Dnase I Hypersensitive Sites within the Intergenic Spacer of Ribosomal RNA Genes in Reconstructed Barley Karyotypes

Dimitrova, A.; Ananiev, E. D.; Gecheff, K.

doi:10.1080/13102818.2009.10817608

Cited by 3 publications

(2 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, rDNA active copies are much more numerous in meristematic cells than in differentiated cells (Qian et al ., ). In this context, our most interesting finding was that rDNA loci were more frequently mapped between 18S, 5.8S and 26S units than inside them by DNase I‐MeDIP‐SEQ reads, which is consistent with previous localization of DNase hypersensitive sites in barley ( Hordeum vulgare ) rDNA supposed to co‐localize with Pol I binding sites (Dimitrovna et al ., ). In addition, CHH contexts were poorly methylated, which is consistent with 5S rDNA low CHH methylation as a consequence of demethylation targeting by DEMETER and DEMETER‐LIKE enzymes in A. thaliana (Woo et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene‐body DNA methylation in open chromatin state

Lafon‐Placette

Faivre-Rampant²,

Delaunay

et al. 2012

New Phytologist

View full text Add to dashboard Cite

SummaryDNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification.Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels.While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes.Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.

show abstract

Section: Discussionmentioning

confidence: 97%

Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene‐body DNA methylation in open chromatin state

Lafon‐Placette

Faivre-Rampant²,

Delaunay

et al. 2012

New Phytologist

View full text Add to dashboard Cite

show abstract

“…The local presence of DHSs within a few plant genes was identified using DNase I cleavage coupled with Southern blot hybridization, including the Adh gene in maize and Arabidopsis [Wu et al, 1979;Vega-Palas and Ferl, 1995], ribosomal RNA genes (rRNA) in barley [Dimitrova et al, 2009] and wheat [Thompson and Flavell, 1988], rbcS in pea [Gorz et al, 1988], heat-shock and abscisic acid inducible genes in wheat [Loer and Spiker, 1992], Proteinase inhibitor I in tomato [Conconi and Ryan, 1993], and HSP 70A and RBCS2 in Chlamydomonas [Lodha and Schroda, 2005]. Remarkably, this Southern blot-based method was used to identify all DHSs within an 80-kb genomic region in Arabidopsis [Kodama et al, 2007a, b].…”

Section: Identification Of Dhss In Plantsmentioning

confidence: 99%

Open Chromatin in Plant Genomes

Wen-li¹,

Zhang²,

Wu³

et al. 2014

Cytogenet Genome Res

View full text Add to dashboard Cite

Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq). DHSs are most frequently associated with various cis-regulatory DNA elements, including promoters, enhancers, and silencers in both animal and plant genomes. Genome-wide identification of DHSs provides an efficient method to interpret previously un-annotated regulatory DNA sequences. In this review, we provide an overview of the historical perspective of DHS research in eukaryotes. We summarize the main achievements of DHS research in model animal species and review the recent progress of DHS research in plants. We finally discuss possible future directions of using DHS as a tool in plant genomics research.

show abstract