Gene expression RNAseq profiles of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells with or without transgenic inducible DUX4 (iDUX4) activation.
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ABSTRACT:
PROVIDER: PRJNA1130513 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29668200_1.fastq.gz | Fastqsanger.gz | |||
| SRR29668200_2.fastq.gz | Fastqsanger.gz | |||
| SRR29668201_1.fastq.gz | Fastqsanger.gz | |||
| SRR29668201_2.fastq.gz | Fastqsanger.gz | |||
| SRR29668202_1.fastq.gz | Fastqsanger.gz |
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Project description:Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024. PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA), totipotent, and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent epigenetic reprogramming to clonal blastomere-like stem cells. TIRN stem cells concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as a panoply of four-cell (4C)-specific (e.g., TPRXL, HOX clusters), eight-cell (8C)-specific (e.g., DUXA, GSC, GATA6), primitive endoderm-specific (e.g., GATA4, SOX17), trophectoderm-specific (e.g., CDX2, TFAP2C), and naïve epiblast-specific (e.g., DNMT3L, NANOG, POU5F1(OCT4)) factors; all in a hybrid, combinatorial single-cell manner. Mapping of proteomic and single-cell expressions of TIRN cells against human preimplantation embryo references identified them as relatively homogenous 4C-8C stage populations. The bulk RNA-seq and proteomics analyses of TIRN cells (+/- iDUX4) revealed acquisition of pre-lineage embryonic transcriptional programs. To determine if TIRN +/- iDUX4 cells were mixed populations or clonal blastomere-like cells, single cell (sc)RNA-seq was performed to investigate transcriptional heterogeneity at a single cell level. Overall, single, unmodified TIRN cells shared high transcriptional identity with single TIRN+iDUX4 cells, and single primed hPSC and TIRN +/- iDUX4 cells expressed comparable and uniformly homogenous levels of core pluripotency factors (e.g., NANOG, POU5F1 (OCT4), SOX2, KLF4, CMYC). However, single TIRN and TIRN+iDUX4 populations homogenously co-expressed not only higher levels of naïve ICM-specific genes (e.g., DNMT3L, SP5, ERVH48-1, GDF3, and IFITM1) (Park et al., 2020; Zimmerlin et al., 2016), but also hundreds of diverse and antagonistic lineage-specifying genes (e.g., HOX-PRD, T-BOX, FOX, GATA families) that are co-expressed simultaneously only during 4C-to-morula human embryonic stages (Petropoulos et al., 2016; Zou et al., 2022). Transcript levels of 4C-specific (i.e., TPRXL, HOXA1, EBF2), 8C-specific (i.e., GATA6, FOXB1), trophectoderm lineage-specific (i.e., CDX2, TFAP2C), and endoderm lineage-specific (i.e., GATA4, SOX17) pioneer factors were co-expressed in the same single cell populations; with expressions that were further augmented following iDUX4 activation.
2025-05-12 | GSE271242 | GEO
Project description:Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024. PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA), totipotent, and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent epigenetic reprogramming to clonal blastomere-like stem cells. TIRN stem cells concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as a panoply of four-cell (4C)-specific (e.g., TPRXL, HOX clusters), eight-cell (8C)-specific (e.g., DUXA, GSC, GATA6), primitive endoderm-specific (e.g., GATA4, SOX17), trophectoderm-specific (e.g., CDX2, TFAP2C), and naïve epiblast-specific (e.g., DNMT3L, NANOG, POU5F1(OCT4)) factors; all in a hybrid, combinatorial single-cell manner. Mapping of proteomic and single-cell expressions of TIRN cells against human preimplantation embryo references identified them as relatively homogenous 4C-8C stage populations. The bulk RNA-seq and proteomics analyses of TIRN cells (+/- iDUX4) revealed acquisition of pre-lineage embryonic transcriptional programs. To determine if TIRN +/- iDUX4 cells were mixed populations or clonal blastomere-like cells, single cell (sc)RNA-seq was performed to investigate transcriptional heterogeneity at a single cell level. Overall, single, unmodified TIRN cells shared high transcriptional identity with single TIRN+iDUX4 cells, and single primed hPSC and TIRN +/- iDUX4 cells expressed comparable and uniformly homogenous levels of core pluripotency factors (e.g., NANOG, POU5F1 (OCT4), SOX2, KLF4, CMYC). However, single TIRN and TIRN+iDUX4 populations homogenously co-expressed not only higher levels of naïve ICM-specific genes (e.g., DNMT3L, SP5, ERVH48-1, GDF3, and IFITM1) (Park et al., 2020; Zimmerlin et al., 2016), but also hundreds of diverse and antagonistic lineage-specifying genes (e.g., HOX-PRD, T-BOX, FOX, GATA families) that are co-expressed simultaneously only during 4C-to-morula human embryonic stages (Petropoulos et al., 2016; Zou et al., 2022). Transcript levels of 4C-specific (i.e., TPRXL, HOXA1, EBF2), 8C-specific (i.e., GATA6, FOXB1), trophectoderm lineage-specific (i.e., CDX2, TFAP2C), and endoderm lineage-specific (i.e., GATA4, SOX17) pioneer factors were co-expressed in the same single cell populations; with expressions that were further augmented following iDUX4 activation.
