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

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...

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Published inScience (American Association for the Advancement of Science) Vol. 371; no. 6532
Main Authors Payne, Andrew C, Chiang, Zachary D, Reginato, Paul L, Mangiameli, Sarah M, Murray, Evan M, Yao, Chun-Chen, Markoulaki, Styliani, Earl, Andrew S, Labade, Ajay S, Jaenisch, Rudolf, Church, George M, Boyden, Edward S, Buenrostro, Jason D, Chen, Fei
Format Journal Article
LanguageEnglish
Published United States The American Association for the Advancement of Science 26.02.2021
Subjects
Animals
Base Sequence
Biological properties
Biological samples
Cell Nucleus - genetics
Cell Nucleus - ultrastructure
Chromatin - chemistry
Chromatin - ultrastructure
Chromosome Positioning
Chromosomes
Chromosomes, Human - ultrastructure
Chromosomes, Mammalian - ultrastructure
Deoxyribonucleic acid
Developmental Stages
DNA
DNA sequencing
DNA structure
Embryo, Mammalian
Embryonic Development
Epigenesis, Genetic
Epigenetics
Fibroblasts
Gene expression
Gene loci
Genetics
Genome
Genome, Human
Genomes
Genomic analysis
High-Throughput Nucleotide Sequencing
Humans
Mice
Nucleotide sequence
Sequence Analysis, DNA
Single-Cell Analysis
Spatial Analysis
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Summary: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.
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These authors contributed equally to this work.
A.C.P. and P.L.R. developed the protocol and performed experiments. Z.D.C. developed the computational processing pipeline. A.C.P., Z.D.C., P.L.R., S.M.M., J.D.B., and F.C. performed analyses. E.M., C.-C. Y., and A.S.L. performed supplementary experiments. S.M. performed embryo preparation under the supervision of R.J. A.S.E. designed the interactive Shiny app. A.C.P., Z.D.C., P.L.R., E.S.B., J.D.B., and F.C. wrote the manuscript with input from all authors. G.M.C., E.S.B., J.D.B., and F.C. supervised this work.
Author contributions
ISSN:0036-8075
1095-9203
1095-9203
DOI:10.1126/science.aay3446