H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

AbstractGene repression and silencers are poorly understood. We reasoned that H3K27me3-rich regions (MRRs) of the genome defined from clusters of H3K27me3 peaks may be used to identify silencers that can regulate gene expression via proximity or looping. MRRs were associated with chromatin interactions and interact preferentially with each other. MRR component removal at interaction anchors by CRISPR led to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. The MRR knockout cells also showed changes in phenotype associated with cell identity, and altered xenograft tumor growth. MRR-associated genes and long-range chromatin interactions were susceptible to H3K27me3 depletion. Our results characterized H3K27me3-rich regions and their mechanisms of functioning via looping.

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H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

Nature Communications ◽

10.1038/s41467-021-20940-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yichao Cai ◽

Ying Zhang ◽

Yan Ping Loh ◽

Jia Qi Tng ◽

Mei Chee Lim ◽

...

Keyword(s):

Gene Expression ◽

Tumor Growth ◽

Target Genes ◽

Gene Repression ◽

Xenograft Tumor ◽

Regulate Gene Expression ◽

Chromatin Interactions ◽

Genomic Regions ◽

Xenograft Tumor Growth ◽

Regulate Gene

AbstractThe mechanisms underlying gene repression and silencers are poorly understood. Here we investigate the hypothesis that H3K27me3-rich regions of the genome, defined from clusters of H3K27me3 peaks, may be used to identify silencers that can regulate gene expression via proximity or looping. We find that H3K27me3-rich regions are associated with chromatin interactions and interact preferentially with each other. H3K27me3-rich regions component removal at interaction anchors by CRISPR leads to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. Cells with H3K27me3-rich regions knockout also show changes in phenotype associated with cell identity, and altered xenograft tumor growth. Finally, we observe that H3K27me3-rich regions-associated genes and long-range chromatin interactions are susceptible to H3K27me3 depletion. Our results characterize H3K27me3-rich regions and their mechanisms of functioning via looping.

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Cohesin disrupts polycomb-dependent chromosome interactions

10.1101/593970 ◽

2019 ◽

Cited By ~ 6

Author(s):

JDP Rhodes ◽

A Feldmann ◽

B Hernández-Rodríguez ◽

N Díaz ◽

JM Brown ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Embryonic Stem ◽

Cell Types ◽

Gene Repression ◽

Chromosome Conformation ◽

Regulate Gene Expression ◽

Topologically Associating Domains ◽

Chromosome Organisation ◽

Regulate Gene

AbstractHow chromosome organisation is related to genome function remains poorly understood. Cohesin, loop-extrusion, and CTCF have been proposed to create structures called topologically associating domains (TADs) to regulate gene expression. Here, we examine chromosome conformation in embryonic stem cells lacking cohesin and find as in other cell types that cohesin is required to create TADs and regulate A/B compartmentalisation. However, in the absence of cohesin we identify a series of long-range chromosomal interactions that persist. These correspond to regions of the genome occupied by the polycomb repressive system, depend on PRC1, and we discover that cohesin counteracts these interactions. This disruptive activity is independent of CTCF and TADs, and regulates gene repression by the polycomb system. Therefore, in contrast to the proposal that cohesin creates structure in chromosomes, we discover a new role for cohesin in disrupting polycomb-dependent chromosome interactions to regulate gene expression.

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CircFOXK2 Promotes Tumor Growth and Metastasis of Pancreatic Ductal Adenocarcinoma via Complexing with RNA Binding Proteins and Sponging MiR-942

10.1101/792101 ◽

2019 ◽

Author(s):

Chi Hin Wong ◽

Ut Kei Lou ◽

Youjia Li ◽

Stephen Lam Chan ◽

Joanna Hung-Man Tong ◽

...

Keyword(s):

