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Epigenetic inheritance in plants

Ian R. Henderson, Steven E. Jacobsen
2007 Nature  
Ong and all members of the Jacobsen laboratory for useful comments and discussion. We apologize to colleagues whose research we did not have space to discuss.  ...  to be induced by other cues. d, During flower development, the anthers and ovaries are sites of meiotic differentiation, giving rise to haploid cells known as microspores and megaspores, respectively. e,  ...  (jacobsen@ucla.edu).  ... 
doi:10.1038/nature05917 pmid:17522675 fatcat:qhqpuezlcjfmlgtrg4lm5ypm6a

Gene silencing: Maintaining methylation patterns

Steven E. Jacobsen
1999 Current Biology  
Recent studies of an Arabidopsis gene family have shown that inverted repeats can be potent silencers of other identical sequences in the genome, causing them to become stably methylated at cytosine residues. From mutations affecting this process we are beginning to understand how methylation patterns are maintained. DNA methylation is thought to have evolved in bacteria as a defense against foreign DNA. For instance, the prokaryotic methylation-restriction systems consist of specific
more » ... that act at short palindromic sequences, and restriction enzymes that cleave these sequences if, and only if, they are unmethylated (as they are likely to be in the context of invading bacteriophage DNA). In eukaryotes, cytosine methylation has evolved into a mechanism that allows dividing cells to stably inherit states of gene activity. DNA methylation is involved in a myriad of epigenetic regulatory processes found in the vast majority of eukaryotes, including plants, fungi and animals. DNA methylation is absent -probably lost -in several fungal and animal lineages that include the much-used model organisms Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans. Recent evidence suggests that a key difference between the METI-type and chromomethylase-type enzymes is R618 Current Biology, Vol 9 No 16 Figure 1 The PAI gene families of two wild-type Arabidopsis ecotypes, WS and Columbia. M represents a methylated cytosine. WS ecotype Columbia ecotype Current Biology PAI1 PAI2 PAI3 M M MMM MMM PAI1 PAI2 PAI3 M M M MMMM M MMMM
doi:10.1016/s0960-9822(99)80388-1 pmid:10469582 fatcat:hoqaf6jh6rfh5lojp42nurjhxq

Determining DNA Methylation Profiles Using Sequencing [chapter]

Suhua Feng, Liudmilla Rubbi, Steven E. Jacobsen, Matteo Pellegrini
2011 Msphere  
Cytosine methylation is an epigenetic mark that has a significant impact on the regulation of transcription and replication of DNA. DNA methylation patterns are highly conserved across cell divisions and are therefore highly heritable. Furthermore, in multicellular organisms, DNA methylation patterning is a key determinant of cellular differentiation and tissue-specific expression patterns. Lastly, DNA demethylases can affect global levels of DNA methylation during specific stages of
more » ... . Bisulfite sequencing is considered the gold standard for measuring the methylation state of cytosines. Sodium bisulfite converts unmethylated cytosines to uracils (which after PCR are converted to thymines), while leaving methylated cytosines unconverted. By mapping bisulfite treated DNA back to the original reference genome, it is then possible to determine the methylation state of individual cytosines. With the advent of next-generation sequencers during the past few years, it is now possible to determine the methylation state of an entire genome. Here, we describe in detail two protocols for preparing bisulfite treated libraries, which may be sequenced using Illumina GAII sequencers. The first of these uses premethylated adapters, which are not affected by bisulfite treatments, while the second uses a two-stage adapter strategy and does not require premethylation of the adapters. We also describe the specialized protocol for mapping bisulfite converted reads. These approaches allow one to determine the methylation state of each cytosine in the genome.
doi:10.1007/978-1-61779-089-8_16 pmid:21431774 fatcat:pkc3keamr5fzrhrh5pnogo356y

Hypermethylated SUPERMAN Epigenetic Alleles in Arabidopsis

Steven E. Jacobsen, Elliot M. Meyerowitz
1997 Science  
E.  ...  Jacobsen and Elliot M. Meyerowitz* Mutations in the SUPERMAN gene affect flower development in Arabidopsis.  ... 
doi:10.1126/science.277.5329.1100 pmid:9262479 fatcat:spvyt4hrbfdl7aiw6puhv6t5je

Interplay between Two Epigenetic Marks

Lianna M. Johnson, Xiaofeng Cao, Steven E. Jacobsen
2002 Current Biology  
Finally, we find that the reduction of DNA methylation itself does not lead to a reduction in 4 Correspondence jacobsen@ucla.edu bation overnight with rotation, 60 l SS DNA/Protein A agarose was added  ... 
doi:10.1016/s0960-9822(02)00976-4 pmid:12194816 fatcat:lribrw6q2ffg7acrf5jaeidgdu

