SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers

Guo, Zhi-Wei; Xie, Chen; Li, Kun; Zhai, Xiang-Ming; Cai, Geng-Xi; Yang, Xu; Wu, Yanni

doi:10.1093/database/baz027

Cited by 21 publications

(19 citation statements)

References 22 publications

(30 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, seRNAs can be divided into cis-acting and trans-acting seRNA according to distinct function approaches ( Fig. 2a, b) [18]. Cis-acting seRNA recruits protein complexes from its synthetic site to activate adjacent genes, where the whole length or TSS of cis-acting seRNA is covered by SE [10].…”

Section: Serna's Characteristics and Its Functionsmentioning

confidence: 99%

“…DNA translocations, small insertions and deletions (indels), focal amplification, singlenucleotide polymorphisms (SNPs), TFs implication and viral infections mediate aberrant SE generation, and the SE further transcribes into seRNA [15][16][17]. The recent studies have discovered two types of seRNA, cis-acting and transacting seRNA [18]. Meanwhile, according to different transcriptional directions, seRNA is defined as 1d-and 2d-seRNA [19].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Oncogenic seRNA functional activation: a novel mechanism of tumorigenesis

Tan

Tang

2020

Mol Cancer

View full text Add to dashboard Cite

seRNA is a noncoding RNA (ncRNA) transcribed from active super-enhancer (SE), through which SE exerts biological functions and participates in various physiological and pathological processes. seRNA recruits cofactor, RNA polymerase II and mediator to constitute and stabilize chromatin loop SE and promoter region, which regulates target genes transcription. In tumorigenesis, DNA insertion, deletion, translocation, focal amplification and carcinogen factor mediate oncogenic SE generation, meanwhile, oncogenic SE transcribes into tumor-related seRNA, termed as oncogenic seRNA. Oncogenic seRNA participates in tumorigenesis through activating various signal-pathways. The recent reports showed that oncogenic seRNA implicates in a widespread range of cytopathological processes in cancer progression including cell proliferation, apoptosis, autophagy, epithelial-mesenchymal transition, extracellular matrix stiffness and angiogenesis. In this article, we comprehensively summarized seRNA's characteristics and functions, and emphatically introduced inducible formation of oncogenic seRNA and its functional mechanisms. Lastly, some research strategies on oncogenic seRNA were introduced, and the perspectives on cancer therapy that targets oncogenic seRNA were also discussed.

show abstract

Section: Serna's Characteristics and Its Functionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Oncogenic seRNA functional activation: a novel mechanism of tumorigenesis

Tan

Tang

2020

Mol Cancer

View full text Add to dashboard Cite

show abstract

“…Driver genes are collected on March 23 rd 2018. The cis-acting differentially expressed super-enhancer associated lncRNAs for different cancers are retrieved from the SELER database [20] (June 23 th 2019).…”

Section: Data Sources and Data Processingmentioning

confidence: 99%

“…Super-enhancers are groups of putative enhancers that are spatially proximal to the mediator binding sites [48]. They regulate gene expression by increasing the gene transcription [20]. Disease-related variations occur in the super-enhancer regions.…”

Section: Inferring Functional Mechanisms For the Super-enhancer Assocmentioning

confidence: 99%

Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors

Olgun

Taştan

2020

Preprint

View full text Add to dashboard Cite

The dysregulation of long non-coding RNAs' (lncRNAs) expressions has been implicated in cancer. Since most of the lncRNAs' are not functionally characterized well, investigating the set of perturbed lncRNAs are is challenging. Existing methods that inspect lncRNAs functionally rely on the co-expressed coding genes, which are far better characterized functionally. LncRNAs can be known to act as transcriptional regulators; they may activate or repress the neighborhood's coding genes on the genome. Based on this, in this work, we aim to analyze the deregulated lncRNAs in cancer by taking into account their ability to regulate nearby loci on the genome. We perform functional analysis on differentially expressed lncRNAs for 28 different cancers considering their adjacent coding genes. We identify that some deregulated lncRNAs are cancer-specific, but a substantial number of lncRNAs are shared across cancers. Next, we assess the similarities of the cancer types based on the functional enrichment of the deregulated lncRNA sets. We find some cancers are very similar in the functions and biological processes related to the deregulated lncRNAs. We observe that some of the cancers for which we find similarity can be linked through primary, metastatic site relations. We investigate the similarity of enriched functional terms for the deregulated lncRNAs and the mRNAs. We further assess the enriched functions' similarity to the functions and processes that the known cancer driver genes take place. We believe that our methodology help to understand the impact of the lncRNAs in cancer functionally.

show abstract

“…Recent studies have revealed that SE-lncRNAs are usually emerging as master RNA regulators in diverse gene expression programs and activate the gene expression by mechanisms of transcription factor trapping, chromatin looping, chromatin modi cation, PolII loading, and release of transcriptional repressor [7][8][9][10][11]. SE-lncRNAs are intimately involved in regulating tumorigenesis [11,12]. A good example is that CCAT1-L positively regulates MYC expression by mediating chromatin looping between the MYC promoter and its enhancers to promote CRC progression [11].…”

mentioning

confidence: 99%

Super-enhancer Associated Long Non-coding RNA AC005592.2 Promotes Tumor Progression by Regulating OLFM4 in Colorectal Cancer

Liu

Chen

Tang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Super-enhancer-associated long non-coding RNAs (SE-lncRNAs) have been reported to play essential roles in tumorigenesis, but the fundamental mechanism of SE-lncRNAs in colorectal cancer (CRC) remains largely unknown. Methods: A microarray was performed to identify the differentially expressed SE-lncRNAs between CRC tissues and peritumoral tissues. A novel SE-lncRNA AC005592.2 was selected from these differentially expressed SE-lncRNAs to explore its effects in the CRC development. Fluorescence quantitative real-time PCR (qRT-PCR) was used to assay the expression of AC005592.2 in CRC tissues and cell lines. Functional assays were applied to identify the biological effects of AC005592.2 in CRC cells. Furthermore, RNA-seq was employed to predict potential targets of AC005592.2. Results: AC005592.2 was significantly increased in CRC tissues and cells. And the high expression of AC005592.2 was significantly associated with TNM stage and tumor differentiation of CRC patients. Knockdown of AC005592.2 suppressed CRC cell proliferation, invasion and migration, but promoted apoptosis, while AC005592.2 overexpression exerted precisely the opposite effects on CRC cells. Besides, AC005592.2 positively regulated the expression of olfactomedin 4 (OLFM4), which was also up-regulation in CRC tissues. Conclusion: The findings suggested that AC005592.2 is a crucial promoter of CRC progression, and may serve as an attractive therapeutic target for CRC.

show abstract

SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers

Cited by 21 publications

References 22 publications

Oncogenic seRNA functional activation: a novel mechanism of tumorigenesis

Oncogenic seRNA functional activation: a novel mechanism of tumorigenesis

Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors

Super-enhancer Associated Long Non-coding RNA AC005592.2 Promotes Tumor Progression by Regulating OLFM4 in Colorectal Cancer

Contact Info

Product

Resources

About