Roles of long noncoding RNAs in chromosome domains

The role of long non-coding RNAs in cardiovascular diseases: A comprehensive review

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide, posing significant challenges to healthcare systems. Despite advances in medical interventions, the molecular mechanisms underlying CVDs are not yet fully understood. For decades, protein-coding genes have been the focus of CVD research. However, recent advances in genomics have highlighted the importance of long non-coding RNAs (lncRNAs) in cardiovascular health and disease. Changes in lncRNA expression specific to tissues may result from various internal or external factors, leading to tissue damage, organ dysfunction, and disease. In this review, we provide a comprehensive discussion of the regulatory mechanisms underlying lncRNAs and their roles in the pathogenesis and progression of CVDs, such as coronary heart disease, atherosclerosis, heart failure, arrhythmias, cardiomyopathies, and diabetic cardiomyopathy, to explore their potential as therapeutic targets and diagnostic biomarkers.

Knockdown of LncRNA MEG3 promotes damage of vascular endothelial cells induced by vibration

Hand-arm vibration syndrome (HAVS) is caused by long-term exposure to hand-transmitted vibration (HTV), and its pathogenesis has not been elucidated fully. We explored the molecular mechanism of HAVS and provided clues and a theoretical basis for the early prevention and treatment of HAVS. After vibration, samples were collected from the plasma of human workers, plasma of rat tails, and human umbilical vein endothelial cells (HUVECs). ELISAs were used to measure the expression of vasoactive factors. Cell Counting Kit-8 and electron microscopy were used to detect cell damage. Flow cytometry was employed to detect apoptosis. Real-time reverse transcription-polymerase chain reaction was used to measure the expression of long non-coding RNAs (lncRNAs). Western blotting was used to measure the expression of apoptosis-related proteins. Vibration could cause cell damage, apoptosis, and changes in the expression vasoactive factors and lncRNAs. The lncRNA maternally expressed gene 3 (MEG3) had a significant regulatory effect on cell damage, apoptotic proteins, and vascular regulatory factors in the HUVEC damage induced by vibration, as shown by the further decrease in viability and aggravation of injury after knockdown of MEG3 expression in HUVECs treated with vibration. Expression of vasoactive factors and apoptosis-related proteins was changed after interfering with MEG3 expression. In conclusion, vibration can affect the expression of vasoactive factors and lncRNA, and cause damage to vascular endothelial cells. MEG3 may be involved in the inflammatory damage to vascular endothelial cells induced by vibration.

SpecLoop predicts cell type-specific chromatin loop via transcription factor cooperation

Cell-type-Specific Chromatin Loops (CSCLs) are crucial for gene regulation and cell fate determination. However, the mechanisms governing their establishment remain elusive. Here, we present SpecLoop, a network regularization-based machine learning framework, to investigate the role of transcription factors (TFs) cooperation in CSCL formation. SpecLoop integrates multi-omics data, including gene expression, chromatin accessibility, sequence, protein-protein interaction, and TF binding motif data, to predict CSCLs and identify TF cooperations. Using high resolution Hi-C data as the gold standard, SpecLoop accurately predicts CSCL in GM12878, IMR90, HeLa-S3, K562, HUVEC, HMEC, and NHEK seven cell types, with the AUROC values ranging from 0.8645 to 0.9852 and AUPR values ranging from 0.8654 to 0.9734. Notably SpecLoop demonstrates improved accuracy in predicting long-distance CSCLs and identifies TF complexes with strong predictive ability. Our study systematically explores the TFs and TF pairs associated with CSCL through effective integration of diverse omics data. SpecLoop is freely available at https://github.com/AMSSwanglab/SpecLoop.

The ELEANOR non-coding RNA expression contributes to cancer dormancy and predicts late recurrence of ER-positive breast cancer

