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Mus musculus

ABSTRACT: Genome-wide analysis of next generation sequencing for Lsh+/+ and Lsh-/- mouse embryonic fibroblasts

PROVIDER: PRJNA246421 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1274830.fastq.gz	Fastqsanger.gz
	SRR1274821.fastq.gz	Fastqsanger.gz
	SRR1274831.fastq.gz	Fastqsanger.gz
	SRR1274822.fastq.gz	Fastqsanger.gz
	SRR1274832.fastq.gz	Fastqsanger.gz

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Transcription profiling of Mus musculus wild type vs mutant with knocked out Lsh to investigate mouse embryonic fibroblasts (MEFs)

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Transcription profiling of Mus musculus MEFs wide type and knocked out gene Lsh to investigate DNA methylation status

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2009-11-30 | E-MEXP-2383 | biostudies-arrayexpress

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Project description:We report here the distribution of the histone variant macroH2A in murine embryonic fibroblasts derived fom Lsh-/- embryos or Lsh+/+ embryos day 14 gestation using ChIP-seq analysis. We find that macroH2A1 and macroH2A2 deposition are reduced in the absence of Lsh in contrast to H2B deposition. The study identifies Lsh as important regulator of genome wide macroH2A deposition.

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Genome-wide analysis of H3K4me1 in Lsh-/- mouse embryonic fibroblasts

Project description:We report here differentiated enrichment of H3K4me1 at Lsh WT and KO mouse embryonic fibroblasts (MEFs). We found a subset of differentially enriched H3K4me1 regions in Lsh KO MEFs, and they clustered at neuronal lineage genes and overlapping with known cis-regulatory elements present in brain tissue. Reprogramming of Lsh?/? MEFs into induced pluripotent stem (iPS) cells leads to increased neuronal lineage gene expression of premarked genes and enhanced differentiation potential of Lsh?/? iPS cells toward the neuronal lineage pathway compared with WT iPS cells in vitro and in vivo. The state of H3K4me1 enrichment is partially maintained in Lsh?/? iPS cells, suggesting the regions are preserved as potential enhancers. Genome-wide maps of H3K4me1 in Lsh WT and KO primary MEFs.

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Cell-autonomous function of LSH ATPase in de novo DNA methylation

Project description:Purpose: We aimed to determine whether the expression of either wild-type or catalytically inactive LSH, carrying a single point mutation in its ATP binding site (K237Q), could restore the levels and patterns of DNA methylation in Lsh-/- mouse embryonic fibroblasts (MEFs). Methods: Lsh-/- MEFs were transduced with lentiviral particles carrying empty pMSCV vector, pMSCV-LSH-3xFLAG and pMSCV-LSH K/Q-3xFLAG, respectively. Clonal cell lines were generated and tested for LSH expression. Two independent cell lines expressing wild-type LSH and two expressing LSH K/Q were used for further analyses and comparison with wild-type MEFs and Lsh-/- MEFs carrying the empty vector. Genomic DNA was purified from all six cell lines and methylated DNA immunoprecipitation (MeDIP) was performed as described in Weber et al., 2007, Nat Genetics. MeDIP libraries were generated and sequenced on Illumina HiSeq 2000 instrument. Results and conclusions: Our experiments demonstrate that the expression of wild-type LSH, but not the catalytically inactive LSH K/Q, in Lsh-/- MEFs leads to reestablishment of DNA methylation at repetitive sequences and unique developmentally regulated loci in a cell-autonomous manner. Analyses of DNA methylation upon expression of either wild-type or catalytically-inactive LSH in Lsh-/- mouse embryonic fibroblasts.

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