ADCP1: a novel plant H3K9me2 reader

C. Jake Harris, Steven E. Jacobsen
2018 Cell Research  
H3K9 methylation is an epigenetic mark associated with heterochromatin. Zhao and colleagues characterize a novel H3K9me reader protein, ADCP1, that plays a role in heterochromatin maintenance and shows functional similarities to animal HP1 proteins. Eukaryotic genomes are broadly compartmentalized into nonoverlapping transcriptionally permissive 'euchromatic' and repressed 'heterochromatic' regions. These regions are decorated by a suite of distinct epigenetic marks, which help to reinforce and
more » ... demarcate their transcriptional state. In Arabidopsis, the majority of heterochromatin is confined to the central portion of each chromosome near the centromere, and this spatial separation from euchromatin makes it an attractive model to study epigenetic states. Di-methylation of lysine 9 of histone H3 (H3K9me2) is a key epigenetic mark associated with heterochromatin in plants, functionally analogous to H3K9me3 in mammals. 1 A large body of work has described epigenetic feedback loops in Arabidopsis, which act to maintain H3K9me2, together with DNA methylation. 1 For instance, three partially redundant proteins, KRYPTONITE (KYP, also known as SUVH4), SUVH5 and SUVH6 work together with CHROMOMETHYLASE3 (CMT3) to form a selfreinforcing feedback loop for coincident maintenance of CHG methylation and H3K9me2. The SRA domain of KYP binds to methylated DNA, and establishes H3K9me2 via its C-terminal SET histone methyltransferase domain. Reciprocally, the N-terminal BAH and chromo domains of CMT3 bind to H3K9me2, and the Cterminal DNA methyltransferase domain establishes CHG methylation. KYP/SUHV5/SUVH6 also operate in a similar feedback loop with CMT2 to maintain CHH methylation. Because these proteins contain both heterochromatic 'reader' and 'writer' domains, they form straightforward epigenetic feedback loops. Much less is known about factors that act downstream of H3K9me2 to enforce transcriptional repression. Zhao and colleagues describe a novel protein, ADCP1, which by its domain structure, appears to have a strict H3K9me2 'reader' function. 2 However, the authors show that ADCP1 also clearly contributes to H3K9me2 and DNA methylation maintenance, although it is currently unclear whether these effects are direct or indirect. Importantly, the adcp1 mutant also shows derepression of many transposons marked with H3K9me2, and shows a partial decondensation of the chromocenters (dense nuclear bodies containing the pericentromeric heterochromatin). Interestingly, a recent paper by Zhang and colleagues also identified the same protein from a different proteomics screen (calling it 'AGDP1′), and reported largely similar results. 3 ADCP1 was initially identified from a previously published labon-chip histone reader screen by the same research group. 4
doi:10.1038/s41422-018-0119-2 pmid:30514899 pmcid:PMC6318331 fatcat:ue7xjgvu4bedhaphbsry4nevoe

Sequencing sliced ends reveals microRNA targets

Ian R Henderson, Steven E Jacobsen
2008 Nature Biotechnology  
Global sequencing of cleaved mRNAs enables identification of the targets of microRNA silencing Hundreds of microRNAs (miRNAs) have been identified in plants and animals by cloning and sequencing, but assigning these miRNAs to their cognate target genes remains technically challenging1,2. In this issue, German et al.3 describe the use of high-throughput sequencing to globally sample degraded RNAs in Arabidopsis thaliana and thereby identify new miRNAs and their targets. Similar techniques have
more » ... en developed in two other recent reports4,5; together, the three studies provide powerful new tools for miRNA discovery and the analysis of mRNA turnover.
doi:10.1038/nbt0808-881 pmid:18688239 pmcid:PMC2989925 fatcat:vmsodhehdfhj3bpbytuqcieyn4

Epigenetic Reprogramming in Plant and Animal Development

Suhua Feng, Steven E. Jacobsen, Wolf Reik
2010 Science  
Epigenetic modifications of the genome are generally stable in somatic cells of multicellular organisms. In germ cells and early embryos, however, epigenetic reprogramming occurs on a genome-wide scale, which includes demethylation of DNA and remodeling of histones and their modifications. Mechanisms of genome-wide erasure of DNA methylation are being unraveled, which involve modifications to 5-methylcytosine (5mC) and DNA repair. Epigenetic reprogramming has important roles in imprinting, the
more » ... atural as well as experimental acquisition of totipotency and pluripotency, control of transposons, and epigenetic inheritance across generations. Small RNAs and inheritance of histone marks may also contribute to epigenetic inheritance and reprogramming. Reprogramming occurs in flowering plants and in mammals and the similarities and differences illuminate developmental and reproductive strategies.
doi:10.1126/science.1190614 pmid:21030646 pmcid:PMC2989926 fatcat:rqsekz2havczdlb34ipsvlfqfi

