Epigenetics & Chromatin最新文献

Background: MED12 is a key regulator of transcription and chromatin architecture, essential for normal hematopoiesis. While its dysregulation has been implicated in hematological malignancies, the mechanisms driving its upregulation in acute myeloid leukemia (AML) remain poorly understood. We investigated MED12 expression across AML subgroups by integrating chromatin accessibility profiling, histone modification landscapes, and DNA methylation (DNAm) patterns. Functional assays using DNMT inhibition were performed to dissect the underlying regulatory mechanisms.

Results: MED12 shows subtype-specific upregulation in AML compared to hematopoietic stem and progenitor cells, independent of somatic mutations. Chromatin accessibility profiling reveals that the MED12 locus is epigenetically primed in AML blasts, with increased DNase hypersensitivity at regulatory elements. Histone modification analysis demonstrates strong H3K4me3 and H3K27ac enrichment around the transcription start site (TSS), consistent with promoter activation, while upstream and intragenic regions exhibit enhancer-associated marks (H3K4me1, H3K27ac). Notably, hypermethylation within TSS-proximal regulatory regions (TPRRs)-including promoter-overlapping and adjacent CpG islands-correlates with ectopic MED12 overexpression, challenging the canonical view of DNAm as strictly repressive. Functional studies show that DNMT inhibition via 5-azacytidine reduces MED12 expression despite promoter demethylation in cells with hypermethylated TPRRs, suggesting a noncanonical role for DNA methylation in maintaining active transcription. Furthermore, MED12 expression positively correlates with DNMT3A and DNMT3B expression, implicating these methyltransferases in sustaining its epigenetic activation.

Conclusion: This study identifies a novel regulatory axis in which aberrant DNA methylation, rather than genetic mutation, drives MED12 upregulation in AML. Our findings suggest that TPRR hypermethylation may function noncanonically to support transcriptional activation, likely in cooperation with enhancer elements. These results underscore the importance of epigenetic mechanisms in AML and highlight enhancer-linked methylation as a potential contributor to oncogene dysregulation. Future studies should further explore the role of noncanonical methylation-mediated gene activation in AML pathogenesis and therapeutic targeting.

DNA methylation is a conserved epigenetic modification that plays important roles in silencing transposable elements, regulating gene expression, and maintaining genome stability. In plants, DNA methylation is de novo established by the RNA-directed DNA methylation pathway and maintained during each cell cycle. It can be actively removed by the REPRESSOR OF SILENCING 1/DEMETER family proteins through the base excision repair pathway. Active DNA demethylation is essential for plant growth, development, reproduction and stress adaptation. During the past two decades, significant progress has been made in our understanding of active DNA demethylation. In this review, we will discuss the molecular mechanisms, regulation, and biological functions of active DNA demethylation in plants.

The TIP60 complex is an evolutionarily conserved, multifunctional chromatin remodeling complex involved in critical cellular processes, including DNA repair, transcription regulation, and cell cycle control. Although its molecular organization and functions have been extensively studied, a comparative synthesis of its context-specific roles across evolutionarily distant species and pathological conditions is important to fully grasp its biological and clinical significance. In this review, we provide an integrative overview of the TIP60 complex, emphasizing its composition and conserved functions in Homo sapiens and Drosophila melanogaster, with comparative insights from plant systems. We explore how TIP60 complex dysregulation contributes to the molecular pathology of cancer and neurodevelopmental disorders, highlighting recent mechanistic insights. We also examine the emerging interplay between TIP60 complex subunits and long non-coding RNAs, which are increasingly recognized as pivotal regulators of genome accessibility and transcriptional programs. Finally, in this intriguing scenario, we highlight the non-canonical functions of the TIP60 complex in mitosis and cytokinesis, underscoring its moonlighting roles in maintaining genomic and cellular integrity, beyond its established contribution to epigenetic regulation. By connecting these diverse aspects, our review aims to provide an integrated perspective on the TIP60 complex and its expanding functional landscape in health and disease.

Characterization of DNA binding sites for specific proteins is of fundamental importance in molecular biology. It is commonly addressed experimentally by chromatin immunoprecipitation and sequencing (ChIP-seq) of bulk samples (10³-10⁷ cells). We have developed an alternative method that uses a Chromatin Antibody-mediated Methylating Protein (ChAMP) composed of a GpC methyltransferase fused to protein G. By tethering ChAMP to a primary antibody directed against the DNA-binding protein of interest, and selectively switching on its enzymatic activity in situ, we generated distinct and identifiable methylation patterns adjacent to the protein binding sites. This method is compatible with methods of single-cell methylation-detection and single molecule methylation identification. Indeed, as every binding event generates multiple nearby methylations, we were able to confidently detect protein binding in long single molecules.

