High-throughput Chromatin Accessibility Profiling at Single-cell Resolution

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Sep 9

PMID 30194434

Citations 82

Authors

Anja Mezger

Sandy Klemm

Ishminder Mann

Kara Brower

Alain Mir

Magnolia Bostick

Andrew Farmer

Polly Fordyce

Sten Linnarsson

William Greenleaf

Affiliations

Soon will be listed here.

Abstract

Here we develop a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 h on-chip processing time) and library preparation cost (~81¢ per cell) compared to prior microfluidic implementations. We apply this method to measure regulatory variation in peripheral blood mononuclear cells (PBMCs) and show robust, de novo clustering of single cells by hematopoietic cell type.

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References

Corces M, Buenrostro J, Wu B, Greenside P, Chan S, Koenig J . Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016; 48(10):1193-203. PMC: 5042844. DOI: 10.1038/ng.3646. View

Di Tullio A, Manh T, Schubert A, Castellano G, Mansson R, Graf T . CCAAT/enhancer binding protein alpha (C/EBP(alpha))-induced transdifferentiation of pre-B cells into macrophages involves no overt retrodifferentiation. Proc Natl Acad Sci U S A. 2011; 108(41):17016-21. PMC: 3193237. DOI: 10.1073/pnas.1112169108. View

Schep A, Wu B, Buenrostro J, Greenleaf W . chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat Methods. 2017; 14(10):975-978. PMC: 5623146. DOI: 10.1038/nmeth.4401. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Cusanovich D, Reddington J, Garfield D, Daza R, Aghamirzaie D, Marco-Ferreres R . The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. 2018; 555(7697):538-542. PMC: 5866720. DOI: 10.1038/nature25981. View

Thurman R, Rynes E, Humbert R, Vierstra J, Maurano M, Haugen E . The accessible chromatin landscape of the human genome. Nature. 2012; 489(7414):75-82. PMC: 3721348. DOI: 10.1038/nature11232. View

Lloberas J, Soler C, Celada A . The key role of PU.1/SPI-1 in B cells, myeloid cells and macrophages. Immunol Today. 1999; 20(4):184-9. DOI: 10.1016/s0167-5699(99)01442-5. View

Pott S . Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells. Elife. 2017; 6. PMC: 5487215. DOI: 10.7554/eLife.23203. View

Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, Bernstein B . Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. PMC: 2592715. DOI: 10.1186/gb-2008-9-9-r137. View

10.

Buenrostro J, Wu B, Litzenburger U, Ruff D, Gonzales M, Snyder M . Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015; 523(7561):486-90. PMC: 4685948. DOI: 10.1038/nature14590. View

11.

Chen H, Zhang P, Voso M, Hohaus S, Gonzalez D, Glass C . Neutrophils and monocytes express high levels of PU.1 (Spi-1) but not Spi-B. Blood. 1995; 85(10):2918-28. View

12.

Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G . Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature. 2015; 528(7580):142-6. PMC: 4697938. DOI: 10.1038/nature15740. View

13.

Cusanovich D, Daza R, Adey A, Pliner H, Christiansen L, Gunderson K . Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015; 348(6237):910-4. PMC: 4836442. DOI: 10.1126/science.aab1601. View

14.

Xu J, Carter A, Gendrel A, Attia M, Loftus J, Greenleaf W . Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nat Genet. 2017; 49(3):377-386. PMC: 5357084. DOI: 10.1038/ng.3769. View

15.

Buenrostro J, Giresi P, Zaba L, Chang H, Greenleaf W . Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013; 10(12):1213-8. PMC: 3959825. DOI: 10.1038/nmeth.2688. View

16.

Laiosa C, Stadtfeld M, Xie H, de Andres-Aguayo L, Graf T . Reprogramming of committed T cell progenitors to macrophages and dendritic cells by C/EBP alpha and PU.1 transcription factors. Immunity. 2006; 25(5):731-44. DOI: 10.1016/j.immuni.2006.09.011. View