2025-05-12 | GSE267577 | GEO
Project description:Gene expression profiles at the single cell level of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells with or without transgenic inducible DUX4 (iDUX4) activation.
| PRJNA1111869 | ENA
Project description:Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024. PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA) and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent proteogenomic reprogramming to a functional blastomere-like state. Tankyrase-PARP1 inhibitor-regulated naïve stem cells (TIRN-SC) concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as two- to eight-cell (2C-8C) (e.g., TPRXL, HOX clusters, EOMES, DUXA, GATA6), pre-lineage morula (e.g., GATA4, SOX17, FOXA2), and naïve epiblast (e.g., LEFTY2, DNMT3L, NANOG) lineage-specifying pioneer factors; all in a hybrid, single-cell manner. Mapping of the single-cell transcriptome of TIRN-SC to human embryo references identified populations expressing hybrid transcriptional programs that not only spanned 2C-4C (pre-ZGA) and morula-ICM stages, but that were also augmented following brief induction of DUX4 expression (iDUX4). Here, we performed ChIP-Seq profiling of PARP1, the core pluripotency factors NANOG, SOX2 and OCT4, phosphorylated-STAT3, BRD4 and modified histones H3K4me3, H3K27me3, H3K27ac. Co-binding analyses of core NANOG-SOX2-OCT4 (NSO) pluripotency factors with PARP1 (NSOP) identified genome-wide reprogramming of novel NSOP sites to DUX4-accessible distal and cis-regulatory enhancer regions in TIRN-SC. Gained NSOP enhancer regions possessed co-binding motifs for hundreds of the same 2C-8C-ICM-specific embryonic, and extraembryonic lineage-specifying pioneer factors (e.g., HOX, FOX, GATA, SOX, TBX families) that were concurrently co-expressed in TIRN-SC; suggesting that PARP1 and DUX4 chromatin co-binding cooperated with NSO core factors to regulate ZGA-associated lineage plasticity.
2025-05-12 | GSE291713 | GEO
Project description:Bulk RNA sequencing was performed on a CML derived cell line, which contains an TET-ON inducible system for DUX4 inducible expression (DIE). Due to the unconventional cellular background used for the generation of an inducible FSHD cell line, bulk RNA seq was performed to determine if, and otherwise to what extend, this cellular background inteferes with the transcriptional program DUX4 is known to activate in muscle cells.
2020-07-29 | GSE154649 | GEO
Project description:We determined the effects of short pulses of DUX4 expression on genome-wide transcription, mimicking the embryonic expression of this gene, using a DUX4-inducible cell culture model of FSHD (MB135iDUX4). We found that a second pulse of DUX4 has a synergistic effect and shows greater induction of DUX4 targets. Knockdown of DUX4-induced histone variants H3.X and H3.Y has no effect on DUX4 targets with a single pulse of DUX4 but eliminates the superinduction seen with a second pulse, showing that these histones are required for this increase in expression.
2019-08-31 | GSE119402 | GEO
Project description:We determined the effects of short pulses of DUX4 expression on genome-wide transcription, mimicking the embryonic expression of this gene, using a DUX4-inducible cell culture model of FSHD (MB135iDUX4). We found that a second pulse of DUX4 has a synergistic effect and shows greater induction of DUX4 targets. Knockdown of DUX4-induced histone variants H3.X and H3.Y has no effect on DUX4 targets with a single pulse of DUX4 but eliminates the superinduction seen with a second pulse, showing that these histones are required for this increase in expression.
