcriptome of NIPBL patient derived Hematopoietic progenitors and patient-derived megakaryocytes to healthy unaffected individuals Methods: HPC transcriptome profiles of three CdLS patient iPSCs harboring mutations in the NIPBL gene and megakaryocytes generated from patient-iPSCS were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the human genome and identified transcripts in CdLS-HPCs and transcripts in CdLS-MEGs. Conclusion: Our data supports dysregulation of megakaroyctye maturation and growth arrest in response to multiple conserved developmental pathways.
2019-11-01 | GSE119828 | GEO
Project description:While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not well understood. Recently, we and others have proposed that direct interactions with transcription factors (TFs) lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of protein-protein interaction (PPI) motifs within the NIPBL sequence that regulate NIPBL dynamics, interactome, and NIPBL-dependent transcriptional programs. These PPIMs directly interact with chromatin-associated proteins, including TFs and one of them is necessary for the maintenance of the NIPBL-MAU2 heterodimer. Finally, using the glucocorticoid receptor (GR) as a model, we investigate its interaction surfaces with NIPBL and MAU2 using AlphaFold2 and surface plasmon resonance to uncover a TF-NIPBL-MAU2 ternary complex and present its importance in GR-dependent gene regulation.
2025-04-17 | PXD058574 | Pride
Project description:The purpose of this study was to compare the transcriptome of NIPBL patient derived iPSCs and patient-derived cardiomyocytes to healthy unaffected individuals Methods: iPSC transcriptome profiles of three CdLS patient iPSCs harboring mutations in the NIPBL gene and cardiomyocytes derived from patient-iPSCS were generated by deep sequencing, in triplicate, using Illumina XXXXXX. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the human genome and identified XXXX transcripts in CdLS-iPSCs and XXXXXX transcripts in control-iPSCs with XXXX workflow. Conclusion: Our data is the represents the first human developmental model for studying CdLS through pluripotent stem cells and lineage commited subtypes (cardiomyocytes). This data highlights NIPBLs role in regulating transcriptional regulation and has significant consequences on DNA nucleosome involvement as it relates to global gene expression. This work provides preliminary evidence that NIPBL is required for normal epigenetic and DNA landscape establishment during embryonic cardiomyocyte generation.
2018-02-22 | GSE102873 | GEO
Project description:Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, Nipbl/Scc2 were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanism driving the CdLS phenotypes are not understood. Apart from its canonical role in sister chromatid cohesion, cohesin has also been involved in the regulation of the spatial organization of the genome. Here, we investigated the transcriptome of CdLS-derived primary fibroblasts (gene expression microarray data included in the manuscript as an excel file) and observed the downregulation of genes involved in development and system skeletal organization providing a link to the developmental alterations and limb abnormalities characteristics of the CdLS patients. Genome-wide distribution studies demonstrated a global reduction of Nipbl at the Nipbl-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at Nipbl-occupied sites at CpG islands probably due to reduced cohesin translocation along chromosomes and fewer cohesin peaks colocalize with CTCF.
2021-05-27 | GSE145966 | GEO
Project description:Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin loading factor and has recently been associated with the BET (Bromodomains and Extra Terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins in mouse P19 teratocarcinoma cells. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2.
2020-01-01 | GSE132785 | GEO
Project description:Cohesin rings interact with DNA and modulate expression of thousands of genes. NIPBL loads cohesin onto chromosomes and WAPL takes it off. Heterozygous mutations in NIPBL lead to a developmental disorder called Cornelia de Lange syndrome. Nipbl heterozygous mice are a good model for this disease. Mutations in WAPL were not known to cause disease or gene expression changes in mammals. Here we show dysregulation of >1000 genes in Wapl-/+embryonic mouse brains. The patterns of dysregulation are highly similar in Wapl and Nipbl heterozygotes, suggesting that Wapl mutations may cause disease in humans. Since WAPL and NIPBL have opposite effects on cohesin’s association with DNA, we asked whether a heterozygous Wapl mutation could correct phenotypes seen in Nipbl heterozygous mice. In fact, both gene expression and embryonic growth are partially corrected. Our data are consistent with the view that cohesin dynamics play a key role in regulating gene expression.
2022-10-11 | GSE203014 | GEO
Project description:Rattus norvegicus Nipbl, NIPBL, cohesin loading factor [Source:RGD Symbol;Acc:1306393], is differentially expressed in 22 experiment(s);
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Project description:Monodelphis domestica NIPBL, NIPBL cohesin loading factor [Source:NCBI gene;Acc:100014459], is expressed in 2 baseline experiment(s);
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Project description:Rattus norvegicus Nipbl, NIPBL, cohesin loading factor [Source:RGD Symbol;Acc:1306393], is expressed in 4 baseline experiment(s);
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Project description:Mus musculus Nipbl, NIPBL cohesin loading factor [Source:MGI Symbol;Acc:MGI:1913976], is differentially expressed in 102 experiment(s);
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