Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants

Fuchs, Jörg; Schubert, Ingo

doi:10.1007/978-0-387-70869-0_9

Cited by 25 publications

(31 citation statements)

References 151 publications

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“…The histone marks were acetylation of lysine 56 (H3K56ac), trimethylation of lysine 4 (H3K4me3), and trimethylation of lysine 27 (H3K27me3). H3K4me3 is a euchromatic mark associated almost exclusively with genes and is highly conserved among eukaryotes (Fuchs and Schubert, 2012). H3K4me3 also shows a consistent distribution in cytologically visible euchromatic regions in cells from various zones of the developing maize root (Yan et al, 2014).…”

Section: Association Of Other Chromatin Features With Replication Timementioning

confidence: 97%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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Section: Association Of Other Chromatin Features With Replication Timementioning

confidence: 97%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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show abstract

“…Surprisingly, no C-banding-positive centromeric/pericentromeric heterochromatin could be cytologically detected in the entire material. Histone H3 dimethylated at lysine 9 (H3K9me2), a repressive histone mark frequently decorating heterochromatin (Fuchs and Schubert, 2012), generated a dull fluorescence or alternatively produced tiny and hard to detect immunosignals dispersed along the chromosomes ( Figure 2D). The latter pattern may reflect H3K9me2 silencing of scattered mobile elements (Houben et al, 2003).…”

Section: Partially and Fully Condensed Chromosomesmentioning

confidence: 99%

“…On prophase-early metaphase chromosomes in which the latecondensing distal chromosome regions are still diffuse, the colocalized H3K4me2 and H3K27me3 labelings are not strictly at the very ends of chromosomes; that is, the terminal heterochromatin can still be seen distal to them ( Figures 2H to 2J). H3K4me2 is a euchromatic mark, distributed within genes and their promoters, thus enriched in the gene-rich euchromatin but absent from heterochromatic regions (Fuchs and Schubert, 2012). H3K27me3, a repressive mark, together with permissive H3K4 methylations, often decorates euchromatin, acting together as a means for poising genes for rapid induction during cellular differentiation (Orkin and Hochedlinger, 2011).…”

Section: Partially and Fully Condensed Chromosomesmentioning

confidence: 99%

Translocations of Chromosome End-Segments and Facultative Heterochromatin Promote Meiotic Ring Formation in Evening Primroses

2014

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Due to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled endsegments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories.

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“…A well-known example is the acetylation of lysine 9 of H3, which neutralizes the positive charge of the histones and decreases their affinity for negatively charged DNA, and thus promotes the accessibility of other proteins to the DNA [56]. In general, H3K9ac is enriched in euchromatin at active genes and normally peaks at translation start sites (ATG).…”

Section: Drought-responsive Alterations Of Histone Modification Patternsmentioning

confidence: 99%

“…A typical repressive mark is H3K9me2, which provides binding sites for HP1 [56] and is necessary for DNA methylation-mediated gene silencing [63]. H3K9me2 is enriched in heterochromatin and chromocenters, and is associated with transposons without any preference along gene territory [57,63,64].…”

Section: Drought-responsive Alterations Of Histone Modification Patternsmentioning

confidence: 99%

Drought Stress-Related Physiological Changes and Histone Modifications in Barley Primary Leaves at HSP17 Gene

2017

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Abstract:Stress-inducible genes undergo epigenetic modifications under stress conditions. To investigate if HSP17, of which transcripts accumulate in plant cells under stress, is regulated through epigenetic mechanisms under drought stress, 5-day-old barley (Hordeum vulgare cv. Carina) plants were subjected to progressive drought through water withholding for 22 days. Changes in physiological status and expression of HSP17 gene were monitored in primary leaves of control and drought-treated plants every two days. Twelve days after drought started, control and drought-treated plants were analyzed by chromatin-immunoprecipitation using antibodies against three histone modifications (H3K4me3, H3K9ac, and H3K9me2) and H3 itself. Already after four days of drought treatment, stomatal conductance was severely decreased. Thereafter, maximum and quantum yield of photosystem II (PSII), regulated and non-regulated energy dissipation in PSII, and later also chlorophyll content, were affected by drought, indicating the stress-induced onset of senescence. At the 12th day of drought, before leaf water content declined, expression of HSP17 gene was increased two-fold in drought-treated plants compared to the controls. Twelve days of drought caused an increase in H3 and a loss in H3K9me2 not only at HSP17, but also at constitutively transcribed reference genes ACTIN, PROTEIN PHOSPHATASE 2A (pp2A), and at silent regions BM9, CEREBA. In contrast, H3K4me3 showed a specific increase at HSP17 gene at the beginning and the middle part of the coding region, indicating that this mark is critical for the drought-responsive transcription status of a gene.

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Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants

Cited by 25 publications

References 151 publications

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Translocations of Chromosome End-Segments and Facultative Heterochromatin Promote Meiotic Ring Formation in Evening Primroses

Drought Stress-Related Physiological Changes and Histone Modifications in Barley Primary Leaves at HSP17 Gene

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