Mutations at the SPINDLY Locus of Arabidopsis Alter Gibberellin Signal Transduction

Steven E. Jacobsen, Neil E. Olszewski
1993 The Plant Cell  
Petri dishes were incubated at 23% under cool white fluorescent lights (35 p E m-2 sec-l).  ...  30.7 f 2.4 a,b 39.7 f 2.8 c 39.6 f 3.6 c 17.7 f 1.2 d 0.6 f 0.1 e 20.8 f 1.1 d 32.7 f 1.5 a 23.5 f 1.5 b,d a Table 6 . 6 Response of the SPY-7 qal-2 Double Mutant to GA?  ... 
doi:10.2307/3869657 pmid:8400871 pmcid:PMC160324 fatcat:2ow5yesg7nh77athotec52vzke

DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes

Robert K. Tran, Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, Steven Henikoff
2005 Current Biology  
doi:10.1016/j.cub.2005.01.008 pmid:15668172 fatcat:l6kjfvtfmfaq3bgilq437bhsay

Accurate sodium bisulfite sequencing in plants

Ian R. Henderson, Simon R. Chan, Xiaofeng Cao, Lianna Johnson, Steven E. Jacobsen
2010 Epigenetics  
As CHH sites are typically methylated at low frequency, the chances of two independent clones possessing an identical CHH methylation distribution are very unlikely. 1 Lianna Johnson 4 and steven E.  ...  Jacobsen 4,5, * department of plant sciences; University of cambridge; downing street, cambridge, UK; 2 section of plant Biology; University of california, davis; davis, ca Usa; state Key Laboratory of  ... 
doi:10.4161/epi.5.1.10560 pmid:20081358 pmcid:PMC2829377 fatcat:qpi35fsksrbtlhar4mu2axb5ie

Discovery of FeBi2

James P. S. Walsh, Samantha M. Clarke, Yue Meng, Steven D. Jacobsen, Danna E. Freedman
2016 ACS Central Science  
Experimental details, Rietveld refinement parameters, and cell parameters used for BM3 fits (PDF) Crystallographic information for FeBi 2 (CIF) ■ AUTHOR INFORMATION Corresponding Author *E-mail: danna.freedman  ... 
doi:10.1021/acscentsci.6b00287 pmid:27924316 pmcid:PMC5126710 fatcat:6fvttzklyjfrxjrv6yu4tzyozm

Epigenetic modifications in plants: an evolutionary perspective

Suhua Feng, Steven E Jacobsen
2011 Current opinion in plant biology  
Steve Jacobsen is an investigator of the Howard Hughes Medical Institute.  ...  Research in the Jacobsen laboratory is supported by the National Institutes of Health (GM60398) and the National Science Foundation Genome Research Program (#0701745).  ...  PRC2 contains a key subunit called Enhancer of zeste, E(z), which is a SET domain histone methyltransferase specific for H3K27 tri-methylation.  ... 
doi:10.1016/j.pbi.2010.12.002 pmid:21233005 pmcid:PMC3097131 fatcat:exawoukwmzhp5hcsw52mymauwa

CRISPR-CAS mediated transcriptional control and epi-mutagenesis

Jason Gardiner, Basudev Ghoshal, Ming Wang, Steven E Jacobsen
2022 Plant Physiology  
E. Direct fusion, SunTag, and MS2 based CRISPR-dCAS9 systems and how these have been combined in the CRISPR ACT 3.0 system. MS2 coat protein (MCP), Single chain variable fragment (ScFV).  ...  DNA methylation is a mitotically and meiotically heritable mark (Law and Jacobsen, 2010) . Maintenance of methylation by RdDM in euchromatic regions depends on siRNAs.  ... 
doi:10.1093/plphys/kiac033 pmid:35134247 pmcid:PMC8968285 fatcat:xflmofm2anaq3ovooq5wxejkru

Mechanisms of anomalous compressibility of vitreous silica

Alisha N. Clark, Charles E. Lesher, Steven D. Jacobsen, Sabyasachi Sen
2014 Physical Review B  
Further details of the associated experimental methodology can be found elsewhere [30] . e V = 2L t . f K S = ρ V 2 P − 4 3 V 2 S . g G = ρV 2 S . III.  ...  sample B v-SiO 2 sample C Density (g cm − 3) a 2.199 ± 0.002 2.203 ± 0.002 2.207 ± 0.002 OH content (ppm) b 268 ± 7 7 9 ± 4 244 ± 5 T f (deg C) c 985 ± 20 1260 ± 30 1500 ± 40 V P (m/s) d,e  ... 
doi:10.1103/physrevb.90.174110 fatcat:f47qcoizh5hunpcof5dly5tu7a
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