Unraveling the 3D Genome Architecture in Plants: Present and Future

Ouyang, Weizhi; Xiong, Dan; Li, Guoliang; Li, Xingwang

doi:10.1016/j.molp.2020.10.002

Cited by 59 publications

(56 citation statements)

References 160 publications

(200 reference statements)

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“…Hence, nCUT&Tag may be scalable for highthroughput or single-nucleus profiling of histone marks in plants. Importantly, the PAT-or PGT-mediated chromatin immunocleavage strategies may greatly facilitate the development of single-cell ligation-free 3D genome mapping technologies (Ouyang et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag

et al. 2021

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Characterizing genome-wide histone posttranscriptional modifications and transcriptional factor occupancy is crucial for deciphering their biological functions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for genome-wide profiling of histone modifications and transcriptional factor-binding sites. However, the current ChIP-seq experimental procedure in plants requires significant material and several days for completion. CUT&Tag is an alternative method of ChIP-seq for low-sample and single-cell epigenomic profiling using protein A-Tn5 transposase fusion proteins (PAT). In this study, we developed a nucleus CUT&Tag (nCUT&Tag) protocol based on the live-cell CUT&Tag technology. Our results indicate that nCUT&Tag could be used for histone modifications profiling in both monocot rice and dicot rapeseed using crosslinked or fresh tissues. In addition, both active and repressive histone marks such as H3K4me3 and H3K9me2 can be identified using our nCUT&Tag. More importantly, all the steps in nCUT&Tag can be finished in only 1 day, and the assay can be performed with as little as 0.01 g of plant tissue as starting materials. Therefore, our results demonstrate that nCUT&Tag is an efficient alternative strategy for plant epigenomic studies.

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Section: Discussionmentioning

confidence: 99%

Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag

et al. 2021

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“…2004 ). However, whether these cohesins have similar functions is still unclear ( Ouyang et al. 2020 ).…”

Section: Chromosomal Architecture Featuresmentioning

confidence: 99%

“…Recent research has revealed that the information and function of a genome are not only modulated via epigenetic marks in the linear DNA sequence but also by the occupancy and three-dimensional (3D) chromatin organization within the nucleus ( Doğan and Liu 2018 , Grob 2020 ). This occupancy and 3D organization have important functional implications for DNA replication, DNA repair and transcription regulation ( Ouyang et al. 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years

Zhang

Wang

2021

Plant and Cell Physiology

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Over the past few decades, eukaryotic linear genomes and epigenomes have been widely and extensively studied for understanding gene expression regulation. More recently, the three-dimensional (3-D) chromatin organization was found to be important for determining genome functionality, finely tuning physiological processes for appropriate cellular responses. With the development of visualization techniques and chromatin conformation capture (3C)-based techniques, increasing evidence indicates that chromosomal architecture characteristics and chromatin domains with different epigenetic modification in the nucleus are correlated to transcriptional activities. Subsequent studies have further explored the intricate interplay between 3-D genome organization and the function of interacting regions. In this review, we summarize spatial distribution patterns of chromatin, including chromatin positioning, configurations and domains, with a particular focus on the effect of a unique form of interaction between a variety of factors that shapes the 3-D genome conformation in plants. We further discuss the methods, advantages and limitations of various chromatin conformation capture (3C)-based techniques, highlighting the applications of these technologies in plants to identify chromatin domains, and address their dynamic changes and functional implications in evolution, and adaptation to development and changing environmental conditions. Moreover, the future implications and emerging research directions of 3-D genome organization are discussed.

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“…Hi-C studies of Arabidopsis , rice ( Oryza sativa ), and maize ( Zea mays ) interphase chromatin, revealed an important role of repeat content in shaping local chromatin domains ( Dong et al, 2020 ). In contrast to plants with large genomes, like rice, that exhibit TAD-like domains ( Ouyang et al, 2020 ), Arabidopsis features few domain-like structures. At the same time, rice and Arabidopsis are characterized by additional functional long-range interacting domains that may be plant-specific – inactive heterochromatic islands (IHIs) or KNOT engaged Elements (KEEs).…”

Section: Fish-visualization Of Chromatin Domains In Model Organismsmentioning

confidence: 99%

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

Maslova

Krasikova

2021

Front. Cell Dev. Biol.

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The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.

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Unraveling the 3D Genome Architecture in Plants: Present and Future

Cited by 59 publications

References 160 publications

Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag

Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag

Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

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