Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression

Seem, Karishma; Kaur, Simardeep; Kumar, Suresh; Mohapatra, Trilochan

doi:10.1080/10409238.2024.2320659

Cited by 2 publications

(1 citation statement)

References 300 publications

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“…Identification of epigenetic marks and their role in stress memory is another challenging task. However, once a heritable mark is identified, a CRISPR-based epigenome-editing tool might be utilized for targeted/ site-specific alteration in the epigenome to achieve the desired phenotype (Seem et al 2024). A comprehensive understanding of the epigenetic-epitranscriptomic regulation of gene expression might enable us the development of climate-smart crops in the near future.…”

Section: Future Perspectivesmentioning

confidence: 99%

Recent advances in epigenomic techniques: Analysis of DNA base modifications

Kumar,

Singh

et al. 2024

IJGPB

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Epigenetics refers to the study of modifications in DNA bases, histone proteins and/or alterations in non-coding-RNA biogenesis that cause changes in gene expression without affecting the underlying nucleotide sequence. Epigenetic variation is emerging as one of the regulators of developmental processes and stress responses in animals and plants. Identification and interrogation of epigenetic changes provide unprecedented opportunities for resolving some of the enigmas that could not be solved based on genetic principles. Moreover, epigenome editing might become a preferred technique for the manipulation of gene expression in the desired organism. Although epigenetics is still in its infancy, the need of the day is to identify epigenetic marks and associate them with heritable phenotypes. Several techniques have been developed to analyze the epigenetic changes and associate them with molecular/physiological processes. It is necessary to examine them in a site- and cell-specific manner. Though considerable progress has been made in the last decade towards mapping DNA modifications as well as other epigenetic changes, there is a need to improve the specificity, sensitivity, and resolving power of the techniques to conduct epigenetic research in a cell-specific manner. The recent technological advancements are currently driving the field of epigenetics, and facilitating a better understanding of the field of functional genomics. The present review outlines the recent advances in epigenomic tools and techniques and presents the future perspectives of epigenomic studies.

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Section: Future Perspectivesmentioning

confidence: 99%

Recent advances in epigenomic techniques: Analysis of DNA base modifications

Kumar,

Singh

et al. 2024

IJGPB

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Transcriptional and epigenetic response of rapeseed (Brassica napusL.) to PEG-triggered osmotic stress

Prasad,

Shetty,

Pal

et al. 2024

Preprint

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Drought hinders growth, development, and productivity of higher plants. While physiological and molecular background of plant responses to drought has extensively studied, the role of epigenetic modifications in response to dehydration remains largely elusive. In this study, we deciphered genome-wide transcriptomic and epigenetic responses of rapeseed (Brassica napusL.) to dehydration. High-throughput transcript profiling (RNA-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) of PEG-treated rapeseed plants revealed genome-scale changes in transcription and histone methylation patterns, focusing on histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 tri-methylated lysine 27 (H3K27me3). We have identified large gene sets with altered transcript profiles and changed histone methylation marks in response to osmotic stress, revealed a close correlation between gain or loss of histone methylation and activation or repression of gene expression. Significant epigenetic regulation of Delta 1-Pyrroline-5-Carboxylate Synthetase (P5CS) genes, which control the key step in proline synthesis, was discovered as several PEG-inducedBnP5CSAgenes displayed enhanced H3K4me3 and/or H3K36me3 marks. Targeted bisulphite sequencing revealed that oneBnP5CSAgene has stress-dependent gene body DNA methylation also. By integrating physiological, transcriptional and epigenetic data, our study facilitates better understanding drought response control in higher plants.

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Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression

Cited by 2 publications

References 300 publications

Recent advances in epigenomic techniques: Analysis of DNA base modifications

Recent advances in epigenomic techniques: Analysis of DNA base modifications

Transcriptional and epigenetic response of rapeseed (Brassica napusL.) to PEG-triggered osmotic stress

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