UCSC Smooth Muscle Methylome Browser

Department of Physiology and Cell Biology

The UCSC SM Methylome Browser is an interactive browser which was built with custom tracks representing the methylome and transcriptome of Dnmt1-WT and Dnmt1-KO murine jejunal smooth muscle. This browser provides a comprehensive reference for genomic DNA methylation status at CpG sites in Dnmt1-WT and Dnmt1-KO. The browser can also interact with the genome bioinformatics (e.g. ENCODE) data publically available in the UCSC Genome Browser.  

Access the UCSC Smooth Muscle Methylome Browser
(Opens in New Window; Requires Google Chrome and may take a few minutes to upload the large files)

Applications

  1. Searching for CpG methylation sensitive or DNMT1 regulated genes
  2. Searching for methylation status at specific CpG sites within a genomic location
  3. Searching for CpG methylation status at genetically variable regions (e.g. SNPs)
  4. Searching for CpG methylation status at genetic and epigenetic regulatory regions (e.g. binding sites of transcription factors, enhancers, insulators, locus control regions, and novel elements)
  5. Searching for epigenetic regulators (e.g. histone modifiers, enhancers, insulators, promoters, locus control regions, and novel elements) that are associated with CpG methylation

Search instructions

  1. To search for the methylation status at specific CpG sites in a gene body, type the gene name, and click "go."
  2. Under "Custom Tracks," select the view option (e.g., "full") for each sample (e.g., "Dnmt1-KOme", "Dnmt1-WTme", "Dnmt1-KO", and/or "Dnmt1-WT), and click "refresh."
  3. Select the bioinformatics data of interest (e.g., click on "full" under "RefSeq Genes" in "Genes and Gene Predictions" and/or "show" under "Expression and Regulation" for CpG Islands), and then click "refresh."
  4. Select options in each bioinformatics data (e.g., click "Caltech TFBS," select "SRF," change the display mode to "full," and click "Submit").
  5. Click "configure" to optimize views (for changing image width and text size).
  6. To remove any unwanted data, select "hide" in the view option and click "refresh."
  7. Zoom in or out to change the view.
  8. To download any DNA sequence, go to "View", select "DNA", and click "get DNA" (or "extended case/color options" to modify formatting options).

Methylome

Methyl-MidiSeq was performed on Dnmt1-WT and Dnmt1-KO murine jejunal smooth muscle through extraction of gDNA, fragmentation, end modification, bisulfite conversion, limited amplification and finally sequencing. After sequencing was complete, bioinformatic processing was utilized to compare the amount of methylation at CpG sites between Dnmt1-WT and Dnmt1-KO samples.

Methyl-MidiSeq Data
SampleTotal Read (pairs)MappingUnique CpGsAvg CpG coverageBisulfite conversion rate
Dnmt1-WTme 240,783,359 53% 15,259,699 9X 99%
Dnmt1-KOme 237,493,706 53% 14,680,291 11X 99%

Transcriptome

RNA-seq libraries were generated from Dnmt1-WT and Dnmt1­-KO murine jejunal smooth muscle using an Illumina kit for sequencing on an Illumina HiSeq 2000 (paired-end sequencing run with 101 nt read length). Sequencing reads were assembled and annotated to the reference genome (mm10) using TopHat v1.4.1 software.

Transcriptome Data
SampleTotal readMapped readKnown gene
Dnmt1-WT 341,290,850 291,592,121 14,319
Dnmt1-KO 252,046,246 206,053,958 16,993

Reference

Jorgensen BG*, Berent RM*, Ha S*, Horiguchi K, Sasse KC, Becker LS, Ro S. DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease. *Equally contributed In review