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      Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

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          Most cited references 42

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          Imaging individual mRNA molecules using multiple singly labeled probes

          We describe a method for imaging individual mRNA molecules in fixed cells by probing each mRNA species with 48 or more short, singly labeled oligonucleotide probes. This makes each mRNA molecule visible as a computationally identifiable fluorescent spot via fluorescence microscopy. We demonstrate simultaneous detection of three mRNA species in single cells and mRNA detection in yeast, nematodes, fruit fly wing discs, mammalian cell lines and neurons.
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            RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

            Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here, we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 to 1000 distinct RNA species in hundreds of individual cells. Correlation analysis of the ~10(4) to 10(6) pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.
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              Organization and function of the 3D genome

              Understanding how chromatin is organized within the nucleus and how this 3D architecture influences gene regulation, cell fate decisions and evolution are major questions in cell biology. Despite spectacular progress in this field, we still know remarkably little about the mechanisms underlying chromatin structure and how it can be established, reset and maintained. In this Review, we discuss the insights into chromatin architecture that have been gained through recent technological developments in quantitative biology, genomics and cell and molecular biology approaches and explain how these new concepts have been used to address important biological questions in development and disease.
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                Author and article information

                Journal
                Nature Protocols
                Nat Protoc
                Springer Science and Business Media LLC
                1754-2189
                1750-2799
                January 22 2020
                Article
                10.1038/s41596-019-0269-9
                © 2020

                http://www.springer.com/tdm

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