3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.

PMID:32719531

IF: 47.990

Cited by: 91

Abstract

There is a need for methods that can image chromosomes with genome-wide coverage, as well as greater genomic and optical resolution. We introduce OligoFISSEQ, a suite of three methods that leverage fluorescence in situ sequencing (FISSEQ) of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. Applying OligoFISSEQ to human diploid fibroblast cells, we show how four rounds of sequencing are sufficient to produce 3D maps of 36 genomic targets across six chromosomes in hundreds to thousands of cells, implying a potential to image thousands of targets in only five to eight rounds of sequencing. We also use OligoFISSEQ to trace chromosomes at finer resolution, following the path of the X chromosome through 46 regions, with separate studies showing compatibility of OligoFISSEQ with immunocytochemistry. Finally, we combined OligoFISSEQ with OligoSTORM, laying the foundation for accelerated single-molecule super-resolution imaging of large swaths of, if not entire, human genomes.

Keywords

ISS

Spatial Genomics

FISSEQ

MeSH terms

Chromosome Painting

Chromosomes

Genome, Human

Humans

Oligonucleotide Array Sequence Analysis

Oligonucleotide Probes

Physical Chromosome Mapping

Authors

Nguyen, Huy Q

Chattoraj, Shyamtanu

Castillo, David

Nguyen, Son C

Nir, Guy

Lioutas, Antonios

Hershberg, Elliot A

Martins, Nuno M C

Reginato, Paul L

Hannan, Mohammed

Beliveau, Brian J

Church, George M

Daugharthy, Evan R

Marti-Renom, Marc A

Wu, C-Ting

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