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Enhancers are cis-acting elements that have the ability to increase the expression of target genes. Recent studies have shown that enhancers can act as transcriptional units for the production of enhancer RNAs (eRNAs), which are hallmarks of activity enhancers and are involved in the regulation of gene transcription. The in-depth study of eRNAs is of great significance for us to better understand enhancer function and transcriptional regulation in various diseases. Therefore, eRNAs may be a potential therapeutic target for diseases. Here, we review the current knowledge of the characteristics of eRNAs, the molecular mechanisms of eRNAs action, as well as diseases related to dysregulation of eRNAs.

Cancer is still one of the greatest medical challenges in the world. The p53 protein plays an important role in the process of cancer formation. In addition, p53 is found as the most common mutant gene in cancers. Because of the central role of p53 in oncology, it is necessary to construct effective sensors to detect this protein. However, there are few methods to detect wild type p53 protein (WTP53) or to distinguish the wild type and mutant p53 proteins. In our study, we designed and constructed a p53 genetic sensor that detected the expression of WTP53 in cells. Moreover, we combined the p53 sensor with diphtheria toxin using the CRISPR-Cas9 system to construct a p53 genetic sensor that specifically killed p53-deficient cells such as tumor cells. Our study therefore developed a new way to treat cancers by using an available genetic sensor based on p53 protein.

Enhancers are transcriptional regulatory elements that increase target gene expression. It has reported that enhancers could universally transcribe into enhancer RNAs (eRNAs) with stimulation. Increasing evidence showed eRNAs participated in various disease processes including malignant tumors. P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer. However, the relationship between P2RY2e and bladder cancer (BCa) is unclear. In the study, we discovered that P2RY2e was upregulated in BCa tissues and estrogen-treated cells. Estrogen promoted the malignant abilities of BCa cells. P2RY2e knockdown by CRISPR-Cas13a inhibit the cell multiplication, invasion and migration. Additionally, the cell apoptosis was facilitated. What's more, downregulation of P2RY2e could weaken the cancer-promoting effects of estrogen on BCa. Our study revealed that P2RY2e played a carcinogenic role in BCa and estrogen might promote the initiation of BCa by inducing P2RY2e. We provide a potential therapeutic target for BCa and a new perspective for the tumorigenesis of bladder cancer.

The growth arrest-specific transcript 5 (GAS5) is a long noncoding RNA with low expression in multiple cancers. This meta-analysis aims to explore the association between GAS5 expression levels and cancer patients' prognosis. We collected all the relevant literatures about GAS5 expression levels associated with overall survival (OS), lymph node metastasis (LNM) and high tumor stage (II/III/IV) (HTS) from the PubMed and Web of Science. The hazard ratio (HR) and the corresponding 95% confidence interval (CI) were calculated to evaluate the link strength between GAS5 and cancer prognosis. A total of 934 patients from 14 studies were included to the present meta-analysis, according to the inclusion and exclusion criteria. The results demonstrated that low expression of GAS5 could predict poor OS in cancer patients (HR = 1.955, 95% CI: 1.551–2.465, P < 0.001). Meanwhile we also analyzed the following cancers independently: hepatocellular carcinoma (HR = 1.893, 95% CI: 1.103–3.249, P = 0.021) and urothelial carcinoma (HR = 1.653, 95% CI: 1.185–2.306, P = 0.003). Compared to the high GAS5 expression group, additionally, patients with low GAS5 expression in tumor tissues were more prone to lymph node metastasis (OR = 0.234, 95%CI: 0.153–0.358, P < 0.001) and high tumor stage (OR = 0.185, 95% CI:0.102–0.333, P < 0.001). In conclusion, this meta-analysis showed that GAS5 might be served as a novel biomarker for predicting prognosis in various types of cancers.

Background Genes are comprised of DNA codes and contain promoters and other control elements for reading these codes. The rapid development of clustered regularly interspaced short palindromic repeats (CRISPR) technology has made possible the construction of a novel code-reading system with low dependency on the native control elements. Results We develop CRISPReader, a technology for controlling promoterless gene expression in a robust fashion. We demonstrate that this tool is highly efficient in controlling transcription and translation initiation of a targeted transgene. A notable feature of CRISPReader is the ability to “read” the open reading frames of a cluster of gene without traditional regulatory elements or other cofactors. In particular, we use this strategy to construct an all-in-one AAV-CRISPR-Cas9 system by removing promoter-like elements from the expression cassette to resolve the existing AAV packaging size problem. The compact AAV-CRISPR-Cas9 is also more efficient in transactivation, DNA cleavage, and gene editing than the dual-AAV vector encoding two separate Cas9 elements, shown by targeting both reporter and endogenous genes in vitro and in vivo. Conclusions CRISPReader represents a novel approach for gene regulation that enables minimal gene constructs to be expressed and can be used in potential biomedical applications. Electronic supplementary material The online version of this article (10.1186/s13059-019-1712-5) contains supplementary material, which is available to authorized users.

As a novel and robust gene-editing tool, the Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated protein 9 (CRISPR-Cas9) system has revolutionized gene therapy. Plasmid vector delivery is the most commonly used method for integrating the CRISPR-Cas9 system into cells. However, such foreign cytosolic DNAs trigger an innate immune response (IIR) within cells, which can hinder gene editing by inhibiting transgene expression. Although some small molecules have been shown to avoid the action of IIR on plasmids, they only work on a single target and may also affect cell viability. A genetic approach that works at a comprehensive level for manipulating IIR is still lacking. Here, we designed and constructed several artificial nucleic acid molecules (ANAMs), which are combinations of aptamers binding to two key players of IIR (β-catenin and NF-κB). ANAMs strongly inhibited the IIR in cells, thus improving transgene expression. We also used ANAMs to improve the gene-editing efficiency of the CRISPR-Cas9 system and its derivatives, thus enhancing the apoptosis of cancer cells induced by CRISPR-Cas9. ANAMs can be valuable tools for improving transgene expression and gene editing in mammalian cells. K E Y W O R D S CRISPR-Cas9, innate immune response, mammalian cells, transgene expression 1 INTRODUCTION The Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated protein 9 (CRISPR-Cas9) system is a novel and robust gene-editing tool, which has This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.