|
| Status |
Public on Mar 13, 2014 |
| Title |
Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes |
| Organisms |
Phaeodactylum tricornutum; Emiliania huxleyi; Cryptococcus neoformans; Leishmania major; Thalassiosira pseudonana; Micromonas pusilla; Bathycoccus prasinos; Aureococcus anophagefferens; Cyanidioschyzon merolae; Fragilariopsis cylindrus; Ostreococcus sp. 'lucimarinus' |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.
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| |
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| Overall design |
DNA methylation, RNA and nucleosome sequencing data for diverse eukaryotes
|
| |
|
| Contributor(s) |
Huff JT, Zilberman D |
| Citation(s) |
24630728 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| T32 HG000047 |
Genomics |
UNIVERSITY OF CALIFORNIA BERKELEY |
Rokhsar |
|
| |
| Submission date |
May 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason T Huff |
| Organization name |
University of California, Berkeley
|
| Department |
Plant & Microbial Biology
|
| Lab |
Daniel Zilberman
|
| Street address |
211 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platforms (12)
|
| GPL17121 |
Illumina HiSeq 2000 (Aureococcus anophagefferens) |
| GPL17122 |
Illumina HiSeq 2000 (Cyanidioschyzon merolae) |
| GPL17123 |
Illumina HiSeq 2000 (Cryptococcus neoformans var. grubii) |
| GPL17124 |
Illumina HiSeq 2000 (Emiliania huxleyi) |
| GPL17125 |
Illumina HiSeq 2000 (Fragilariopsis cylindrus) |
| GPL17126 |
Illumina HiSeq 2000 (Micromonas pusilla) |
| GPL17127 |
Illumina HiSeq 2000 (Ostreococcus 'lucimarinus') |
| GPL17128 |
Illumina HiSeq 2000 (Phaeodactylum tricornutum) |
| GPL17129 |
Illumina HiSeq 2000 (Thalassiosira pseudonana) |
| GPL18353 |
Illumina HiSeq 2000 (Bathycoccus prasinos) |
| GPL18354 |
Illumina HiSeq 2000 (Leishmania major) |
| GPL18355 |
Illumina HiSeq 2500 (Ostreococcus 'lucimarinus') |
|
| Samples (26)
|
| GSM1134612 |
C. neoformans dnmt5Δ bisulfite sequencing |
| GSM1134613 |
C. neoformans WT47 bisulfite sequencing |
| GSM1134614 |
C. neoformans WT47 RNA sequencing |
| GSM1134615 |
C. neoformans WT bisulfite sequencing |
| GSM1134616 |
E. huxleyi bisulfite sequencing |
| GSM1134617 |
E. huxleyi RNA sequencing |
| GSM1134618 |
F. cylindrus bisulfite sequencing |
| GSM1134619 |
F. cylindrus RNA sequencing |
| GSM1134620 |
M. pusilla CCMP1545 bisulfite sequencing |
| GSM1134621 |
M. pusilla CCMP1545 MNase sequencing |
| GSM1134622 |
M. pusilla CCMP1545 RNA sequencing |
| GSM1134623 |
O. lucimarinus bisulfite sequencing |
| GSM1134624 |
O. lucimarinus MNase sequencing |
| GSM1134625 |
O. lucimarinus RNA sequencing |
| GSM1134626 |
P. tricornutum bisulfite sequencing |
| GSM1134627 |
P. tricornutum RNA sequencing |
| GSM1134628 |
T. pseudonana bisulfite sequencing |
| GSM1134629 |
T. pseudonana RNA sequencing |
| GSM1337409 |
B. prasinos bisulfite sequencing |
| GSM1337410 |
L. major bisulfite sequencing |
| GSM1337411 |
O. lucimarinus naked DNA control mock assembly MNase sequencing |
| GSM1337412 |
O. lucimarinus natively methylated in vitro assembled nucleosomes MNase sequencing |
| GSM1337413 |
O. lucimarinus unmethylated in vitro assembled nucleosomes MNase sequencing |
|
| Relations |
| BioProject |
PRJNA201680 |
| SRA |
SRP022147 |
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