3C Technologies in plants

Hövel, Iris; Louwers, Marieke; Stam, Maike

doi:10.1016/j.ymeth.2012.06.010

Cited by 14 publications

(5 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…According to this model, the chromatin fiber is packed into 1-Mb domains in meta-stable conformational states [Mirny, 2011;Dekker et al, 2013]. In plants, the 3C method has only recently been used [Hovel et al, 2012], and no equivalent or alternative model is available for plant CT organisation yet.…”

Section: Chromosome Territoriesmentioning

confidence: 99%

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of Arabidopsis thaliana

Prete

Arpòn

Sakai

et al. 2014

Cytogenet Genome Res

View full text Add to dashboard Cite

The interphase cell nucleus is extraordinarily complex, ordered, and dynamic. In the last decade, remarkable progress has been made in deciphering the functional organisation of the cell nucleus, and intricate relationships between genome functions (transcription, DNA repair, or replication) and various nuclear compartments have been revealed. In this review, we describe the architecture of the Arabidopsis thaliana interphase cell nucleus and discuss the dynamic nature of its organisation. We underline the need for further developments in quantitative and modelling approaches to nuclear organization.

show abstract

Section: Chromosome Territoriesmentioning

confidence: 99%

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of Arabidopsis thaliana

Prete

Arpòn

Sakai

et al. 2014

Cytogenet Genome Res

View full text Add to dashboard Cite

show abstract

“…Tissue was collected from biological triplicate inner husk leaves at silking and from inner stem leaves from A619 Pl1-Rhoades ( Pl-Rh ) V5 seedlings. Interacting chromatin was isolated from these tissues as described for 3C experiments [ 79 , 121 , 122 ]. In short, 2-3g tissue was crosslinked in 1X PBS with 2% formaldehyde for 1 hour.…”

Section: Methodsmentioning

confidence: 99%

Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats

Deans,

Talbot,

et al. 2024

PLoS Genet

Self Cite

View full text Add to dashboard Cite

Exceptions to Mendelian inheritance often highlight novel chromosomal behaviors. The maize Pl1-Rhoades allele conferring plant pigmentation can display inheritance patterns deviating from Mendelian expectations in a behavior known as paramutation. However, the chromosome features mediating such exceptions remain unknown. Here we show that small RNA production reflecting RNA polymerase IV function within a distal downstream set of five tandem repeats is coincident with meiotically-heritable repression of the Pl1-Rhoades transcription unit. A related pl1 haplotype with three, but not one with two, repeat units also displays the trans-homolog silencing typifying paramutations. 4C interactions, CHD3a-dependent small RNA profiles, nuclease sensitivity, and polyadenylated RNA levels highlight a repeat subregion having regulatory potential. Our comparative and mutant analyses show that transcriptional repression of Pl1-Rhoades correlates with 24-nucleotide RNA production and cytosine methylation at this subregion indicating the action of a specific DNA-dependent RNA polymerase complex. These findings support a working model in which pl1 paramutation depends on trans-chromosomal RNA-directed DNA methylation operating at a discrete cis-linked and copy-number-dependent transcriptional regulatory element.

show abstract

“…Two techniques are used to investigate 3D chromatin organization, i.e. , fluorescence in situ hybridization (FISH), which allows direct visualization of the spatial organization of genomic sequences by cytology and microscopy approaches in individual nuclei, and methods derived from chromosome conformation capture (3C), which allow high-throughput and high-resolution analyses of genomic interactions at local to genome-wide scales [ 103 , 104 , 105 ].…”

Section: On the Path From 1d To 3dmentioning

confidence: 99%

One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation

Prete

Mikulski

Schubert

et al. 2015

Genes

View full text Add to dashboard Cite

Polycomb group (PcG) proteins contribute to the formation and maintenance of a specific repressive chromatin state that prevents the expression of genes in a particular space and time. Polycomb repressive complexes (PRCs) consist of several PcG proteins with specific regulatory or catalytic properties. PRCs are recruited to thousands of target genes, and various recruitment factors, including DNA-binding proteins and non-coding RNAs, are involved in the targeting. PcG proteins contribute to a multitude of biological processes by altering chromatin features at different scales. PcG proteins mediate both biochemical modifications of histone tails and biophysical modifications (e.g., chromatin fiber compaction and three-dimensional (3D) chromatin conformation). Here, we review the role of PcG proteins in nuclear architecture, describing their impact on the structure of the chromatin fiber, on chromatin interactions, and on the spatial organization of the genome in nuclei. Although little is known about the role of plant PcG proteins in nuclear organization, much is known in the animal field, and we highlight similarities and differences in the roles of PcG proteins in 3D gene regulation in plants and animals.

show abstract

3C Technologies in plants

Cited by 14 publications

References 48 publications

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of <b><i>Arabidopsis thaliana</i></b>

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of <b><i>Arabidopsis thaliana</i></b>

Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats

One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation

Contact Info

Product

Resources

About