Background: Histone modifications are key epigenetic regulators of cell differentiation and have been intensively studied in many cell types and tissues. Nevertheless, we still lack a thorough understanding of how combinations of histone marks at the same genomic location, so-called chromatin states, are linked to gene expression, and how these states change in the process of differentiation. To receive insight into the epigenetic changes accompanying the differentiation along the chondrogenic lineage we analyzed two publicly available datasets representing (1) the early differentiation stages from embryonic stem cells into chondrogenic cells and (2) the direct differentiation of mature chondrocyte subtypes.

Results: We used ChromHMM to define chromatin states of 6 activating and repressive histone marks for each dataset and tracked the transitions between states that are associated with the progression of differentiation. As differentiation-associated state transitions are likely limited to a reduced set of genes, one challenge of such global analyses is the identification of these rare transitions within the large-scale data. To overcome this problem, we have developed a relativistic approach that quantitatively relates transitions of chromatin states on defined groups of tissue-specific genes to the background. In the early lineage, we found an increased transition rate into activating chromatin states on mesenchymal and chondrogenic genes while mature chondrocytes are mainly enriched in transition between activating states. Interestingly, we also detected a complex extension of the classical bivalent state (H3K4me3/H3K27me3) consisting of several activating promoter marks besides the repressive mark H3K27me3. Within the early lineage, mesenchymal and chondrogenic genes undergo transitions from this state into active promoter states, indicating that the initiation of gene expression utilizes this complex combination of activating and repressive marks. In contrast, at mature differentiation stages the inverse transition, the gain of H3K27me3 on active promoters, seems to be a critical parameter linked to the initiation of gene repression in the course of differentiation.

Conclusions: Our results emphasize the importance of a relative analysis of complex epigenetic data to identify chromatin state transitions associated with cell lineage progression. They further underline the importance of serial analysis of such transitions to uncover the diverse regulatory potential of distinct histone modifications like H3K27me3.

Background: Anopheles mosquitoes and the malaria parasites they transmit remain a significant global health problem. Most genomic and functional genomic studies of mosquitoes have focused on the protein-coding genome, and comparatively little is known about the importance of noncoding transcriptional enhancers in controlling their gene expression and phenotypic variation. Here we evaluate nine enhancers previously identified in a STARR-seq screen and present in a genetic locus that was identified as a major influence on susceptibility to malaria infection in wild Anopheles coluzzii mosquitoes.

Result: We developed an analytical pipeline to filter nine enhancers in the malaria susceptibility locus on chromosome 2L. First, ATAC-seq revealed that only three of the nine enhancers were located in open chromatin and thus likely to be active in somatic cells. Next, we cloned these three enhancers from malaria-susceptible and resistant mosquitoes and measured their enhancer activity by luciferase reporter assays. Only two of the three open-chromatin enhancers displayed significantly different enhancer activity between resistant and susceptible alleles. Finally, alleles of just one of these enhancers, ENH_2L-03, contained nucleotide variants which also segregated in wild mosquitoes, and ENH_2L-03 was prioritized for further study. A noncoding RNA was detected within ENH_2L-03, consistent with an enhancer RNA (eRNA), which we depleted in mosquitoes using RNAi in order to silence the enhancer activity. Transcriptional profiling of ENH_2L-03-silenced mosquitoes revealed 15 differentially expressed genes, which share a transcription factor binding motif suggestive of coordinate regulation. However, silencing ENH_2L-03 did not influence infection levels of either human or rodent malaria parasites.

Conclusion: Despite the absence of an ENH_2L-03 effect on infection outcome, multiple enhancers can cooperate to influence a phenotype, and further examination of this enhancer is warranted. Overall, we provide a pipeline for the in vivo functional study of transcriptional enhancers in Anopheles, towards understanding how enhancer function may control important vector phenotypes.

Epigenetic factors underlie cellular identity through the regulation of transcriptional networks that establish a cell's phenotype and function. Cell conversions are directed by transcription factor binding at target DNA which induce changes to identity-specific gene regulatory programs. The degree of cell plasticity is determined by the interplay of epigenetic mechanisms to create a landscape susceptible to such binding events. 5-hydroxymethylcytosine, a key intermediate during the process of DNA demethylation, is an epigenetic modification involved in controlling these epigenetic dynamics related to cell identity. Here, the role of 5-hydroxcymethylcytosine during cell identity conversions, including its relationship with other main epigenetic mechanisms, is reviewed.