ISWI ATP-ases, Smarca5 and Smarca1, are required for normal murine neocortical development
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA722856 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14270606_1.fastq.gz | Fastqsanger.gz | |||
| SRR14270606_2.fastq.gz | Fastqsanger.gz | |||
| SRR14270607_1.fastq.gz | Fastqsanger.gz | |||
| SRR14270607_2.fastq.gz | Fastqsanger.gz | |||
| SRR14270608_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:Chromatin remodeling complexes modulate DNA accessibility permitting neuronal progenitor cells to proliferate and differentiate to form the mammalian neocortex. Smarca5 and Smarca1 are the ISWI ATP-ase proteins, within a variety of chromatin remodelling complexes. We created a mouse model with a truncated Smarca1, which inactivates the ATPase nucleosome rearranging activity of the protein. Secondly, using the cre/loxp system, we conditionally removed exon 5 of the Smarca5 gene, resulting in a null allele solely in the cortex of the mouse. Ultimately, we knockout (KO) both the Smarca5 and Smarca1 genes to analyze neocortical neurogenesis at E13.5 and identify their cooperative role during embryonic brain development. The DKO mice reveal significant forebrain hypoplasia.
2023-04-12 | GSE172294 | GEO
Project description:Regulation of the transcriptome to promote meiosis is important for sperm development and fertility. However, how chromatin remodeling directs the transcriptome during meiosis in male germ cells is largely unknown. Here, we demonstrate that the ISWI family ATP-dependent chromatin remodeling factor SMARCA5 (SNF2H) plays a critical role in regulating meiotic prophase progression during spermatogenesis. Males with germ cell-specific depletion of SMARCA5 are infertile and unable to form sperm. Loss of Smarca5 results in failure of meiotic progression with abnormal spermatocytes beginning at the pachytene stage and an aberrant global increase in chromatin accessibility, especially at genes important for meiotic prophase.
2024-12-05 | GSE279216 | GEO
Project description:We hypothesize that the ISWI ATPase Smarca5 plays a role in hematopoietic stem cell development via its interaction partners, and to study the role, we used a mouse model with transgenic expression of SMARCA5 coupled with mass spectrometry analysis. The study uses transgenic SMARCA5 mouse model with conditional hypomorphic allele (lower expression on protein level compared to controls) incorporated into Rosa26 locus, transgenic allele uses endogenous Rosa26 promoter. The transgenic human SMARCA5 protein has a FLAG tag at its C-terminus, which allows specific immunoprecipitation and also differentiation from the endogenous protein (human and mouse SMARCA5 are almost identical at the protein level). To ensure the highest possible expression of the transgenic allele, we used a model that also had one endogenous Smarca5 allele deleted. Various organs (thymus, spleen, brain, kidney, liver, testes, muscle, fetal liver) were isolated from transgenic mice, lysed and then immunoprecipitated using anti-FLAG antibody. The immunoprecipitates were then analyzed using mass spectrometry to determine SMARCA5 interactomes in various tissues. Transgenic human SMARCA5 was confirmed to form all the expected complexes and capable of replacing the functions of the mouse protein. For details, see the publication of Turkova et al. 2024 in Communications Biology.
2024-06-22 | PXD049034 | Pride
Project description:Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
2023-03-01 | GSE160459 | GEO
Project description:Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
2023-03-01 | GSE160458 | GEO
Project description:Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
2023-03-01 | GSE220778 | GEO
Project description:Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
2023-03-01 | GSE160469 | GEO
Project description:Genetic models suggested that SMARCA5 was required for DNA templated events including transcription, DNA replication and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch (ISWI) complexes, in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6hr of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
2023-03-01 | GSE160468 | GEO
Project description:Zygotic genome activation in mice happens in two waves, a minor wave in the 1 cell embryo, and a major wave at the two-cell stage, both accompanied by global transcriptional and epigenetic reprogramming. However, the orchestration of these reprogramming events by maternal factors deposited in the oocyte is not yet entirely understood. We and others have recently shown that epigenetic modifiers such as SMARCA5 (the main ATPase in ISWI complexes), can initiate the ZGA transcriptional programme in vitro. So far, the role of SMARCA5 in ZGA in vivo has not been addressed, as constitutive knock-out mice lacking SMARCA5 are not viable. We have overcome this issue by using the targeted protein-depletion system Trim-Away. Degradation of SMARCA5 in early zygotes in combination with single cell multi-omics methods allow us to investigate its role in transcription, DNA methylation and chromatin accessibility during ZGA, as well as the wider impact of the lack of maternal SMARCA5 on embryonic development. We show that in absence of SMARCA5, major ZGA transcription is downregulated, whereas maternal and other genes are upregulated. Our results show that the global accessibility at the two-cell stage is higher than in a wild-type context, and that major ZGA gene promoters are not following that global trend but remain less accessible in SMARCA5 depleted embryos. Moreover, while the accessibility of repeat elements like MERVL increases, so does the methylation level in these regions, suggesting that SMARCA5 might indirectly influence more than just the chromatin accessibility during these stages.
2024-09-18 | GSE248180 | GEO
Project description:Zygotic genome activation in mice happens in two waves, a minor wave in the 1 cell embryo, and a major wave at the two-cell stage, both accompanied by global transcriptional and epigenetic reprogramming. However, the orchestration of these reprogramming events by maternal factors deposited in the oocyte is not yet entirely understood. We and others have recently shown that epigenetic modifiers such as SMARCA5 (the main ATPase in ISWI complexes), can initiate the ZGA transcriptional programme in vitro. So far, the role of SMARCA5 in ZGA in vivo has not been addressed, as constitutive knock-out mice lacking SMARCA5 are not viable. We have overcome this issue by using the targeted protein-depletion system Trim-Away. Degradation of SMARCA5 in early zygotes in combination with single cell multi-omics methods allow us to investigate its role in transcription, DNA methylation and chromatin accessibility during ZGA, as well as the wider impact of the lack of maternal SMARCA5 on embryonic development. We show that in absence of SMARCA5, major ZGA transcription is downregulated, whereas maternal and other genes are upregulated. Our results show that the global accessibility at the two-cell stage is higher than in a wild-type context, and that major ZGA gene promoters are not following that global trend but remain less accessible in SMARCA5 depleted embryos. Moreover, while the accessibility of repeat elements like MERVL increases, so does the methylation level in these regions, suggesting that SMARCA5 might indirectly influence more than just the chromatin accessibility during these stages.
2024-09-18 | GSE248179 | GEO