The recurrence risk of estrogen receptor (ER)-positive breast cancer remains high for a long period of time, unlike the other types of cancer. The late recurrence reflects the ability of cancer cells to remain dormant through various events, including cancer stemness acquisition, but the detailed mechanism is unknown. ESR1 locus enhancing and activating non-coding RNAs (ELEANORS) are a cluster of nuclear non-coding RNAs originally identified in a recurrent breast cancer cell model. Although their functions as chromatin regulators in vitro are well characterized, their roles in vivo remain elusive. In this study, we evaluated the clinicopathological features of ELEANORS, using primary and corresponding metastatic breast cancer tissues. The ELEANOR expression was restricted to ER-positive cases and well-correlated with the ER and progesterone receptor expression levels, especially at the metastatic sites. ELEANORS were detected in both primary and metastatic tumors (32% and 29%, respectively), and frequently in postmenopausal cases. Interestingly, after surgery, patients with ELEANOR-positive primary tumors exhibited increased relapse rates after, but not within, 5 years. Multivariate analysis showed that ELEANORS are independent recurrence risk factor. Consistently, analyses with cell lines, mouse xenografts and patient tissues revealed that ELEANORS upregulate a breast cancer stemness gene, CD44, and maintain the cancer stem cell population, which may facilitate tumor dormancy. Our findings highlight a new role of nuclear long non-coding RNAs and their clinical potential as predictive biomarkers and therapeutic targets for late recurrence of ER-positive breast cancer.

Linking RNA Processing and Function

RNA processing is critical for eukaryotic mRNA maturation and function. It appears there is no exception for other types of RNAs. Long noncoding RNAs (lncRNAs) represent a subclass of noncoding RNAs, have sizes of >200 nucleotides (nt), and participate in various aspects of gene regulation. Although many lncRNAs are capped, polyadenylated, and spliced just like mRNAs, others are derived from primary transcripts of RNA polymerase II and stabilized by forming circular structures or by ending with small nucleolar RNA-protein complexes. Here we summarize the recent progress in linking the processing and function of these unconventionally processed lncRNAs; we also discuss how directional RNA movement is achieved using the radial flux movement of nascent precursor ribosomal RNA (pre-rRNA) in the human nucleolus as an example.

The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis

MCF7 cells acquire estrogen-independent proliferation after long-term estrogen deprivation (LTED), which recapitulates endocrine therapy resistance. LTED cells can become primed for apoptosis, but the underlying mechanism is largely unknown. We previously reported that Eleanor non-coding RNAs (ncRNAs) upregulate the ESR1 gene in LTED cells. Here, we show that Eleanors delineate the topologically associating domain (TAD) of the ESR1 locus in the active nuclear compartment of LTED cells. The TAD interacts with another transcriptionally active TAD, which is 42.9 Mb away from ESR1 and contains a gene encoding the apoptotic transcription factor FOXO3. Inhibition of a promoter-associated Eleanor suppresses all genes inside the Eleanor TAD and the long-range interaction between the two TADs, but keeps FOXO3 active to facilitate apoptosis in LTED cells. These data indicate a role of ncRNAs in chromatin domain regulation, which may underlie the apoptosis-prone nature of therapy-resistant breast cancer cells and could be good therapeutic targets.

Long term estrogen deprivation can result in apoptosis in breast cancer cells. Here, the authors show that this apoptosis is induced by the long-range chromatin interaction of loci containing the ESR1 and FOXO3 genes, resulting in FOXO3-mediated apoptosis.

Non-coding RNAs and chromatin domains

Large-scale transcriptome analyses have identified a variety of non-coding RNAs (ncRNAs) that are not translated into proteins. Many of them are in the nucleus, where they associate with chromatin and regulate its structure and function. Interphase chromosomes are intricately folded into multiple layers and composed of domains. Recent studies using Hi-C technologies have identified a mega-base self-associating chromatin domain: the topologically associating domain (TAD). The domain boundaries are demarcated with the chromatin regulatory proteins CTCF and cohesin, which are often bound to or recruited by ncRNAs. Some ncRNAs form RNA clouds in the nucleus and coordinate the transcription of multiple genes in a chromatin domain. In this review, we describe the emerging link between long ncRNAs and chromatin domains in the nucleus.

New Insights into the Interplay between Non-Coding RNAs and RNA-Binding Protein HnRNPK in Regulating Cellular Functions

The emerging data indicates that non-coding RNAs (ncRNAs) epresent more than the “junk sequences” of the genome. Both miRNAs and long non-coding RNAs (lncRNAs) are involved in fundamental biological processes, and their deregulation may lead to oncogenesis and other diseases. As an important RNA-binding protein (RBP), heterogeneous nuclear ribonucleoprotein K (hnRNPK) is known to regulate gene expression through the RNA-binding domain involved in various pathways, such as transcription, splicing, and translation. HnRNPK is a highly conserved gene that is abundantly expressed in mammalian cells. The interaction of hnRNPK and ncRNAs defines the novel way through which ncRNAs affect the expression of protein-coding genes and form autoregulatory feedback loops. This review summarizes the interactions of hnRNPK and ncRNAs in regulating gene expression at transcriptional and post-transcriptional levels or by changing the genomic structure, highlighting their involvement in carcinogenesis, glucose metabolism, stem cell differentiation, virus infection and other cellular functions. Drawing connections between such discoveries might provide novel targets to control the biological outputs of cells in response to different stimuli.

