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H3K27ac ChIP-seq Analysis in WT and MIER1 Depletion Liver Tissues at 0 h and 24 h after 70% Partial Hepatectomy

ABSTRACT: To explore how Mier1 influence the genome H3K27ac levels during liver regeneration, we performed H3K27ac chromatin immunoprecipitation followed by sequencing in control and liver-specific Mier1 ko liver tissues at 0 h and 24 h after 70% partial hepatectomy (PHx). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals.Then we performed 70% partial hepatectomy, 3 weeks after AAV injection. Consistent with the increased expression of cell cycle genes during liver regeneration, we observed increased signals of H3K27ac at 24 h after hepatectomy, especially near some cell cycle genes, after MIER1 depletion in liver tissue.

ORGANISM(S): Mus musculus

PROVIDER: GSE188742 | GEO | 2022/12/30

REPOSITORIES: GEO

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Analysis of Control and Liver-specific Mier1 KO Liver Transcriptomes after 70% Partial Hepatectomy

Project description:To explore how Mier1 affiects liver regeneration, we specifically knocked out Mier1 in mouse liver through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy, 3 weeks after AAV injection. We then performed RNA sequencing analysis on liver tissues collected from control and Mier1 ko groups at 0 h, 24 h, 36 h, 48 h and 72 h after partial hepatectomy. Interestingly, although MIER1 depletion did not cause a significant difference in expression of cell cycle genes before surgery, the increase of cell cycle gene expression during liver regeneration was significantly enhanced after MIER1 loss. Further analysis showed that after partial hepatectomy, MIER1 loss caused significant upregulation of genes enriched in cell proliferation relevant pathways.

2022-12-30 | GSE188421 | GEO

RNA-seq Analysis of Mier1 Effects in HFD Aging and Adipose Tissue Lipe Knockout Mice after 70% Partial Hepatectomy

Project description:To explore how Mier1 affiects high-fat diet-fed, aging and adipose tissue Lipe knockout mice liver regeneration, we specifically knocked out liver Mier1 in high-fat diet-fed, aging and adipose tissue Lipe knockout mice through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy on high-fat diet-fed, aging and adipose tissue Lipe knockout mice. We then performed RNA sequencing analysis on liver tissues collected from control and Mier1 ko groups at 0 h, 48h or 36 h after partial hepatectomy. RNA-seq analysis showed that after partial hepatectomy, MIER1 loss caused significant upregulation of genes enriched in cell proliferation relevant pathways.

2022-12-31 | GSE212628 | GEO

ATAC-seq Analysis in Control and Mier1 KO Mice Liver at 0 h and 24 h after 70% Partial Hepatectomy

Project description:To explore how Mier1 affects liver regeneration, we specifically knocked out Mier1 in mouse liver through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy, 3 weeks after AAV injection. We then performed ATAC-seq in Control and Mier1 liver-sepcific knockout mice liver tissues at 0 h and 24 h after PHx to explore the influence of Mier1 on the chromation opening during liver regeneration.

2022-12-31 | GSE212626 | GEO

MIER1-FLAG ChIP-seq Analysis in Liver at 0 h and 24 h after 70% Partial Hepatectomy

Project description:To explore how Mier1 influence liver regeneration, we performed chromatin immunoprecipitation followed by sequencing in liver tissues at 0 h and 24 h after 70% partial hepatectomy (PHx). Due to a lack of available MIER1 antibody for ChIP-seq analysis, exogenous liver expression of MIER1-FLAG under TBG promoter was executed using AAV vectors, and ChIP-seq was conducted using FLAG antibody. Liver tissues from animals receiving empty vectors were also collected for ChIP-seq with FLAG antibody as negative control to remove possible non-specific binding signals from FLAG antibody. We observed in total 9310 sites bound by MIER1 in total, with a majority of these binding sites around the transcription start sites or present in introns or exons. Further analysis combining the results from RNA-seq revealed a significant set of genes involved in cell cycle, DNA replication and chromosome organization, that were bound by MIER1 and upregulated after MIER1 loss in liver tissues 24 hours after surgery, indicating a direct functional regulation of these genes via MIER1.

2022-12-30 | GSE188747 | GEO

Analysis of the role of Mcu in the regenerating mouse liver after partial hepatectomy

Project description:In this study, we analyzed global liver gene expression in MCU knock-down (KD) mice. MCUloxp/loxp male mice were treated with an AAV8-Cre under the control of a hepatocyte specific promoter (TBG) to generate liver-specific MCU KD mice. AAV8-TBG-Null treated littermates were used as controls. Knockdown was verified 3 weeks after injection by protein and mRNA (80%). 5 weeks after injection mice were subjected to 70% partial hepatectomy and liver semples were collected 30h after the sugery. Mouse Clariom S (Affymetrix, Santa Clara, CA) arrays were used to obtain global gene expression data from pooled liver samples (pools of 4 biological replicates per array).