Gene Expression ◽

Tumor Growth ◽

Pancreatic Ductal Adenocarcinoma ◽

Ductal Adenocarcinoma ◽

List Type ◽

Interacting Proteins ◽

Loss Of Function ◽

Gain Of Function ◽

Regulate Gene Expression ◽

Regulate Gene

AbstractObjectiveCircular RNA (circRNA) is a novel class of non-coding RNAs that regulate gene expression. However, the role of circRNAs in pancreatic ductal adenocarcinoma (PDAC) is largely unknown.DesignWe performed circRNA sequencing of non-tumor HPDE and PDAC cells. We investigated the functions of circFOXK2 in PDAC by gain-of-function and loss-of-function assays. Bioinformatics analysis, luciferase assay and microRNA pulldown assays were performed to identify circFOXK2 interacting-miRNAs. To further investigate the mechanism, we performed circRNA-pulldown and mass spectrometry to identify circFOXK2-interacting proteins in PDAC.ResultsWe identified 169 differentially expressed circRNAs in PDAC cells. We validated that one of the circRNAs circFOXK2 was significantly up-regulated in PDAC cells and in 63 % of primary tumor (53 out of 84). Gain-of-function and loss-of-function assays demonstrated that circFOXK2 promoted PDAC cell growth, migration and invasion. CircFOXK2 was also involved in cell cycle progression and apoptosis. circFOXK2 functioned as sponge for miR-942, and in turn promoted the expression of miR-942 targets ANK1, GDNF and PAX6. Furthermore, circFOXK2 interacted with 94 proteins, which were involved in cell adhesion and mRNA splicing. Among these circFOXK2-interacting proteins, YBX1 and hnRNPK were validated by RNA immunoprecipitation. Importantly, circFOKX2 interacted with YBX1 and hnRNPK targets NUF2 and PDXK in PDAC cells. Knockdown of circFOXK2 reduced the binding of YBX1 and hnRNPK to NUF2 and PDXK, and in turn decreased their expressions in PDAC cells.ConclusionWe identified that circFOXK2 promoted PDAC cells growth and metastasis. Also, circFOXK2 complexed with YBX1 and hnRNPK to promote the expressions of oncogenic proteins.Significance of this studyWhat is already known on this subject?Differentially expressed circRNAs are involved in carcinogenesis of many cancers.CircRNAs function as microRNA sponges to regulate gene expression.The roles of circRNAs in PDAC progression is largely unknown.What are the new findings?circFOXK2 is upregulated in PDAC primary tumors.circFOXK2 promotes PDAC tumor growth and liver metastasis.circFOXK2 functions as sponges for miR-942 to promote the expressions of oncogenic ANK1, GDNF and PAX6.circFOXK2 complexes with YBX1 and hnRNPK to promote the expressions of oncogenic proteins in PDAC.How might it impact on clinical practice in the foreseeable future?circFOXK2 upregulation in PDAC may function as a novel biomarker for diagnosis.circFOXK2 may be a novel therapeutic target in treating PDAC.

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Correlation between miRNA-targeting-specific promotermethylation and miRNA regulation of target genes

F1000Research ◽

10.12688/f1000research.2-21.v1 ◽

2013 ◽

Vol 2 ◽

pp. 21

Author(s):

Y-h Taguchi

Keyword(s):

Gene Expression ◽

Promoter Methylation ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Gene Expression Omnibus ◽

Mirna Regulation ◽

P Values ◽

Regulate Gene Expression ◽

Mirna Targeting ◽

Regulate Gene

Background miRNA regulation of target genes and promoter methylation were known to be the primary mechanisms underlying the epigenetic regulation of gene expression. However, how these two processes cooperatively regulate gene expression has not been extensively studied. Methods Gene expression and promoter methylation profiles of 271 distinct human cell lines were obtained from gene expression omnibus. P-values that describe both miRNA-targeting-specific promoter methylation and miRNA regulation of target genes were computed with the MiRaGE method proposed recently by the author. Results We found that promoter methylation was miRNA-targeting-specific. In other words, changes in promoter methylation were associated with miRNA binding at target genes. It was also found that miRNA-targeting-specific promoter hypomethylation was related to miRNA regulation; the genes with miRNA-targeting-specific promoter hypomethylation were downregulated during cell senescence and upregulated during cellulardierentiation. Promoter hypomethylation was especially enhanced for genes targeted by miR-548 miRNAs, which are non-conserved, and primate-specific miRNAs that are typically expressed at lower levels than the frequently investigated conserved miRNAs. Conclusions It was found that promoter methylation was affected by miRNA targeting. Furthermore, miRNA-targeting-specific promoter hypomethylation was suggested to facilitate gene regulation by miRNAs that are not strongly expressed (e.g., miR-548 miRNAs).

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Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

10.1101/2020.07.03.186783 ◽

2020 ◽

Author(s):

Nikki R. Kong ◽

Mahmoud A. Bassal ◽

Hong Kee Tan ◽

Jesse V. Kurland ◽

Kol Jia Yong ◽

...

Keyword(s):

Gene Expression ◽

Dna Binding ◽

Cancer Cells ◽

Zinc Finger ◽

Target Genes ◽

Zinc Finger Protein ◽

Embryonic Stem ◽

Regulate Gene Expression ◽

Protein Binding Microarray ◽

Regulate Gene

SummaryThe zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.

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