SE-lncRNAs in Cancer: Classification, Subcellular Localisation, Function and Corresponding TFs

Overview

Journal J Cell Mol Med

Specialties Cell Biology
Molecular Biology

Date 2024 Dec 17

PMID 39690143

Authors

Yuxin Bao

Songling Teng

Hanjie Zhai

Yuanzhuang Zhang

Yeqiu Xu

Chenghao Li

Zhenjun Chen

Fu Ren

Yong Wang

Affiliations

Soon will be listed here.

Abstract

Emerging evidence highlights certain long noncoding RNAs (lncRNAs) transcribed from or interacting with super-enhancer (SE) regulatory elements. These lncRNAs, known as SE-lncRNAs, are strongly linked to cancer and regulate cancer progression through multiple interactions with downstream targets. The expression of SE-lncRNAs is controlled by various transcription factors (TFs), and dysregulation of these TFs can contribute to cancer development. In this review, we discuss the characteristics, classification and subcellular distribution of SE-lncRNAs and summarise the role of key TFs in the transcription and regulation of SE-lncRNAs. Moreover, we examine the distinct functions and potential mechanisms of SE-lncRNAs in cancer progression.

References

Statello L, Guo C, Chen L, Huarte M . Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol. 2020; 22(2):96-118. PMC: 7754182. DOI: 10.1038/s41580-020-00315-9. View

Baluapuri A, Wolf E, Eilers M . Target gene-independent functions of MYC oncoproteins. Nat Rev Mol Cell Biol. 2020; 21(5):255-267. PMC: 7611238. DOI: 10.1038/s41580-020-0215-2. View

Zhou H, Schmidt S, Jiang S, Willox B, Bernhardt K, Liang J . Epstein-Barr virus oncoprotein super-enhancers control B cell growth. Cell Host Microbe. 2015; 17(2):205-16. PMC: 4539236. DOI: 10.1016/j.chom.2014.12.013. View

Zhang T, Song X, Zhang Z, Mao Q, Xia W, Xu L . Aberrant super-enhancer landscape reveals core transcriptional regulatory circuitry in lung adenocarcinoma. Oncogenesis. 2020; 9(10):92. PMC: 7568720. DOI: 10.1038/s41389-020-00277-9. View

Mattick J, Amaral P, Carninci P, Carpenter S, Chang H, Chen L . Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023; 24(6):430-447. PMC: 10213152. DOI: 10.1038/s41580-022-00566-8. View

Polytarchou C, Iliopoulos D, Struhl K . An integrated transcriptional regulatory circuit that reinforces the breast cancer stem cell state. Proc Natl Acad Sci U S A. 2012; 109(36):14470-5. PMC: 3437881. DOI: 10.1073/pnas.1212811109. View

Chen H, Liu H, Qing G . Targeting oncogenic Myc as a strategy for cancer treatment. Signal Transduct Target Ther. 2018; 3:5. PMC: 5837124. DOI: 10.1038/s41392-018-0008-7. View

Zhou Z, Du Z, Wei J, Zhuo L, Pan S, Fu X . MHAM-NPI: Predicting ncRNA-protein interactions based on multi-head attention mechanism. Comput Biol Med. 2023; 163:107143. DOI: 10.1016/j.compbiomed.2023.107143. View

Yan L, Chen H, Tang L, Jiang P, Yan F . Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer. BMC Cancer. 2021; 21(1):187. PMC: 7903608. DOI: 10.1186/s12885-021-07900-x. View

10.

Conn V, Gabryelska M, Toubia J, Kirk K, Gantley L, Powell J . Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia. Cancer Cell. 2023; 41(7):1309-1326.e10. DOI: 10.1016/j.ccell.2023.05.002. View

11.

Keyes W, Pecoraro M, Aranda V, Vernersson-Lindahl E, Li W, Vogel H . ΔNp63α is an oncogene that targets chromatin remodeler Lsh to drive skin stem cell proliferation and tumorigenesis. Cell Stem Cell. 2011; 8(2):164-76. PMC: 4373450. DOI: 10.1016/j.stem.2010.12.009. View

12.

Wang E, Lu S, Pastore A, Chen X, Imig J, Chun-Wei Lee S . Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell. 2019; 35(3):369-384.e7. PMC: 6424627. DOI: 10.1016/j.ccell.2019.01.010. View

13.

Jia Q, Tan Y, Li Y, Wu Y, Wang J, Tang F . JUN-induced super-enhancer RNA forms R-loop to promote nasopharyngeal carcinoma metastasis. Cell Death Dis. 2023; 14(7):459. PMC: 10361959. DOI: 10.1038/s41419-023-05985-9. View

14.

Debek S, Juszczynski P . Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim Biophys Acta Rev Cancer. 2022; 1877(2):188697. DOI: 10.1016/j.bbcan.2022.188697. View

15.

Katoh M . Frequent up-regulation of WNT2 in primary gastric cancer and colorectal cancer. Int J Oncol. 2001; 19(5):1003-7. DOI: 10.3892/ijo.19.5.1003. View

16.

Henriques T, Scruggs B, Inouye M, Muse G, Williams L, Burkholder A . Widespread transcriptional pausing and elongation control at enhancers. Genes Dev. 2018; 32(1):26-41. PMC: 5828392. DOI: 10.1101/gad.309351.117. View

17.

Tay Y, Rinn J, Pandolfi P . The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014; 505(7483):344-52. PMC: 4113481. DOI: 10.1038/nature12986. View

18.

Su T, Zhang N, Wang T, Zeng J, Li W, Han L . Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis. Cancer Res. 2023; 83(24):4080-4094. DOI: 10.1158/0008-5472.CAN-23-0544. View

19.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M . An atlas of active enhancers across human cell types and tissues. Nature. 2014; 507(7493):455-461. PMC: 5215096. DOI: 10.1038/nature12787. View

20.

Wei H, Wang F, Wang Y, Li T, Xiu P, Zhong J . Verteporfin suppresses cell survival, angiogenesis and vasculogenic mimicry of pancreatic ductal adenocarcinoma via disrupting the YAP-TEAD complex. Cancer Sci. 2016; 108(3):478-487. PMC: 5378285. DOI: 10.1111/cas.13138. View