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Shawn J. Cokus
Researcher at University of California, Los Angeles
Publications - 41
Citations - 11823
Shawn J. Cokus is an academic researcher from University of California, Los Angeles. The author has contributed to research in topics: DNA methylation & RNA-Directed DNA Methylation. The author has an hindex of 31, co-authored 41 publications receiving 10734 citations. Previous affiliations of Shawn J. Cokus include University of California, Berkeley.
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Journal ArticleDOI
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Shawn J. Cokus,Suhua Feng,Xiaoyu Zhang,Zugen Chen,Barry Merriman,Christian D. Haudenschild,Sriharsa Pradhan,Stanley F. Nelson,Matteo Pellegrini,Steven E. Jacobsen +9 more
TL;DR: A map at single-base-pair resolution of methylated cytosines for Arabidopsis is generated by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology.
Journal ArticleDOI
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.
Xiaoyu Zhang,Junshi Yazaki,Ambika Sundaresan,Shawn J. Cokus,Simon W. L. Chan,Huaming Chen,Ian R. Henderson,Paul Shinn,Matteo Pellegrini,Steve E. Jacobsen,Joseph R. Ecker +10 more
TL;DR: This is the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model and finds that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated.
Journal ArticleDOI
Conservation and divergence of methylation patterning in plants and animals
Suhua Feng,Shawn J. Cokus,Xiaoyu Zhang,Pao-Yang Chen,Magnolia Bostick,Mary G. Goll,Jonathan Hetzel,Jayati Jain,Steven H. Strauss,Marnie E. Halpern,Chinweike Ukomadu,Kirsten C. Sadler,Sriharsa Pradhan,Matteo Pellegrini,Steven E. Jacobsen +14 more
TL;DR: Comparisons of DNA methylation in eight diverse plant and animal genomes found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals.
Journal ArticleDOI
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by Aid deficiency
Christian Popp,Wendy Dean,Suhua Feng,Shawn J. Cokus,Simon Andrews,Matteo Pellegrini,Steven E. Jacobsen,Wolf Reik +7 more
TL;DR: The results reveal that erasure of DNA methylation in the germ line is a global process, hence limiting the potential for transgenerational epigenetic inheritance, and indicates that AID has a critical function in epigenetic reprogramming and potentially in restricting the inheritance of epimutations in mammals.
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Relationship between nucleosome positioning and DNA methylation.
Ramakrishna K. Chodavarapu,Suhua Feng,Yana V. Bernatavichute,Pao-Yang Chen,Hume Stroud,Yanchun Yu,Jonathan Hetzel,Frank Kuo,Jin Kim,Shawn J. Cokus,David Casero,María Bernal,Peter Huijser,Amander T. Clark,Ute Krämer,Ute Krämer,Sabeeha S. Merchant,Xiaoyu Zhang,Steven E. Jacobsen,Matteo Pellegrini +19 more
TL;DR: It is found that nucleosomal DNA was more highly methylated than flanking DNA and that DNA methyltransferases preferentially target nucleosome-bound DNA, indicating that the relationships between nucleosomes and DNA methyl transferases are conserved.