A Method to Identify Nucleolus-Associated Chromatin Domains (NADs)

Carpentier, Marie-Christine; Picart-Picolo, Ariadna; Pontvianne, Frédéric

doi:10.1007/978-1-4939-7318-7_7

Cited by 11 publications

(9 citation statements)

References 13 publications

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“…Pattern analyses of plant LADs confirmed the previous conclusion that the plant nuclear periphery is a repressive environment [39]. On the other hand, the identification of NADs was achieved by isolating intact nucleoli [41,42]. In addition to ribosomal RNA loci, NADs are clearly enriched with lowly expressed protein-coding genes, as well as inactive chromatin marks and transposons [41].…”

Section: Identifying Plant Lads and Nadssupporting

confidence: 72%

Chromatin domains in space and their functional implications

Pontvianne

Liu

2020

Current Opinion in Plant Biology

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Genome organization exhibits functional compartmentalization. Several factors, including epigenetic modifications, transcription factors, chromatin remodelers, and RNAs shape chromatin domains and the three-dimensional genome organization. Various types of chromatin domains with distinct epigenetic and spatial features exhibit different transcriptional activities. As part of the efforts to better understand plant functional genomics, over the past a few years, spatial distribution patterns of plant chromatin domains have been brought to light. In this review, we discuss chromatin domains associated with the nuclear periphery and the nucleolus, as well as chromatin domains staying in proximity and showing physical interactions. The functional implication of these domains is discussed, with a particular focus on the transcriptional regulation and replication timing. Finally, from a biophysical point of view, we discuss potential roles of liquid-liquid phase separation in plant nuclei in the genesis and maintenance of spatial chromatin domains.

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Section: Identifying Plant Lads and Nadssupporting

confidence: 72%

Chromatin domains in space and their functional implications

Pontvianne

Liu

2020

Current Opinion in Plant Biology

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“…CNVs of rRNA genes were determined using probes amplifying the 18S, the loci AT4G05475 and AT4G16580 that are not duplicated are controls, and the loci AT4TE12140 and AT4G05030 allow the identification of the largest duplication of TDDO4. et al 2016a; Carpentier et al 2018). Preceding studies have clearly shown that in wild-type Col-0 leaf cells, NOR4-derived rRNA genes are expressed and associate with the nucleolus.…”

Section: Impact Of Low Rdna and Tddo On 3d Genome Organizationmentioning

confidence: 99%

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

et al. 2020

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“…Perinucleolar regions might provide the molecular architectures, such as nucleolus-associated chromatin domains (NADs), which correspond to regions of low transcriptional levels [ 67 , 68 , 124 , 125 ]. In Arabidopsis, many of 45S rRNA genes are condensed as heterochromatin and silenced by epigenetic mechanisms that include DNA methylation and histone modification at the periphery of the nucleolus [ 114 , 126 , 127 , 128 ].…”

Section: Possible Roles Of As2 Bodies In Epigenetic Repression Of mentioning

confidence: 99%

Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial–Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis

Iwakawa

Takahashi

Machida

et al. 2020

IJMS

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Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal–distal, adaxial–abaxial, and medial–lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial–abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular functions of AS2. A characteristic genetic feature of AS2 is the presence of a number of (about 60) modifier genes, mutations of which enhance the leaf abnormalities of as2. Although genes for proteins that are involved in diverse cellular processes are known as modifiers, it has recently become clear that many modifier proteins, such as NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10), are localized in the nucleolus. Some modifiers including ribosomal proteins are also members of the small subunit processome (SSUP). In addition, AS2 forms perinucleolar bodies partially colocalizing with chromocenters that include the condensed inactive 45S ribosomal RNA genes. AS2 participates in maintaining CpG methylation in specific exons of ETT/ARF3. NUC1 and RH10 genes are also involved in maintaining the CpG methylation levels and repressing ETT/ARF3 transcript levels. AS2 and nucleolus-localizing modifiers might cooperatively repress ETT/ARF3 to develop symmetric flat leaves. These results raise the possibility of a nucleolus-related epigenetic repression system operating for developmental genes unique to plants and predict that AS2 could be a molecule with novel functions that cannot be explained by the conventional concept of transcription factors.

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A Method to Identify Nucleolus-Associated Chromatin Domains (NADs)

Cited by 11 publications

References 13 publications

Chromatin domains in space and their functional implications

Chromatin domains in space and their functional implications

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial–Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis

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