Transcription activation is tightly associated with the openness of chromatin, which allows direct contact between transcriptional regulators, such as transcription factors, and their targeted DNA for downstream gene activation. However, the annotation of open chromatin regions (OCRs) in the wild soybean (Glycine soja) genome is limited. We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and successfully identified 22,333 OCRs in the leaf of W05 (a wild soybean accession). These OCRs were enriched in gene transcription start sites (TSS) and were positively correlated with downstream gene expression. Several known transcription factor (TF)-binding motifs were also enriched at the OCRs. A potential regulatory network was constructed using these transcription factors and the OCR-marked genes. Furthermore, by overlapping the OCR distribution with those of histone modifications from chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that the distribution of the activation histone mark, H3K4me3, but not that of the repressive H3K27me3 mark, was closely associated with OCRs for gene activation. Several putative enhancer-like distal OCRs were also found to overlap with LincRNA-encoding loci. Moreover, our data suggest that homologous OCRs could potentially influence homologous gene expression. Hence, the duplication of OCRs might be essential for plant genome architecture as well as for regulating gene expression.

Glandular trichome (GT) is the dominant site for artemisinin production in Artemisia annua. Several critical genes involved in artemisinin biosynthesis are specifically expressed in GT. However, the molecular mechanism of differential gene expression between GT and other tissue types remains elusive. Chromatin accessibility, defined as the degree to which nuclear molecules are able to interact with chromatin DNA, reflects gene expression capacity to a certain extent. Here, we investigated and compared the landscape of chromatin accessibility in Artemisia annua leaf and GT using the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technique. We identified 5413 GT high accessible and 4045 GT low accessible regions, and these GT high accessible regions may contribute to GT-specific biological functions. Several GT-specific artemisinin biosynthetic genes, such as DBR2 and CYP71AV1, showed higher accessible regions in GT compared to that in leaf, implying that they might be regulated by chromatin accessibility. In addition, transcription factor binding motifs for MYB, bZIP, C2H2, and AP2 were overrepresented in the highly accessible chromatin regions associated with artemisinin biosynthetic genes in glandular trichomes. Finally, we proposed a working model illustrating the chromatin accessibility dynamics in regulating artemisinin biosynthetic gene expression. This work provided new insights into epigenetic regulation of gene expression in GT.

Long noncoding RNA (lncRNA)/microRNA(miRNA)/mRNA triplets contribute to cancer biology. However, identifying significative triplets remains a major challenge for cancer research. The dynamic changes among factors of the triplets have been less understood. Here, by integrating target information and expression datasets, we proposed a novel computational framework to identify the triplets termed as “lncRNA-perturbated triplets”. We applied the framework to five cancer datasets in The Cancer Genome Atlas (TCGA) project and identified 109 triplets. We showed that the paired miRNAs and mRNAs were widely perturbated by lncRNAs in different cancer types. LncRNA perturbators and lncRNA-perturbated mRNAs showed significantly higher evolutionary conservation than other lncRNAs and mRNAs. Importantly, the lncRNA-perturbated triplets exhibited high cancer specificity. The pan-cancer perturbator OIP5-AS1 had higher expression level than that of the cancer-specific perturbators. These lncRNA perturbators were significantly enriched in known cancer-related pathways. Furthermore, among the 25 lncRNA in the 109 triplets, lncRNA SNHG7 was identified as a stable potential biomarker in lung adenocarcinoma (LUAD) by combining the TCGA dataset and two independent GEO datasets. Results from cell transfection also indicated that overexpression of lncRNA SNHG7 and TUG1 enhanced the expression of the corresponding mRNA PNMA2 and CDC7 in LUAD. Our study provides a systematic dissection of lncRNA-perturbated triplets and facilitates our understanding of the molecular roles of lncRNAs in cancers.