Genome sequencing directly in the cell

January 4, 2021

Researchers develop a method to sequence DNA while preserving its physical structure inside the cell

DNA sequencing inside a cell.
Microscopy image showing the DNA sequencing process for a single-cell embryo, with maternal and paternal DNA separated on opposite sides. The four DNA bases are represented by different colors. Credit: Andrew Payne, Zachary Chiang, and Paul Reginato.


HSCI scientists are part of a team that has brought DNA sequencing out of the sequencer machine and directly into cells, revealing an entirely new view of the genome. The new method for in situ genome sequencing allows researchers to see for the first time exactly how DNA sequences are organized and packed inside cells.

Published in the journal Science, the research was led by HSCI Principal Faculty members Fei Chen and Jason Buenrostro, who are assistant professors in Harvard’s Department of Stem Cell and Regenerative Biology, in collaboration with Ed Boyden of MIT.

The technology creates new opportunities to investigate a broad range of biology, from fundamental questions about how DNA’s three-dimensional organization affects its function to the structural changes and chromosomal rearrangements associated with aging, cancer, brain disorders, and other diseases.

The researchers’ approach begins by fixing cells onto a glass surface to preserve their structure. Then, after inserting small DNA markers into the genome, thousands of short segments of DNA — about 20 letters of code apiece — are amplified and sequenced in their original locations inside the cells. Finally, the samples are ground up and put into a sequencer, which sequences all of the cells’ DNA about 300 letters at a time. By finding the location-identified short sequences within those longer segments, the method pinpoints each one’s position within the three-dimensional structure of the cell.

3D computer visualization of DNA inside a cell.
Visualization of how DNA is organized inside a single-cell embryo, with each color representing a different chromosome. Credit: Andrew Payne, Zachary Chiang, and Paul Reginato.


The team applied the method to visualizing a genome as it reorganizes itself during the earliest moments of life. By sequencing inside a mouse embryo, the researchers showed how genetic information inherited from each parent remains distinct and compartmentalized immediately after fertilization, then gradually intertwines as development progresses. Their sequencing also revealed how patterns of genome organization, which very early in life differ from cell to cell, are passed on as cells divide, generating a memory of each cell’s developmental origins. Being able to watch these processes unfold across entire cells instead of piecing them together through less direct means represented a dramatic new view of how an organism develops.

The team continues to improve the resolution of the technique and adapt it to a broader range of cell types, but meanwhile have made their method and associated software freely available to other labs. The researchers hope this new approach to DNA sequencing will change the way people think about studying the structure of the genome and will help illuminate patterns and consequences of genome organization across a variety of contexts.

Read more

The original version of this story was originally published on the McGovern Institute website on December 31, 2020, under the title, “Sequencing inside cells.”

Source article: Payne, A. C., Chiang, Z. D., Reginato, P. L. et al. (2020). In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science. DOI: 10.1126/science.aay3446

This research was supported by the Allen Distinguished Investigator program, National Institutes of Health, John Doerr, Open Philanthropy Project, HHMI–Simons Faculty Scholars Program, Intelligence Advanced Research Projects Activity, U. S. Army Research Office, U.S.–Israel Binational Science Foundation, Natural Sciences and Engineering Research Council of Canada, National Human Genome Research Institute, and Harvard Quantitative Biology Initiative.