2020-01-01 | GSE137891 | GEO

Consequences of beta-PDGFR deletion on hepatic stellate cells during hepatic regeneration

Project description:Purpose: The goal of this study was to determine biological consequences during liver regeneration following partial hepatectomy in mice by next-generation sequencing. A particular interest was to compare mice with either a floxed b-PDGFR allele to mice that harbored a deletion of b-PDGFR in hepatic stellate cells (HSCs), by crossing b-PDGFR fl/fl mice with transgenic GFAP-Cre mice. Methods: b-PDGFR fl/fl mice or mice with a HSC-specific deletion of b-PDGFR underwent either sham operation or 70% partial hepatectomy. Following 72 hours, livers were collected and total RNA was extracted using tizol, followed by a purification using Quiagen spin columns including an on-column DNAse digestion step. Conclusion: Our study represents a detailed analysis of hepatic transcriptome, with biologic replicates, generated by RNA-seq technology of livers following sham operation or partial hepatectomy in b-PDGFR fl/fl mice or b-PDGFRfl/fl/GRAP-Cre mice. Whole liver mRNA profiles of sham operated livers or livers collected 72hours after partial hepatectomy of beta-PDGFR fl/fl and beta-PDGFR fl/fl/GFAP-Cre (creating a hepatic stellate cell-specific deletion of b-PDGFR) mice were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

2013-11-08 | E-GEOD-52234 | biostudies-arrayexpress

Gene expression profiling of HDAC3-depleted mouse liver rescued with wild-type exogenous HDAC3

Project description:We have shown that intravenous injection of HDAC3 floxed mice with adeno-associated virus (AAV) expressing Cre depletes hepatic HDAC3, upregulates lipogenic gene expression, and causes fatty liver. When AAV-Flag-HDAC3 wild-type (WT) is co-injected along with AAV-Cre, the exogenous HDAC3 is expressed at endogenous levels and can completely rescue fatty liver phenotype. Here we profile transcriptome of the rescued WT livers in comparison with HDAC3-depleted (KO) livers. 4-months old C57BL/6 male mice were co-injected with AAV-Cre or AAV-Cre plus AAV-Flag-HDAC3. Mice were fed ad libitum and harvested at 5 pm (ZT10) at 2-weeks post-injection. Liver total RNA was extracted and hybridized to Affymetrix Mouse Gene 1.0ST array.

2013-11-25 | E-GEOD-49386 | biostudies-arrayexpress

Effect of conditional deletion of S6 ribosomal protein following partial hepatectomy

Project description:Deletion of the RPS6 gene in mouse liver results in the inhibition of 40S ribosome biogenesis and the failure of hepatocytes to enter S-phase following partial hepatectomy. This microarray experiment was designed to assess the effects of RPS6 deletion on the expression of genes involved in liver regeneration following partial hepatectomy. Keywords: time course, liver RNA was isolated from mouse livers at different time-points following partial hepatectomy. Conditional deletion of the RPS6 gene was perfomed by injecting polyinosinic-polycytidylic acid in mice harbouring a floxed version of the RPS6 gene and a cre recombinase under the regulation of an interferon responsive promoter (MX-CRE). The mice used a control have also a floxed version of the RPS6 gene but lack the cre recombinaste transgene.

2009-05-01 | E-GEOD-13864 | biostudies-arrayexpress

Consequences of beta-PDGFR deletion on hepatic stellate cells during hepatic regeneration

2013-11-08 | GSE52234 | GEO

ChIP-seq analysis of E2f4, H3K4me2 and H3K27ac in the mouse livers

Project description:Arid1a is the subunit of SWI/SNF complex, which was reported to guide SWI/SNF to DNA. Here, we found that loss of Arid1a in the liver results in improved liver regeneration after partial hepatectomy.Genome-wide analysis showed that after hepatectomy,loss of Arid1a reduces the recruitment and activity of E2F4 on target promoters, resulting in expression programs that favor regeneration during injury. Correspondingly, these promoters showed increased H3k4me2 and H3k27ac marks, indicating de-repression of these E2f target genes. The post partial hepatectomy mice liver cells were fixed and isolated, analysis of genomic occupancy of E2f4,H3K4me2,H3K27ac in hepatocytes from Arid1a WT and Arid1a liver specific KO mice by ChIP-seq.

2016-03-30 | E-GEOD-76927 | biostudies-arrayexpress

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