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| Status |
Public on May 03, 2016 |
| Title |
Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
The epigenetic DNA modification 5-hydroxymethylcytosine (5hmC) has crucial roles in development and gene regulation. Quantifying the abundance of this epigenetic mark at the single-cell level could enable us to understand its roles. We present a single-cell, genome-wide and strand-specific 5hmC sequencing technology based on 5hmC glucosylation and glucosylation-dependent digestion of DNA, that reveals pronounced cell-to-cell variability in the abundance of 5hmC on the two DNA strands of a given chromosome. We develop a mathematical model that reproduces the strand bias and use this model to make two main predictions. First, the variation in strand bias should decrease when 5hmC turnover increases. Second, the strand bias of two sister cells should be strongly anti-correlated. We validate these predictions experimentally, and use our model to reconstruct lineages of 2- and 4-cell mouse embryos, showing that single-cell 5hmC sequencing can be used as a lineage reconstruction tool.
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| Overall design |
In this study, 5-hydroxymethylcytosine (5hmC) was detected on a genome-wide level in single cells from E14tg2a (E14) mouse embryonic stem cells, Vitamin C treated E14 cells, B6/CBA mouse oocytes, 2-cell mouse embryos and 4-cell mouse embryos using a new method called as scAba-seq.
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| Contributor(s) |
Mooijman D, Dey SS, Boisset J, Crosetto N, van Oudenaarden A |
| Citation(s) |
27347753 |
| |
| Submission date |
May 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Siddharth Subhas Dey |
| E-mail(s) |
s.dey@hubrecht.eu
|
| Organization name |
Hubrecht Institute
|
| Lab |
van Oudenaarden lab
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA320216 |
| SRA |
SRP074232 |
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