Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

Emily Hodges, Lindsey N. Guerin, Kelly R. Barnett

Published: 2021-10-17 DOI: 10.1038/s41596-021-00608-z

chromatin accessibility

DNA methylation

ATAC-Me

epigenetic dynamics

time course studies

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can reveal their precise correspondence in genomic space, or te
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- References
- References
References
ACKNOWLEDGMENTS

Albert, I. et al. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446, 572–576 (2007).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).
Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).
Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).
Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).
Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011).
Taberlay, P. C. et al. Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell 147, 1283–1294 (2011).
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010).
Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).
Kelsey, G., Stegle, O. & Reik, W. Single-cell epigenomics: recording the past and predicting the future. Science 358, 69–75 (2017).
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
Hodges, E. et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell 44, 17–28 (2011).
Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).
Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013).
Schubeler, D. Function and information content of DNA methylation. Nature 517, 321–326 (2015).
Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492 (2012).
Brinkman, A. B. et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128–1138 (2012).
King, A. D. et al. Reversible regulation of promoter and enhancer histone landscape by DNA methylation in mouse embryonic stem cells. Cell Rep. 17, 289–302 (2016).
Charlet, J. et al. Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol. Cell 62, 422–431 (2016).
Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J. & Hodges, E. De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome Res. 23, 1601–1614 (2013).
Schmidl, C. et al. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res. 19, 1165–1174 (2009).
Barnett, K. R. et al. ATAC-Me captures prolonged DNA methylation of dynamic chromatin accessibility loci during cell fate transitions. Mol. Cell 77, 1350–1364 e1356 (2020).
Kriaucionis, S. & Klose, R. J. ATACing DNA methylation during differentiation. Mol. Cell 77, 1159–1161 (2020).
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
Adey, A. & Shendure, J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res. 22, 1139–1143 (2012).
Wang, Q. et al. Tagmentation-based whole-genome bisulfite sequencing. Nat. Protoc. 8, 2022–2032 (2013).
Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat. Commun. 9, 781 (2018).
Kelly, T. K. et al. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22, 2497–2506 (2012).
Fujiwara, S., Baek, S., Varticovski, L., Kim, S. & Hager, G. L. High quality ATAC-Seq data recovered from cryopreserved breast cell lines and tissue. Sci. Rep. 9, 516 (2019).
Scharer, C. D. et al. ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells. Sci. Rep. 6, 27030 (2016).
Lara-Astiaso, D. et al. Chromatin state dynamics during blood formation. Science 345, 943 (2014).
Rhie, S. K., Schreiner, S. & Farnham, P. J. Defining regulatory elements in the human genome using nucleosome occupancy and methylome sequencing (NOMe-Seq). Methods Mol. Biol. 1766, 209–229 (2018).
Barnett, K. R. et al. ATAC-Me captures prolonged DNA methylation of dynamic chromatin accessibility loci during cell fate transitions. Mol. Cell http://doi.org/10.1016/j.molcel.2020.01.004 (2020).
Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017).
Trevino, A. E. et al. Chromatin accessibility dynamics in a model of human forebrain development. Science 367, eaay1645 (2020).
Bysani, M. et al. ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes. Sci. Rep. 9, 7785 (2019).
Tierling, S., Schmitt, B. & Walter, J. Comprehensive evaluation of commercial bisulfite-based DNA methylation kits and development of an alternative protocol with improved conversion performance. Genet. Epigenet. 10, 1179237x18766097 (2018).
Montefiori, L. et al. Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Sci. Rep. 7, 2451 (2017).
Schutsky, E. K. et al. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat. Biotechnol. 36, 1083–1090 (2018).
Yu, M. et al. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protoc. 7, 2159–2170 (2012).
Song, C.-X. et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 29, 68–72 (2011).
Yu, M. et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368–1380 (2012).
Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).
Krueger, F. Trim galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. Bioinformatics 516, 517 (2015).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17, 10–12 (2011).
Chen, H., Smith, A. D. & Chen, T. WALT: fast and accurate read mapping for bisulfite sequencing. Bioinformatics 32, 3507–3509 (2016).
Song, Q. et al. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PloS One 8, e81148–e81148 (2013).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137–R137 (2008).
Guerin, L., Barnett, K. R. & Hodges, E. Dual detection of chromatin accessibility and DNA methylation using ATAC-Me. HodgesGenomicsLab/NatProtocols_ATACme, http://doi.org/10.5281/zenodo.5062153 (2021).
Wu, M. & Gu, L. TCseq: time course sequencing data analysis. R package version 1.12.1 (2020).
Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012).
Yan, F., Powell, D. R., Curtis, D. J. & Wong, N. C. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol. 21, 22 (2020).
Li, Z. et al. Identification of transcription factor binding sites using ATAC-seq. Genome Biol. 20, 45 (2019).
Bentsen, M. et al. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat. Commun. 11, 4267 (2020).
Daley, T. & Smith, A. D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325–327 (2013).
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).

Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

推荐阅读