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Orchestrated intron retention regulates normal granulocyte differentiation [Affymetrix arrays]

ABSTRACT: Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression.

ORGANISM(S): Mus musculus

PROVIDER: GSE48306 | GEO | 2013/06/27

SECONDARY ACCESSION(S): PRJNA209626

REPOSITORIES: GEO

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Orchestrated intron retention regulates normal granulocyte differentiation [Affymetrix arrays]

Project description:Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression. We used Affymetrix's Mouse Gene 1.0 ST array to determine accumulation of RNA-transcripts following inhibition of nonsense-mediated decay in primary mouse granulocytes using caffeine.

2013-06-27 | E-GEOD-48306 | biostudies-arrayexpress

Orchestrated intron retention regulates normal granulocyte differentiation [RNA-Seq]

Project description:Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). There was a significant overlap of IR between human and mouse (P=2.85E-22, hypergeometric test), showing that IR is conserved.Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression. Sequencing of polyadenylated RNA from three types of myeloid cells (promyelocytes, myelocytes and granulocytes) using Illumina GAIIx

2013-06-27 | E-GEOD-48305 | biostudies-arrayexpress

Orchestrated intron retention regulates normal granulocyte differentiation [RNA-Seq]

Project description:Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). There was a significant overlap of IR between human and mouse (P=2.85E-22, hypergeometric test), showing that IR is conserved.Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression.

2013-06-27 | GSE48305 | GEO

Macrophage development and activation involve coordinated intron retention in key inflammatory regulators

Project description:Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using mRNA sequencing, bioinformatics analyses and RT-qPCR validation, we identified differential IR and altered expression of key genes involved in macrophage development and function, both in vitro and in vivo. We demonstrate that decreased IR in nuclear-detained mRNA is coupled to increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts in macrophages are rapidly spliced, leading to timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular mechanisms controlling vital regulators of the innate immune response.

2020-05-27 | PXD017391 | Pride

Gene expression, methylome and splicing of THP-1 monocytic cells and THP-1-derived macrophage

2019-04-19 | GSE130011 | GEO

An orchestrated intron retention program in meiosis controls timely usage of transcripts during germ cell differentiation (RNA-Seq)

Project description:Alternative splicing (AS) represents a powerful resource to amplify the coding potential of eukaryotic genomes and to finely tune gene expression during cell differentiation and development. Notably, high-throughput transcriptome analyses identified testis among the tissues displaying the highest proportion of AS events and profiling of whole testis transcriptome during the first wave of mouse spermatogenesis highlighted some AS events that are timely regulated during this process. Thus, AS modulation likely contributes to the fine-tuned regulation of gene expression that occurs during the male germ cell differentiation. In particular, meiotic spermatocytes and post-meiotic spermatids are known to express a highly specific repertoire of protein variants. However, no study has directly investigated whether global splicing-changes occur during the trans-meiotic phases of spermatogenesis to date. Spermatocytes undergo two consecutive meiotic divisions to yield haploid post-meiotic spermatids, which then differentiate into highly specialized and motile spermatozoa. Herein, to achieve a comprehensive characterization of the splicing changes occurring during trans-meiotic differentiation of male germ cells, we performed high-throughput RNA sequencing (RNA-seq) analyses of polyA+ RNA isolated from highly purified populations of meiotic spermatocytes and post-meiotic spermatids. Our analysis uncovered a robust intron retention (IR) program in meiotic spermatocytes. Intron-retaining genes were strongly enriched in functional categories related to differentiation and properties of the male gamete. We found that meiotic intron-retaining transcripts are long-lived mRNAs, which are preserved in the nucleus until they need to be translated. Thus, our study reveals an unexpected physiological role for IR in ensuring proper and timely control of gene expression during male germ cell differentiation.

2017-06-13 | GSE95138 | GEO

Bud13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7

Project description:Intron retention (IR) has emerged as an important mechanism of gene expression control. Despite this, the factors that control IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified Bud13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in Bud13 led to increased IR, decreased mature Irf7 transcript and protein levels, and consequently to a dampened type I interferon response. This impairment of Irf7 production in Bud13 deficient cells compromised their ability to withstand VSV infection. Global analysis of Bud13 knockdown and BUD13 cross-linking to RNA revealed a subset of introns that share many characteristics with the one found in Irf7 and are spliced in a Bud13-dependent manner. Deficiency of Bud13 led to decreased mature transcript from genes containing such introns. Thus, by acting as an antagonist to IR, Bud13 facilitates the expression of genes at which IR occurs.

2018-11-15 | GSE122543 | GEO

Gene expression data of Lsd1fl/fl and Lsd1fl/fl Mx1Cre Gr1dim Mac1 granulocytic progenitor cells.

Project description:We discovered that mice with hematopoietic-specific deletion of Lsd1 lacked Gr-1+ Mac1+ neutrophilic granulocytes whereas the numbers of Gr-1dim Mac1+ granulocytic progenitor cells was increased. To determine the genes altered by Lsd1-loss, Gr-1dim Mac1+ granulocytic progenitor cells from Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were FACS-purified to be analyzed by gene expression profiling.

2013-06-25 | GSE40282 | GEO

Metabolically distinct subpopulations of a secondary AML cell line are associated with differences in stemness and drug response

Project description:In recent years fatty acid metabolism has gained greater attention in haematological cancers, such as myeloid dysplastic syndrome (MDS) and secondary acute myeloid leukaemia (sAML), and has been implicated in increased proliferation and drug resistance. We have characterised two populations of FACS-sorted MDS/sAML cells - SKK-1LOW and SKK-1HIGH - that retain distinct fatty acid uptake phenotypes that are stable over time. Transcriptomic analysis of SKK-1LOW and SKK-1HIGH confirmed differentially expressed genes. Gene ontology analysis revealed gene expression differences principally in fatty acid transport genes and receptor tyrosine kinases, of which KIT was associated with low fatty acid uptake. SKK-1LOW resembled a leukaemic stem cell sub-population on the level of its immunophenotype and exhibited greater resistance to the hypomethylating agent, azacitadine. Overall, this study sheds new light on the relatively under-characterised SKK-1 cell line, which may be useful for the study of MDS-to-sAML transformation.

2021-06-13 | GSE152161 | GEO

The effect of C/EBPepsilon in differentiated granulocytes: cDNA microarray of C/EBPepsilon knock out mice vs C57BL/6 mice bone marrow cells

Project description:To identify target genes of C/EBPepsilon in differentiated granulocytes, total RNA were purified from sorted Gr-1intermediate/Mac-1+ and Gr-1hi/Mac-1+ cells of C/EBPepsilon knock out and C57BL/6 wild type mice using RNeasy Mini Kit (Qiagen). The differences of their expression pattern were compared with Illumina Mouse WG-6v2 Expression Chip platform. Raw Illumina BeadArray data in IDAT format were preprocessed using the open-source Bioconductor package illuminaio with the Illumina array design formation BGX file downloaded from NCBI, GEO accession: GPL6887. Following the preprocessing, the expression data were normalized by applying control background correction, log transformation and inter-quantile normalization using the neqc function from the limma bioconductor package. This allowed us to compare the transcriptomic consequences of C/EBPepsilon in two independent populations.

2017-06-02 | GSE73835 | GEO

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