Long non-coding RNAs (lncRNAs) play key roles in colorectal carcinogenesis. Here, we aimed to identify the risk SNP-induced lncRNAs and to investigate their roles in colorectal carcinogenesis. First, we identified rs6695584 as the causative SNP in 1q41 locus. The A>G mutation of rs6695584 created a protein-binding motif of BATF, altered the enhancer activity, and subsequently activated lncSLCC1 expression. Further validation in two independent CRC cohorts confirmed the upregulation of lncSLCC1 in CRC tissues, and revealed that increased lncSLCC1 expression was associated with poor survival in CRC patients. Mechanistically, lncRNA-SLCC1 interacted with AHR and transcriptionally activated HK2 expression, the crucial enzyme in glucose metabolism, thereby driving the glycolysis pathway and accelerating CRC tumor growth. The functional assays revealed that lncSLCC1 induced glycolysis activation and tumor growth in CRC mediated by HK2. In addition, HK2 was upregulated in colorectal cancer tissues and positively correlated with lncSLCC1 expression and patient survival. Taken together, our findings reveal a risk SNP-mediated oncogene lncRNA-SLCC1 promotes CRC through activating the glycolysis pathway.

DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure.

The histone variant H3.3 is deposited across active genes, regulatory regions, and telomeres. It remains unclear how H3.3 interacts with chromatin modifying enzymes and thereby modulates gene activity. In this study, we performed a co-immunoprecipitation-mass spectrometry analysis of proteins associated with H3.3-containing nucleosomes and identified the nucleosome remodeling and deacetylase complex (NuRD) as a major H3.3-interactor. We show that the H3.3-NuRD interaction is dependent on the H3.3 lysine 4 residue and that NuRD binding occurs when lysine 4 is in its unmodified state. The majority of NuRD binding colocalizes with H3.3 and directly correlates with gene activity. H3.3 depletion led to reduced levels of NuRD at sites previously occupied by H3.3, as well as a global decrease in histone marks associated with gene activation. Our results demonstrate the importance of H3.3 in the maintenance of the cellular epigenetic landscape and reveal a highly prevalent interaction between the histone variant H3.3 and the multiprotein complex NuRD.

Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Infiltration and alterations in non-cardiomyocytes of the human heart involve crucially in the occurrence of DCM and associated immunotherapeutic approaches. We constructed a single-cell transcriptional atlas of DCM and normal patients. Then, the xCell algorithm, EPIC algorithm, MCP counter algorithm, and CIBERSORT method were applied to identify DCM-related cell types with a high degree of precision and specificity using RNA-seq datasets. We further analyzed the heterogeneity among cell types, performed trajectory analysis, examined transcription factor regulatory networks, investigated metabolic heterogeneity, and conducted intercellular communication analysis. Finally, we used bulk RNA-seq data to confirm the roles of M2-like2 subpopulations and GAS6 in DCM. We integrated and analyzed Single-cell sequencing (scRNA-seq) data from 7 DCM samples and 3 normal heart tissue samples, totaling 70,958 single-cell data points. Based on gene-specific expression and prior marker genes, we identified 9 distinct subtypes, including fibroblasts, endothelial cells, myeloid cells, pericytes, T/NK cells, smooth muscle cells, neuronal cells, B cells, and cardiomyocytes. Using machine learning methods to quantify bulk RNA-seq data, we found significant differences in fibroblasts, T cells, and macrophages between DCM and normal samples. Further analysis revealed high heterogeneity in tissue preference, gene expression, functional enrichment, immunodynamics, transcriptional regulatory factors, metabolic changes, and communication patterns in fibroblasts and myeloid cells. Among fibroblast subpopulations, proliferative F3 cells were implicated in the fibroblast transition process in DCM, while myofibroblast F6 cells promoted the fibroblast transition to a late cell state in DCM. Additionally, two subpopulations of M2 macrophages, M2-like1 and M2-like2, were identified with distinct features. The M2-like2 cell subpopulation, which was enriched in glycolysis and fatty acid metabolism, involved in inflammation inhibition and fibrosis promotion. Cell‒cell communication analysis indicated the GAS6-MERTK axis might exhibit interaction between M2 macrophage and M2-like1 macrophage. Furthermore, deconvolution analysis for bulk RNA-seq data revealed a significant increase in M2-like2 subpopulations in DCM, suggesting a more important role for this cell population in DCM. We revealed the heterogeneity of non-cardiomyocytes in DCM and identified subpopulations of myofibroblast and macrophages engaged in DCM, which suggested a potential significance of non-cardiomyocytes in treatment of DCM.

Long non-coding RNAs (lncRNAs) are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. Although the cold responsive lncRNAs have been reported in plants, no data is available on screening and functional prediction of lncRNAs in cold acclimation in fish so far. Here we compared the expression profile of lncRNAs in cold acclimated zebrafish embryonic fibroblast cells (ZF4) cultured at 18°C for 30 days with that of cells cultured at 28°C as control by high-throughput sequencing. Totally 8,363 novel lncRNAs were identified. Including known and novel lncRNAs, there are 347 lncRNAs up-regulated and 342 lncRNAs down-regulated in cold acclimated cells. Among the differentially expressed lncRNAs, 74 and 61 were detected only in control cells or cold-acclimated cells, respectively. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses of adjacent genes to the differentially expressed lncRNAs showed that the enriched genes are involved in electron transport, cell adhesion, oxidation-reduction process, and so on. We also predicted the target genes of the differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNAs, and constructed an interaction network. In summary, our genome-wide systematic identification and functional prediction of cold responsive lncRNAs in zebrafish cells suggests a crucial role of lincRNAs in cold acclimation in fish.

Accumulating evidence indicates that heat shock protein 90 (HSP90) plays essential roles in modulation of phenotypic plasticity in vertebrate development, however, the roles of HSP90 in modulation of cold tolerance capacity in fish are still unclear. In the present study, we showed that transient inhibition of embryonic HSP90 function by a chemical inhibitor or low conductivity stress promoted variation of cold tolerance capacity in adult zebrafish. Further work showed that embryonic HSP90 inhibition enhanced cold tolerance in adult zebrafish could be transmitted to their offspring. RNA-seq data showed that embryonic HSP90 inhibition enhanced cold tolerance involves variation of gene expression related to proteasome, lysosome, autophagy, and ribosome. Experiments with zebrafish ZF4 cells showed that two differentially expressed genes atg9b and psmd12 were up-regulated by radicicol treatment and provided protective roles for cells under cold stress, indicating that up-regulation of autophagy and proteasome function contributes to enhanced cold tolerance. The present work sheds a light on the roles of HSP90 in regulation of phenotypic plasticity associated with thermal adaptation in fish.