Genome-wide maps of macroH2A and H2B distribution in murine embryonic fibroblasts in dependence of Lsh.
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE142082 | GEO | 2020/08/13
REPOSITORIES: GEO
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Project description:Here we report that the histone variant macroH2A acts as a barrier to induced pluripotency. Using fibroblasts isolated from macroH2A double knockout mice, we observed enhanced reprogramming efficiency compared to fibroblasts from wild type animals. We further show that macroH2A isoforms act synergistically in this process. Genomic analysis in wild type fibroblasts reveals that macroH2A1 and H3K27me3 domains co-localize and occupy pluripotency genes. While the absence of macroH2A does not affect H3K27me3 in fibroblasts, macroH2A1 is highly enriched at a set of Utx target genes that are reactivated early during iPS reprogramming. Mononucleosomes from Dermal Fibroblasts (from wt and macroH2A1 and macroH2A2 double knockout mice) were isolated and ChIP'd with mH2A1, H3K27me3 and H3K27ac antibodies. DNA from Input and ChIP samples was purified and sequenced on Illumina's Hiseq.
2013-03-01 | E-GEOD-40813 | biostudies-arrayexpress
Project description:Here, we characterized de novo chromatin deposition of macroH2A2 using temporal genomic profiling in cells devoid of all macroH2A isoforms. We find that macroH2A2 is first pervasively deposited genome-wide and subsequently pruned to establish mature domains. This transient incorporation occurs preferentially at transcribed regions adjacent to future mature macroH2A2 domains and transcriptional inhibition prevents the clearing of promiscuously incorporated macroH2A2. Furthermore, CRISPR/Cas9-based manipulation of the transcriptional activity at a given locus reveals that transcriptional silencing triggers ectopic macroH2A2 accumulation, while activation depletes pre-existing macroH2A2. We demonstrate that the FACT (facilitates chromatin transcription) complex is required for macroH2A2 removal from transcribed chromatin. Taken together, we have identified a transcription-associated pruning mechanism that establishes and maintains the faithful genomic localization of macroH2A variants.
2018-10-05 | GSE109740 | GEO
Project description:MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Our gene expression studies indicate that macroH2A.1 and macroH2A.2 work together to regulate specific genes. In these studies we examine the distributions of macroH2A.1 and macroH2A.2 nucleosomes to determine if they are localized to the genes that show altered expression in macroH2A knockout mouse liver. MacroH2A.1 and macroH2A.2 nucleosomes prepared from ~ 50 fetal mouse livers were purified by thio-affinity chromatography. Five samples were sequenced: Thiopropyl Sepharose, Normal Liver - contains mononucleosomal DNA from macroH2A.1-containing nucleosomes; Activate Thiol Sepharose, Normal Liver - contains mononucleosomal DNA primarily from macroH2A.2-containing nucleosomes. Starting Material, Normal Liver - this is a reference samplefor the first two samples. It contains mononucleosomal DNA from bulk fetal liver chromatin. Activated Thiol Sepharose, Knockout Livers - this is a control sample that contains mononucleosomal DNA from non-macroH2A nucleosomes that contaminate the macroH2A.2 nucleosomes. This fraction was prepared from macroH2A1/2 double knockout fetal livers; Starting Material, Knockout Liver - this is a reference sample for the fourth sample. It contains mononucleosomal DNA from bulk chromatin prepared from macroH2A1/2 double knockout fetal livers.
2014-10-15 | E-GEOD-57796 | biostudies-arrayexpress
Project description:MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Here we examine macroH2A function in vivo by knocking out both macroH2A1 and macroH2A2 in the mouse. We used microarrays to examine how the absence of macroH2A.1 and macroH2A.2 histone variants affect gene expression late fetal mouse liver. Wild-type and macroH2A1/2 double knockout pre-implantation embryos were collected, mixed and implanted into wild-type recipient females. Livers were collected from the resultant fetuses at 18.5 days post coitum and snap frozen with liquid nitrogen. Total RNA was extracted from the livers using Trizol.
2014-10-15 | E-GEOD-57086 | biostudies-arrayexpress
Project description:Here we report that the histone variant macroH2A acts as a barrier to induced pluripotency. Using fibroblasts isolated from macroH2A double knockout mice, we observed enhanced reprogramming efficiency compared to fibroblasts from wild type animals. We further show that macroH2A isoforms act synergistically in this process. Genomic analysis in wild type fibroblasts reveals that macroH2A1 and H3K27me3 domains co-localize and occupy pluripotency genes. While the absence of macroH2A does not affect H3K27me3 in fibroblasts, macroH2A1 is highly enriched at a set of Utx target genes that are reactivated early during iPS reprogramming.
2013-03-01 | GSE40813 | GEO
Project description:MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Here we examine macroH2A function in vivo by knocking out both macroH2A1 and macroH2A2 in the mouse. We used microarrays to examine how the absence of macroH2A.1 and macroH2A.2 histone variants affect gene expression fasted adult mouse liver.
2014-10-15 | GSE57088 | GEO
Project description:MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Here we examine macroH2A function in vivo by knocking out both macroH2A1 and macroH2A2 in the mouse. We used microarrays to examine how the absence of macroH2A.1 and macroH2A.2 histone variants affect gene expression late fetal mouse liver.
2014-10-15 | GSE57086 | GEO
Project description:The histone variant macroH2A forms large chromatin domains and serves as a transcriptional repression marker. It has been found that the overall quantity of macroH2A deposition on chromatin undergoes dynamic changes during the cell cycle. However, the genomic features relevant to these dynamic changes in macroH2A1 deposition during the cell cycle remain poorly understood. We combined ChIP‑seq and cell synchronization in mouse NIH-3T3 cells to examine the dynamic changes of macroH2A1 deposition on the genome between G1/S phase and metaphase. Interestingly, we observed that macroH2A1 deposition dynamically changes within the large macroH2A1 domain at G1/S phase and metaphase, which was associated with transcriptional activity. These dynamic changes occurring at gene bodies can specifically mark cell-cycle-specific genes. Taken together, we propose that macroH2A1 is a dynamic histone variant associated with cell-cycle-specific genes and plays a crucial role in cell-cycle-specific transcriptional repression.
2023-10-02 | GSE234016 | GEO
Project description:MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Here we examine macroH2A function in vivo by knocking out both macroH2A1 and macroH2A2 in the mouse. We used microarrays to examine how the absence of macroH2A.1 and macroH2A.2 histone variants affect gene expression fasted adult mouse liver. Two month old male mice were fasted overnight (~16 hours). Mice were sacrificed between 9:00 and 10:00 AM, livers were collected and snap frozen with liquid nitrogen. Total RNA was extract with Trizol (life technologies) following standard protocol.
2014-10-15 | E-GEOD-57088 | biostudies-arrayexpress
Project description:Genome-wide maps of macroH2A and H2B distribution in murine embryonic fibroblasts in dependence of Lsh.
| PRJNA595882 | ENA