Simultaneous Quantification of Spatial Genome Positioning and Transcriptomics in Single Cells with scDam&T-Seq

Silke J.A. Lochs, Jop Kind*

*Corresponding author for this work

    Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

    Abstract

    Spatial genome organization is considered to play an important role in mammalian cells, by guiding gene expression programs and supporting lineage specification. Yet it is still an outstanding question in the field what the direct impact of spatial genome organization on gene expression is. To elucidate this relationship further, we have recently developed scDam&T-seq, a method that simultaneously quantifies protein–DNA interactions and transcriptomes in single cells. This method efficiently combines two preexisting methods: DamID for measuring protein–DNA contacts and CEL-Seq2 for quantification of the transcriptome in single cells. scDam&T-seq has been successfully applied to measure DNA contacts with the nuclear lamina, while at the same time revealing the effect of these contacts on gene expression. This method is applicable to many different proteins of interest and can thereby aid in studying the relationship between protein–DNA interactions and gene expression in single cells.

    Original languageEnglish
    Title of host publicationSpatial Genome Organization
    Subtitle of host publicationMethods and Protocols
    EditorsTom Sexton
    PublisherHumana New York
    Chapter11
    Pages215-241
    Number of pages27
    Edition1
    ISBN (Electronic)978-1-0716-2497-5
    ISBN (Print)978-1-0716-2496-8, 978-1-0716-2499-9
    DOIs
    Publication statusPublished - 23 Jul 2022

    Publication series

    NameMethods in Molecular Biology
    PublisherHumana New York
    Volume2532
    ISSN (Print)1064-3745
    ISSN (Electronic)1940-6029

    Keywords

    • CEL-Seq2
    • DamID
    • Lamina-associated domains
    • Protein–DNA interactions
    • Single-cell genomics
    • Single-Cell Analysis/methods
    • Animals
    • Transcriptome
    • Mammals/genetics
    • Genome
    • Proteins/genetics
    • DNA/genetics

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