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Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
- Yuelin Liu,
- Xuan Cindy Li,
- Farid Rashidi Mehrabadi,
- Alejandro A. Schäffer,
- Drew Pratt,
- David R. Crawford,
- Salem Malikić,
- Erin K. Molloy,
- Vishaka Gopalan,
- Stephen M. Mount,
- Eytan Ruppin,
- Kenneth D. Aldape,
- and S. Cenk Sahinalp
Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
...of multiregionally sampled tumor cells from nine metastatic colorectal cancer patients, as well as multiregionally sampled single-cell reduced-representation bisulfite sequencing data from a glioblastoma patient. We show that the tumor lineages constructed reveal a simple model underlying tumor progression...
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Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing,
- Chadi A El Farran,
- Ying Ying Zeng,
- Yao Yi,
- Tushar Warrier,
- Pradeep Gautam,
- James J. Collins,
- Jian Xu,
- Peter Dröge,
- Cheng-Gee Koh,
- Hu Li,
- Li-Feng Zhang,
- and Yuin-Han Loh
Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
...importance to gain comprehensive understanding of cell states. To tackle this, multimodal single-cell methods have been developed for concurrent measurement of and transcriptome (Dey et al. 2015; Macaulay et al. 2015) and of transcriptome and DNA methylome within a single-cell (Angermueller et al. 2016...
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Method: Long-read single-molecule maps of the functional methylome
- Hila Sharim,
- Assaf Grunwald,
- Tslil Gabrieli,
- Yael Michaeli,
- Sapir Margalit,
- Dmitry Torchinsky,
- Rani Arielly,
- Gil Nifker,
- Matyas Juhasz,
- Felix Gularek,
- Miguel Almalvez,
- Brandon Dufault,
- Sreetama Sen Chandra,
- Alexander Liu,
- Surajit Bhattacharya,
- Yi-Wen Chen,
- Eric Vilain,
- Kathryn R. Wagner,
- Jonathan Pevsner,
- Jeff Reifenberger,
- Ernest T. Lam,
- Alex R. Hastie,
- Han Cao,
- Hayk Barseghyan,
- Elmar Weinhold,
- and Yuval Ebenstein
Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
...analysis for clinical and single-cell applications (Guo et al. 2013; Nagano et al. 2013). Nevertheless, bisulfite sequencing and RRBS have limited accessibility to repetitive regions owing to the inherent limitations of short-read sequencing and are often unable to quantify the length and arrangements...
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Perspective: The first five years of single-cell cancer genomics and beyond
- Nicholas E. Navin
Genome Res. October 2015 25: 1499-1507; doi:10.1101/gr.191098.115
...such as the Fluidigm C1 system have alsobeendeveloped for analyzing96 single-cell RNAprofiles inparallel usingnanoliter reactionvolumes.Another innovativemethod uses tens of thousands of microwells and beads with cell-specific barcodes that can potentially perform single-cell RNA sequencing on 10,000 ormore cells (Fan...
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Perspective: Defining cell types and states with single-cell genomics
- Cole Trapnell
Genome Res. October 2015 25: 1491-1498; doi:10.1101/gr.190595.115
...transcriptomics. Nat Methods 11: 637–640. GuoH, Zhu P,WuX, Li X,WenL, Tang F. 2013. Single-cellmethylome landscapes ofmouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res 23: 2126–2135. Hashimshony T,Wagner F, Sher N, Yanai I. 2012. CEL-Seq: single-cell...
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Method: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells
- Christopher Jen-Yue Wei and
- Kun Zhang
Genome Res. April 2020 30: 602-610; Published in Advance March 3, 2020, doi:10.1101/gr.255851.119
....1371/journal.pcbi.0010050 ↵Guo H, Zhu P, Wu X, Li X, Wen L, Tang F. 2013. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res 23: 2126–2135. doi:10.1101/gr.161679.113 ↵Gymrek M, Yuan J, Zielinski D, Willems T...
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Research: Pervasive polymorphic imprinted methylation in the human placenta
- Courtney W. Hanna,
- Maria S. Peñaherrera,
- Heba Saadeh,
- Simon Andrews,
- Deborah E. McFadden,
- Gavin Kelsey,
- and Wendy P. Robinson
Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
...Methylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation...
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Method: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
- Ruben Boers,
- Joachim Boers,
- Bas de Hoon,
- Christel Kockx,
- Zeliha Ozgur,
- Anco Molijn,
- Wilfred van IJcken,
- Joop Laven,
- and Joost Gribnau
Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
...) (Sandoval et al. 2011). Alternatively, bisulfite conversion and sequencing is preceded by a size selection step (reduced representation bisulfite sequencing [RRBS]) (Meissner et al. 2005). Unfortunately, WGBS requires that the is sequenced at 10 times coverage and necessitated the development of a demanding...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...provide an opportunity to map complete DNA methylomes. These technologies include whole- bisulfite sequencing (WGBS, MethylC-seq [Cokus et al. 2008; Lister et al. 2009] or BS-seq [Laurent et al. 2010]), reduced-representation bisulfite-sequencing (RRBS) 16These authors contributed equally to this work. 17...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...) cells, which are enriched for hematopoietic stem cells (HSCs) and in neutrophils using RNA-sequencing. The rationale underlying the choice of these two study populations is that (1) HSC are the disease-initating cell population in MPN, and (2) neutrophils are involved in the inflammatory response...

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