DNA methylation reprogramming during early zebrafish embryo development
Survey
10.1016/j.cell.2013.04.041
GSE44075
5-methylcytosine is a major epigenetic modification that is sometimes called ‘‘the fifth nucleotide.’’ However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes, including zebrafish gametes and early embryos. The oocyte methylome is significantly hypomethylated compared to sperm. Strikingly, the paternal DNA methylation pattern is maintained throughout early embryogenesis. The maternal DNA methylation pattern is maintained until the 16-cell stage. Then, the oocyte methylome is gradually discarded through cell division and is progressively reprogrammed to a pattern similar to that of the sperm methylome. The passive demethylation rate and the de novo methylation rate are similar in the maternal DNA. By the midblastula stage, the embryo’s methylome is virtually identical to the sperm methylome. Moreover, inheritance of the sperm methylome facilitates the epigenetic regulation of embryogenesis. Therefore, besides DNA sequences, sperm DNA methylome is also inherited in zebrafish early embryos.
True
zhuwei
June 11, 2016, 10:16 p.m.
Feb. 12, 2019, 12:58 a.m.
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006624BS | DCD000227SR | tissue | Liu Lab, Beijing Institute of Genomics, CAS | TU | 90 Days-2 Years | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001355AA | DCD012875BR | MeDIP-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001139SQ | DCD001365TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001351AA | DCD012879BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001135SQ | DCD001361TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001350AA | DCD012880BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001134SQ | DCD001360TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001349AA | DCD012881BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001133SQ | DCD001359TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001348AA | DCD012882BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001132SQ | DCD001358TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001346AA | DCD012884BR | RNA-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001130SQ | DCD001356TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006625BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | 2-cell | 0.75 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001356AA | DCD012874BR | MeDIP-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001140SQ | DCD001366TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006626BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | 16-cell | 1.5 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001360AA | DCD012870BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001144SQ | DCD001370TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001359AA | DCD012871BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001143SQ | DCD001369TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001358AA | DCD012872BR | MeDIP-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001142SQ | DCD001368TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001357AA | DCD012873BR | MeDIP-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001141SQ | DCD001367TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006627BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | 32-cell | 1.75 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001365AA | DCD012865BR | TAB-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001149SQ | DCD001375TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001364AA | DCD012866BR | TAB-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001148SQ | DCD001374TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001363AA | DCD012867BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001147SQ | DCD001373TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001362AA | DCD012868BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001146SQ | DCD001372TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001361AA | DCD012869BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001145SQ | DCD001371TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006628BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | 64-cell | 2 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001369AA | DCD012861BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001153SQ | DCD001379TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001368AA | DCD012862BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001152SQ | DCD001378TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001367AA | DCD012863BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001151SQ | DCD001377TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001366AA | DCD012864BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001150SQ | DCD001376TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006629BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | 128-cell | 2.25 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001373AA | DCD012857BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001157SQ | DCD001383TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001372AA | DCD012858BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001156SQ | DCD001382TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001371AA | DCD012859BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001155SQ | DCD001381TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001370AA | DCD012860BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001154SQ | DCD001380TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006630BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | 1k-cell | 3 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001379AA | DCD012851BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001163SQ | DCD001389TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001378AA | DCD012852BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001162SQ | DCD001388TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001377AA | DCD012853BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001161SQ | DCD001387TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001376AA | DCD012854BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001160SQ | DCD001386TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001375AA | DCD012855BR | RNA-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001159SQ | DCD001385TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001374AA | DCD012856BR | MeDIP-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001158SQ | DCD001384TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006631BS | DCD000227SR | whole organism | Liu Lab, Beijing Institute of Genomics, CAS | TU | Germ-ring | 5.66 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001382AA | DCD012848BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001166SQ | DCD001392TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001381AA | DCD012849BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001165SQ | DCD001391TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001380AA | DCD012850BR | RNA-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001164SQ | DCD001390TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006632BS | DCD000227SR | tissue | Liu Lab, Beijing Institute of Genomics, CAS | TU | 90 Days-2 Years | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001388AA | DCD012842BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD001172SQ | DCD001398TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | — | — | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001387AA | DCD012843BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001171SQ | DCD001397TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001386AA | DCD012844BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001170SQ | DCD001396TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001385AA | DCD012845BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001169SQ | DCD001395TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001384AA | DCD012846BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001168SQ | DCD001394TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001383AA | DCD012847BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001167SQ | DCD001393TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006995BS | DCD000227SR | tissue | Liu Lab, Beijing Institute of Genomics, CAS | TU | 90 Days-2 Years | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001354AA | DCD012876BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001138SQ | DCD001364TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001353AA | DCD012877BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001137SQ | DCD001363TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001352AA | DCD012878BR | BS-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001136SQ | DCD001362TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001347AA | DCD012883BR | RNA-seq_Liu_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD001131SQ | DCD001357TR | Liu Lab, Beijing Institute of Genomics, CAS | Illumina | HiSeq 2000 | 01/01/2001 |