Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

By Shawn Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, C. Haudenschild, S. Pradhan, Stanley F. Nelson, Matteo Pellegrini, Steven E. Jacobsen. Nature, 2008

2,259 citations recorded by the source corpus.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/067097b814fba7fe46585e7888bade78d8754367

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In Plant Science

Citations in the corpus

Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, background): “These studies suggest the functional significance of AS as a result of tandem acceptor in plants.”
CNV-seq, a new method to detect copy number variation using high-throughput sequencing (2009, methodology): “Sequencing-based methods are also used to produce genome-wide DNA methylation profiles, detect SNP, study chromosome translocations and RNA transcriptome profiling [13-20].”
DNA methylation: a historical perspective. (2022, positive): “Further advances in sequencing technologies then enabled the first single-base resolution methylation maps in Arabidopsis, mouse, and human ESCs as well as somatic tissues [204,205].”
DNA methylome analysis using short bisulfite sequencing data (2012, background): “Alternatively, all four DNA strands that arise through bisulfite treatment and subsequent PCR amplification can be sequenced with the same frequency in nondirectional libraries 32,37,38 .”
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. (2008, neutral): “2007), and DNA methylation (Cokus et al. 2008).”
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome (2012, positive): “The study of 5mC has been facilitated by the development of whole genome bisulfite sequencing methods that can resolve the genomic location of methylcytosine at single-base resolution (Cokus et al., 2008; Lister et al., 2008; Lister et al., 2009).”
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities (2018, methodology): “[64] CETCh-seq associated protein ChIP-seq against a special protein region added by clustered regularly interspaced short palindromic repeats (CRISPR) genome editing.”
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing (2008, background): “In the context of DNA methylation site detection by shotgun bisulfite sequencing (21), the frequency of erroneous detection of C instead of T and vice versa is of particular interest.”
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data (2013, background): “Next-generation sequencing of bisulfite converted DNA makes it possible to detect genome wide DNA methylation at base-pair resolution [1].”
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles (2012, methodology): “There are multiple techniques that leverage high-throughput bisulfite sequencing such as: reduced representation bisulfite sequencing (RRBS)[10] and its variants [11], wholegenome shotgun bisulfite sequencing (BS-seq) [12], methylC-Seq [13], and target capture bisulfite sequencing [14].”