Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape

Kong, Siyuan; Lu, Yuhui; Tan, Shiyong; Li, Rongrong; Gao, Yan; Li, Kui; Zhang, Yubo

doi:10.3390/genes13071114

Cited by 8 publications

(3 citation statements)

References 100 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, previously published methods also detect nucleosome DNA or protein-free DNA (Fig. 2 A) 10 , 11 , 14 – 16 . To enrich only the DNA-TAF complex, we used DSP because it is long enough to crosslink neighboring nucleosomes, which can be easily removed by centrifugation (Fig.…”

Section: Resultsmentioning

confidence: 99%

Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin

Li,

Nakamura

2023

Sci Rep

View full text Add to dashboard Cite

The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consisting of DNA, histones, and trans-acting factors (TAFs). The binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is crucial for gaining insight into the gene expression mechanism of CIP. In this study, using modified proteomics of TAFs bound to DNA, we identified a protein that shuttles between the nucleus and cytosol in a cell density-dependent manner. We identified TIPARP, PTGES3, CBFB, and SMAD4 as cell density-dependent nucleocytoplasmic shuttling proteins. In low-density cells, these proteins predominantly reside in the nucleus; however, upon reaching high density, they relocate to the cytosol. Given their established roles in gene regulation, our findings propose their involvement as CIP-dependent TAFs. We also identified and characterized potential open chromatin regions sensitive to changes in cell density. These findings provide insights into the modulation of chromatin structure by CIP.

show abstract

Section: Resultsmentioning

confidence: 99%

Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin

Li,

Nakamura

2023

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Genome-wide histone modifications are often positioned by chromatin immunoprecipitation and high-throughput sequencing techniques (ChIP-seq), which can enrich target chromatin fragments carrying specific histone modifications ( Kong et al, 2022 ). ChIP-seq is also commonly used to analyze transcription factor binding sites and other protein-DNA interactions ( Wen and Tang, 2018b ).…”

Section: The Methodological Progress Of Single-cell Omics and Single-...mentioning

confidence: 99%

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Kong

Tian

et al. 2023

Front. Genet.

Self Cite

View full text Add to dashboard Cite

Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.

show abstract

“…For example, the trimethylation of histone H3 at lysine 4 (H3K4me3) is often associated with active promoters, while trimethylation at lysine 27 (H3K27me3) is linked with gene repression [27]. This interplay between DNA methylation and histone modifications is sometimes referred to as the "epigenetic code" (reviewed in Kong et al [28]). While DNA methylation can influence the histone modification state, the reverse is also true: histone modifications can affect the DNA methylation pattern.…”

Section: Interplay Between Histone Modifications and Dna Methylationmentioning

confidence: 99%

Epigenetic Landscape and Therapeutic Implication of Gene Isoforms of Doublecortin-Like Kinase 1 for Cancer Stem Cells

Moore,

Houchen

2023

IJMS

View full text Add to dashboard Cite

While significant strides have been made in understanding cancer biology, the enhancement in patient survival is limited, underscoring the urgency for innovative strategies. Epigenetic modifications characterized by hereditary shifts in gene expression without changes to the DNA sequence play a critical role in producing alternative gene isoforms. When these processes go awry, they influence cancer onset, growth, spread, and cancer stemness. In this review, we delve into the epigenetic and isoform nuances of the protein kinase, doublecortin-like kinase 1 (DCLK1). Recognized as a hallmark of tumor stemness, DCLK1 plays a pivotal role in tumorigenesis, and DCLK1 isoforms, shaped by alternative promoter usage and splicing, can reveal potential therapeutic touchpoints. Our discussion centers on recent findings pertaining to the specific functions of DCLK1 isoforms and the prevailing understanding of its epigenetic regulation via its two distinct promoters. It is noteworthy that all DCLK1 isoforms retain their kinase domain, suggesting that their unique functionalities arise from non-kinase mechanisms. Consequently, our research has pivoted to drugs that specifically influence the epigenetic generation of these DCLK1 isoforms. We posit that a combined therapeutic approach, harnessing both the epigenetic regulators of specific DCLK1 isoforms and DCLK1-targeted drugs, may prove more effective than therapies that solely target DCLK1.

show abstract

Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape

Cited by 8 publications

References 100 publications

Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin

Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Epigenetic Landscape and Therapeutic Implication of Gene Isoforms of Doublecortin-Like Kinase 1 for Cancer Stem Cells

Contact Info

Product

Resources

About