About

Overview

DNA methylation is one major epigenetic modification that is crucial for the development and differentiation of various cell types in an organism. MethBank is a database of DNA methylome programming, dedicating to storing, browsing and mining single-base nucleotide whole-genome methylation data of early embryos spanning different animals. At present, large cohorts of early embryo methylomes for Danio rerio and Mus musculus are available in MethBank.

MethBank features integration and visualization of high-resolution DNA methylomes. Currently MethBank incorporates large cohorts of gamete and early embryo methylomes for Danio Rerio and Mus musculus. For each developmental stage, about 90% of all CpGs in the whole genome are covered, with about 17~20 million and ~20 million methylated CG sites measured for Danio rerio and Mus musculus, respectively. As genetic polymorphisms may disrupt the methylation status and gene expression correlates closely with DNA methylation status, a large number of SNPs and expression profiles are also included in MethBank. Therefore, MethBank can help users retrieve methylation levels for a specific region or gene, locate differentially methylated regions, and unveil the corresponding expression profile and SNP information.

In addition, a user-friendly methylome browser bulit on JBrowse is installed in MethBank, allowing users to visualize high-quality DNA methylation profiles as well as related data (including gene expression, SNP, CpG islands, etc.) in an interactive manner and thus to investigate methylation patterns of gametes and early embryos at different developmental stages within specific genomic regions. Database-mining and statistical tools help users retrieve, filter, and analyze methylation profiles in diverse ways.

Ongoing efforts are focused on incorporation of methylomes and related data from other animals, aiming to provide an important resource for the epigenetic and developmental studies. Methylation data from other labs are also encouraged to be submitted to MethBank.


Data Statistics

Species Number of methylated CG sites Number of DMRs Number of SNPs Number of expressed genes Number of CpG Islands
Zebrafish
  • sperm: 20,606,757
  • egg: 20,987,274
  • 16-cell: 18,948,935
  • 32-cell: 20,825,693
  • 64-cell: 17,836,722
  • 128-cell: 19,889,625
  • 1k-cell: 20,815,960
  • germ ring: 19,258,632
  • testis: 20,095,377
  • Sperm vs Egg: 53,680
  • 1k vs Egg: 51,886
  • 1k vs 57h: 95
  • 57h vs Egg: 36,004
  • TU (female): 3,653,795
  • TL (male): 3,423,892
  • 1k-cell: 12,168
  • germ ring: 12,129
  • sperm: 13,529
  • egg: 11,191
8,768
Mouse
  • sperm: 19,455,209
  • oocyte: 19,100,312
  • 2-cell: 19,844,915
  • 4-cell : 19,637,338
  • E7.5: 19,644,831
  • E6.5: 19,805,268,
  • ICM: 19,523,556
  • E13.5 female: 19,253,566
  • E13.5 male: 19,352,586
  • Sperm vs Oocyte: 2,000
2,561,574 18,259 37,730

Zebrafish

The zebrafish (Danio rerio), a tropical freshwater fish, belongs to the minnow family (Cyprinidae) of the order Cypriniformes. Zebrafish is found in the streams, canals, ponds of the southern Himalayan region including parts of India, Pakistan, Bangladesh, Nepal, and Burma.

Zebrafish are omnivorous, mainly eating zooplankton, insects and insect larvae. The male zebrafish is torpedo-shaped, having gold stripes between the blue stripes; the female is characteristic of larger, whitish belly and sliver stripes between the blue stripes. The length of adult zebrafish can reach 6.4 cm. In captivity, the length is seldom larger than 4 cm. Its lifespan in capivity is around two to three years.

The approximate generation time for zebrafish is about three to four months. Females lay hundreds of eggs at intervals of two to three days with the requirement for the presence of a male. Fertilized eggs immediately become transparent, followed by embryonic development. Precursors to all major organs appear within 36 hours of fertilization. Swimming and feeding behavior begin about 36 hours later. The sex of juvenile zebrafish can not be distinguished except by dissection and sex determinants are not clearly understood.

Zebrafish embryo develops rapidly with its genome fully sequenced and well-understood, therefore, it is commonly used as a model organism for studies of vertebrate development and gene function. The annotated zebrafish genome is about 1.4 giga bases, including 24.2 million CpG sites.


Mouse

The house mouse (Mus musculus), a small mammal, belongs to the order Rodentia, having a pointed snout, small rounded ears and a long naked or almost hairless tail. They are omnivorous, primarily feeding on plants.

An adult house mouse has a body length of 7.5-10 cm (nose to base of tail), and a tail length of 5-10 cm. The lifespan in the lab is up to 2-3 years, while in the wild the average mouse rarely lives beyond 1 year mainly due to predation. In the wild, the color of mice vary from light to dark brown, while in the lab, they are produced in colors from white to champagne to black.

Female house mice have a four to six day long estrous cycle, with estrus itself lasting less than a day. If females are held together, they will usually not have an estrus. They will have estrus after 72 hours with exposure to males. During mating behavior, male house mice emit 10 kHz-110 kHz ultrasonic calls to court females.

After copulation, a copulation plug will be developed in female mice to prevent further copulation. This plug usually exists for about 24 hours. Following a 19-21 day gestation period, female house mice give birth to a litter of 3-14 pups. Within a year, one female can have 5-10 litters.

The house mouse is by far one of the most important model organisms for scientific research. The annotated house mouse genome is about 2.5 giga bases, including about 20 million CpG sites.