2019-08-31 | GSE119401 | GEO
Project description:All types of facioscapulohumeral muscular dystrophy (FSHD) are caused by the aberrant myogenic activation of the somatically silent DUX4 gene, which initiates a cascade of cellular events ultimately leading to FSHD pathophysiology. Therefore, FSHD is a dominant gain-of-function disease that is amenable to modeling by DUX4 overexpression. However, there is large variability in the patient population. Typically, progressive skeletal muscle weakness becomes noticeable in the second or third decade of life, yet there are many genetically FSHD individuals who develop symptoms much later in life or remain relatively asymptomatic throughout their lives. Conversely, in rare cases, FSHD may present clinically prior to 5-10 yrs of age, ultimately manifesting as a very severe early onset form of the disease. Thus, there is a need to control the timing and severity of pathology in FSHD-like models. Methods: We have recently described a line of conditional DUX4 transgenic mice, FLExDUX4, that develop a myopathy upon induction of human DUX4-fl expression in skeletal muscle. Here, we use the FLExDUX4 mouse crossed with the skeletal muscle-specific and tamoxifen inducible line ACTA1-MerCreMer to generate a highly versatile bi-transgenic mouse model with chronic, low-level DUX4-fl expression and mild pathology, that can be induced to develop more severe FSHD-like pathology in a dose-dependent response to tamoxifen. We identified conditions to reproducibly generate models exhibiting mild, moderate, or severe DUX4-dependent pathophysiology, and characterized their progression. Results: We assayed DUX4-fl mRNA and protein levels, fitness, strength, global gene expression, histopathology, and immune response, all of which are consistent with an FSHD-like myopathic phenotype. Importantly, we identified sex-specific and muscle-specific differences that should be considered when using these models for preclinical studies. Conclusions: The ACTA1-MCM;FLExDUX4 bi-transgenic mouse model expresses a chronic low level of DUX4-fl and has mild pathology and detectable muscle weakness. The onset and progression of moderate to severe pathology can be controlled via tamoxifen injection to provide consistent and readily screenable phenotypes for assessing therapies targeting DUX4-fl mRNA and protein. Thus, these FSHD-like mouse models can be used to study a range of DUX4-fl expression and pathology dependent upon investigator need, through controlled mosaic expression of DUX4.
2019-12-01 | GSE122562 | GEO
Project description:Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of the double-homeodomain transcription factor DUX4 in skeletal muscle cells. Many different cell culture models have been developed to study the pathophysiology of FSHD, frequently based on endogenous expression of DUX4 in FSHD cells or by mis-expression of DUX4 in control human muscle cells. Although results generated using each model are generally consistent, differences have also been reported, making it unclear which model(s) faithfully recapitulate DUX4 and FSHD biology. In this study, we systematically compared RNA-seq data generated from three different models of FSHD—lentiviral-based DUX4 expression in myoblasts, doxycycline-inducible DUX4 in myoblasts, and differentiated human FSHD myocytes expressing endogenous DUX4—and show that the DUX4-associated gene expression signatures of each dataset are highly correlated (Pearson’s correlation coefficient, r ~ 0.75-0.85). The few robust differences were attributable to different states of cell differentiation and other differences in experimental design. Our study describes a model system for inducible DUX4 expression that enables reproducible and synchronized experiments and validates the fidelity and FSHD relevance of multiple distinct models of DUX4 expression.
2016-09-21 | GSE85461 | GEO
Project description:Single cell RNA sequencing was performed on a CML derived cell line, which contains a TET-ON inducible system for DUX4 inducible expression (DIE). In attempt of finding key players early in the DUX4 induced process, we performed single-cell RNA sequencing (SCS) on induced DIE cells, as early as 2 hours after induction. In a sequential manner, DIE cells induced for 3, 4, and 6 hours were also collected and used for SCS. By analysing these cells at a single cell level, we aimed to find (subtle) changes in the DIE cell transcriptome, that start early after DUX4 induction.
2021-01-01 | GSE156154 | GEO