Endocrine therapy-resistant breast cancer model cells are inhibited by soybean glyceollin I through Eleanor non-coding RNA

Long-term estrogen deprivation (LTED) of an estrogen receptor (ER) α-positive breast cancer cell line recapitulates cancer cells that have acquired estrogen-independent cell proliferation and endocrine therapy resistance. Previously, we have shown that a cluster of non-coding RNAs, Eleanors (ESR1 locus enhancing and activating non-coding RNAs) formed RNA cloud and upregulated the ESR1 gene in the nuclei of LTED cells. Eleanors were inhibited by resveratrol through ER. Here we prepared another polyphenol, glyceollin I from stressed soybeans, and identified it as a major inhibitor of the Eleanor RNA cloud and ESR1 mRNA transcription. The inhibition was independent of ER, unlike one by resveratrol. This was consistent with a distinct tertiary structure of glyceollin I for ER binding. Glyceollin I preferentially inhibited the growth of LTED cells and induced apoptosis. Our results suggest that glyceollin I has a novel role in LTED cell inhibition through Eleanors. In other words, LTED cells or endocrine therapy-resistant breast cancer cells may be ready for apoptosis, which can be triggered with polyphenols both in ER-dependent and ER-independent manners.

The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions

Long non-coding RNAs (lncRNAs) are emerging as critical regulators of various biological processes and human diseases. The mechanisms of action involve their interactions with proteins, RNA and genomic DNA. Most lncRNAs display strong nuclear localization. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a large family of RNA-binding proteins that are important for multiple aspects of nucleic acid metabolism. hnRNPs are also predominantly expressed in the nucleus. This review discusses the interactions of lncRNAs and hnRNPs in regulating gene expression at transcriptional and post-transcriptional levels or by changing genomic structure, highlighting their involvements in glucose and lipid metabolism, immune response, DNA damage response, and other cellular functions. Toward the end, several techniques that are used to identify lncRNA binding partners are summarized. There are still many questions that need to be answered in this relatively new research area, which might provide novel targets to control the biological outputs of cells in response to different stimuli.

SPRY4-IT1: A novel oncogenic long non-coding RNA in human cancers

Long non-coding RNAs are classified as a kind of RNA, which are longer than 200 nucleotides in length and cannot be translated into proteins. Multiple studies have demonstrated that long non-coding RNAs are involved in various cellular processes, including proliferation, differentiation, cell death, and metastasis. Among numerous long non-coding RNAs, we focus on Sprouty4-Intron 1 (SPRY4-IT1), a well-known long non-coding RNA that is overexpressed in various kinds of tumor tissues and cell lines. Accumulating evidences show that SPRY4-IT1 was dysregulated in various cancers, including melanoma, breast cancer, esophageal squamous cell carcinoma, non-small cell lung cancer, gastric cancer, colon cancer, and hepatocellular carcinoma, and amplification of SPRY4-IT1 was associated with different clinicopathological features of cancer patients. Importantly, SPRY4-IT1 exerts important roles in tumor progression and metastasis. However, detailed molecular mechanisms of SPRY4-IT1 in cancer progression and metastasis were poorly understood. In this review, we have focused on the characteristics of SPRY4-IT1 and illustrated the biological function and mechanism of SPRY4-IT1 in cancer development.

Long Noncoding RNA MEG3 Negatively Regulates Proliferation and Angiogenesis in Vascular Endothelial Cells

Long noncoding RNA (lncRNA) MEG3 is an important tumor suppressor in several types of human cancers. However, the biological function and underlying mechanism of MEG3 in vascular endothelial cells (VECs) remain unknown. In the present study, we demonstrated the functional importance of lncRNA MEG3 in proliferation and angiogenesis of VECs. MEG3 overexpression significantly suppressed the proliferation and in vitro angiogenesis in VECs, whereas knockdown of MEG3 had the opposite effect. Furthermore, we found that MEG3 exerts its function through negatively regulating miR-9 by acting as a microRNA sponge. Taken together, MEG3-miR-9 plays an important role in proliferation and angiogenesis in VECs.

RNAcentral: a comprehensive database of non-coding RNA sequences

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.