Characterization of DNA methylation reader proteins ofArabidopsis thaliana DOI
Jonathan Cahn, James P. B. Lloyd, Ino D. Karemaker

et al.

Genome Research, Journal Year: 2024, Volume and Issue: 34(12), P. 2229 - 2243

Published: Dec. 1, 2024

In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body expressed genes, referred to as gene (gbM). gbM correlated ubiquitously genes; however, its function, or absence thereof, highly debated. The different outputs that mC have raise questions how interpreted—or read—differently these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased affinity pull-down assay combined quantitative mass spectrometry using methylated probes each context. All readers known date preferentially bind probes, along a range new protein candidates. Functional characterization readers, focused on MBD SUVH families, was undertaken by ChIP-seq mapping genome-wide binding sites, their interactors, impact high-order mutations transcriptomic epigenomic profiles. Together, results highlight specific context preferences particular ability MBD2 predominantly gbM. This comprehensive analysis Arabidopsis emphasizes complexity interconnectivity between chromatin remodeling processes plants.

Language: Английский

Profiling the epigenome using long-read sequencing DOI
Tianyuan Liu, Ana Conesa

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

Citations

2
The regulatory potential of transposable elements in maize DOI Creative Commons
Kerry L. Bubb, Morgan O. Hamm,

Thomas W. Tullius

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 14, 2024

The genomes of flowering plants consist largely transposable elements (TEs), some which modulate gene regulation and function. However, the repetitive nature TEs difficulty mapping individual by short-read-sequencing have hindered our understanding their regulatory potential. We demonstrate that long-read chromatin fiber sequencing (Fiber-seq) comprehensively identifies accessible regions (ACRs) CpG methylation across maize genome. uncover stereotypical ACR patterns at young degenerate with evolutionary age, resulting in TE-enhancers preferentially marked a novel plant-specific epigenetic feature: simultaneous hyper-CpG accessibility. show TE ACRs are co-opted as promoters ACR-containing can facilitate amplification. Lastly, we pervasive signature - hypo-5mCpG diffuse accessibility directing to specific loci, including loci sparked McClintock's discovery TEs.

Language: Английский

Citations

4
Mechanisms and technologies in cancer epigenetics DOI Creative Commons
Zaki A. Sherif, Olorunseun O. Ogunwobi, Habtom W. Ressom

et al.

Frontiers in Oncology, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 7, 2025

Cancer's epigenetic landscape, a labyrinthine tapestry of molecular modifications, has long captivated researchers with its profound influence on gene expression and cellular fate. This review discusses the intricate mechanisms underlying cancer epigenetics, unraveling complex interplay between DNA methylation, histone chromatin remodeling, non-coding RNAs. We navigate through tumultuous seas dysregulation, exploring how these processes conspire to silence tumor suppressors unleash oncogenic potential. The narrative pivots cutting-edge technologies, revolutionizing our ability decode epigenome. From granular insights single-cell epigenomics holistic view offered by multi-omics approaches, we examine tools are reshaping understanding heterogeneity evolution. also highlights emerging techniques, such as spatial long-read sequencing, which promise unveil hidden dimensions regulation. Finally, probed transformative potential CRISPR-based epigenome editing computational analysis transmute raw data into biological insights. study seeks synthesize comprehensive yet nuanced contemporary landscape future directions research.

Language: Английский

Citations

0
DNA methylation in wheat: current understanding and future potential for enhancing biotic and abiotic stress tolerance DOI
Uzma Afreen, Kunal Mukhopadhyay, Manish Kumar

et al.

Physiology and Molecular Biology of Plants, Journal Year: 2024, Volume and Issue: 30(12), P. 1921 - 1933

Published: Dec. 1, 2024

Language: Английский

Citations

1
Characterization of DNA methylation reader proteins ofArabidopsis thaliana DOI
Jonathan Cahn, James P. B. Lloyd, Ino D. Karemaker

et al.

Genome Research, Journal Year: 2024, Volume and Issue: 34(12), P. 2229 - 2243

Published: Dec. 1, 2024

In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body expressed genes, referred to as gene (gbM). gbM correlated ubiquitously genes; however, its function, or absence thereof, highly debated. The different outputs that mC have raise questions how interpreted—or read—differently these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased affinity pull-down assay combined quantitative mass spectrometry using methylated probes each context. All readers known date preferentially bind probes, along a range new protein candidates. Functional characterization readers, focused on MBD SUVH families, was undertaken by ChIP-seq mapping genome-wide binding sites, their interactors, impact high-order mutations transcriptomic epigenomic profiles. Together, results highlight specific context preferences particular ability MBD2 predominantly gbM. This comprehensive analysis Arabidopsis emphasizes complexity interconnectivity between chromatin remodeling processes plants.

Language: Английский

Citations

0