Integrative multi-omics analysis unveils the regulatory landscape of diabetic cardiomyopathy: from chromatin accessibility to transcript isoforms and epitranscriptome

Figure 1. Identification and characterization of full-length transcripts in diabetic cardiomyopathy. (A) The bar showing the number of the transcripts and genes detected in all samples. (B) The boxplot showing the lengths of all sample transcripts. (C) The Venn diagram of the overlapping transcripts between reference genome transcripts and the number of detected transcripts. (D) The bar showing the number of transcript types. (E) The number of transcripts of single genes. (F) This figure shows the distribution of reads 3kb upstream and downstream of a gene transcription start site (TSS). (G) The percentage of the number of transcript types.

Figure 2. Functional annotation of differentially expressed transcripts (DET) in diabetic cardiomyopathy. (A) The bar showing the number of differentially expressed transcripts (DETs) based on known and novel. (B) The Scatter plot exhibiting the most enriched GO biological process results of the novel DETs. (C) The bar showing the number of differentially expressed genes (DEGs) for DRS-seq and bulk RNA-seq. (D) The Venn diagram of the overlapping DEGs between DRS-seq and bulk RNA-seq. (E) The Venn diagram of the overlapping genes between differentially expressed transcripts (DETs) and differentially expressed genes (DEGs). (F) The bar showing the average number of the average number of transcripts for each overlapping part. (G) The bar showing the number of gene types for each overlapping part. (H) Hierarchical clustering heat map showing the top enriched GO biological process results of the gene for each overlapping part. (I) Hierarchical clustering heat map showing the top enriched KEGG pathway results of the gene for each overlapping part.

Figure 3. Integration of DET (DRS-seq) and DAR (ATAC-seq) of diabetic cardiomyopathy. (A) Venn diagram showing the DET of DAR. (B–E) Showing the transcripts information from overlapped transcripts (Fam210b, Cdh22, Fbxo10, Cenpx). Left panel: Schematic representation of distinct transcript isoforms identified by DRS-seq (black), along with read coverage from ATAC-seq (blue) and bulk RNA-seq (red). Right panel: Bar plot showing the relative expression levels of individual transcripts in DRS-seq and chromatin accessibility changes in ATAC-seq. Error bars represent mean ± SEM, **P-value < 0.01, *P < 0.05.

Figure 4. m6A modification of transcripts in DRS-seq. (A) The bar showing the number of m6A modified sites in all samples. (B) The ratio of transcripts with a different number of m6A-modified sites. (C) The density of m6A-modified bases along the gene body. The position of each modified site along the gene body was normalized by the length of the transcript using R pipeline MeraPlotR. (D) The ratio of m6A-modified sites distributed in the 5’-UTR, CDS,3’-UTR in all samples. E) Volcano plot showing all differentially expressed transcripts with a different number of m6A-modified sites (DETs). (F) The bar showing the number of m5C modified sites in all samples. (G) The ratio of transcripts with a different number of m5C-modified sites. (H) The density of m5C-modified bases along the gene body. The position of each modified site along the gene body was normalized by the length of the transcript using R pipeline MeraPlotR. (I) The ratio of m5C-modified sites distributed in the 5’-UTR, CDS,3’-UTR in all samples. (J) Volcano plot showing all differentially expressed transcripts with a different number of m5C-modified sites (DETs).

Figure 5. Integrative analysis of DETs, differentially m6A-modified transcripts, and alternative polyadenylation /polyA sites in DRS-seq. (A) Venn diagram showing the overlap of DET and DE-m6A and DE-polyA and DE-APA. (B–E) Showing the ENSMUST00000015456.10 of Gadd45b, ENSMUST00000054301.14 of Lipe, ENSMUST00000035579.10 of Fbxo21, ENSMUST00000090746.3 of Hmgcs2. Top panel: Reads distribution of the transcripts, full structure display, and distribution of APA and m6A sites. Bottom panel: Bar plot showing the expression levels of DETs and the modification ratios of m⁶A sites. Error bars represent mean ± SEM. **P-value < 0.01, *P < 0.05, ***P-value < 0.001.

Figure 6. Fam210b correlates with CD4+ memory T-cell infiltration in DCM. (A) CIBERSORT analysis of cardiac immune microenvironment. (B) Verification of candidate transcript expression in DRS-seq datasets. (C) Pearson correlation matrix between candidate transcript expressions and CD4+ memory T-cell infiltration. **P-value < 0.01, *P < 0.05.