In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Andrew C Payne; Zachary D Chiang; Paul L Reginato; Sarah M Mangiameli; Evan M Murray; Chun-Chen Yao; Styliani Markoulaki; Andrew S Earl; Ajay S Labade; Rudolf Jaenisch; George M Church; Edward S Boyden; Jason D Buenrostro; Fei Chen

doi:10.1126/science.aay3446

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Science. 2021 Feb 26;371(6532):eaay3446. doi: 10.1126/science.aay3446. Epub 2020 Dec 31.

Authors

Andrew C Payne^#^{1

2}, Zachary D Chiang^#^{2

3}, Paul L Reginato^#^{1

2

4

5

6}, Sarah M Mangiameli², Evan M Murray², Chun-Chen Yao^{2

7}, Styliani Markoulaki⁸, Andrew S Earl³, Ajay S Labade³, Rudolf Jaenisch^{8

9}, George M Church^{5

6}, Edward S Boyden^#^{10

4

7

11

12

13

14}, Jason D Buenrostro^#^{15

3}, Fei Chen^#^{15

3}

Affiliations

¹ Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
² Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
³ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
⁴ Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA.
⁵ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁶ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
⁷ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA.
⁸ Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA.
⁹ Department of Biology, MIT, Cambridge, MA 02139, USA.
¹⁰ Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. edboyden@mit.edu jason_buenrostro@harvard.edu chenf@broadinstitute.org.
¹¹ McGovern Institute, MIT, Cambridge, MA 02139, USA.
¹² Koch Institute, MIT, Cambridge, MA 02139, USA.
¹³ Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
¹⁴ Centers for Neurobiological Engineering and Extreme Bionics, MIT, Cambridge, MA 02139, USA.
¹⁵ Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA. edboyden@mit.edu jason_buenrostro@harvard.edu chenf@broadinstitute.org.

^# Contributed equally.

Abstract

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Base Sequence
Cell Nucleus / genetics
Cell Nucleus / ultrastructure
Chromatin / chemistry
Chromatin / ultrastructure
Chromosome Positioning
Chromosomes, Human / ultrastructure
Chromosomes, Mammalian / ultrastructure
Embryo, Mammalian
Embryonic Development
Epigenesis, Genetic
Fibroblasts
Genome*
Genome, Human*
High-Throughput Nucleotide Sequencing
Humans
Mice
Sequence Analysis, DNA*
Single-Cell Analysis
Spatial Analysis

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding