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RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

ABSTRACT: We performed methylome profiling for mouse frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE108762 | GEO | 2019/07/25

REPOSITORIES: GEO

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RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

Project description:RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

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RNA-seq of Egr1-/- and Tet1-/- mouse frontal cortex

Project description:We performed transcriptome profiling for frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.

2019-07-25 | GSE108750 | GEO

RNA-seq of Egr1-/- and Tet1-/- mouse frontal cortex

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Egr1 Recruits Tet1 to Shape the Brain Methylome during Early Postnatal Development

Project description:Early growth response gene-1 (Egr1) is a critical transcription factor involved in many important biological processes, including neuronal plasticity and memory formation. With a rapid increase in expression during the first few weeks after birth, Egr1 controls the selection, maturation and functional integration of newborn neurons. The regulation of Egr1-mediated gene expression has been shown to be under methylation control. However, Egr1 target sites and their epigenetic regulation in the nervous system remains largely unknown. In this study, we performed ChIP-seq for EGR1 in mouse frontal cortex and identified a large number of EGR1 binding sites with their cell-type specific methylation patterns established during postnatal frontal cortex development. More specifically, the CpG dinucleotides within these EGR1 binding sites become hypo-methylated in mature neurons but remain heavily methylated in glia. We further demonstrated that EGR1 recruits a DNA demethylase TET1 to remove DNA methylation at EGR1 binding sites and activate downstream genes. In addition, we found that the frontal cortexes from knockout mice with the loss of Egr1 or Tet1 share strikingly similar profiles in both gene expression and DNA methylation. In summary, our study reveals Egr1 as a key mediator for gene-environment interactions shaping brain methylome together with Tet1 during early postnatal development and provides an important new insight into how early life experience may shape the brain methylome. This SuperSeries is composed of the SubSeries listed below.

2019-07-25 | GSE108768 | GEO

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Project description:UNLABELLED: Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS sequencing data is challenging and specialized alignment/mapping programs are needed. Although such programs have been developed, a comprehensive solution that provides researchers with good quality and analyzable data is still lacking. To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation. AVAILABILITY AND IMPLEMENTATION: SAAP-RRBS is freely available to non-commercial users at the web site http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.

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GENE-SWITCH Pig DNA methylation with Reduced representation bisulfite sequencing (RRBS)

Project description: Not available

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GENE-SWITCH Chicken DNA methylation with Reduced representation bisulfite sequencing (RRBS)

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High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS).

Project description:Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500. All sequencing data are deposited in the GEO database under accession number GSE87097.

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Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses.

Project description:Reduced representation bisulfite sequencing (RRBS) is a powerful method of DNA methylome profiling that can be applied to single cells. However, no previous report has described how PCR-based duplication-induced artifacts affect the accuracy of this method when measuring DNA methylation levels. For quantifying the effects of duplication-induced artifacts on methylome profiling when using ultra-trace amounts of starting material, we developed a novel method, namely quantitative RRBS (Q-RRBS), in which PCR-induced duplication is excluded through the use of unique molecular identifiers (UMIs). By performing Q-RRBS on varying amounts of starting material, we determined that duplication-induced artifacts were more severe when small quantities of the starting material were used. However, through using the UMIs, we successfully eliminated these artifacts. In addition, Q-RRBS could accurately detect allele-specific methylation in absence of allele-specific genetic variants. Our results demonstrate that Q-RRBS is an optimal strategy for DNA methylation profiling of single cells or samples containing ultra-trace amounts of cells.

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Genome-wide maps of TET1 binding in mouse frontal cortex

Project description:With anti-TET1 immunoprecipitated chromatin from mouse frontal cortices, we generated TET1 binding maps with 4496 high-confidence peaks and approximately 90% of TET1 peaks were within intergenic regions.

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