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Functional roles of eRNA transcripts and enhancer transcription. Enhancer RNAs could functionally contribute to gene activation at least partially by modulating the stability of enhancer: promoter (E:P) looping via interacting with looping factors, including cohesin 3 and Mediator, 8 or could regulate the chromatin accessibility of its target promoter region. 7 For some enhancer cohorts, eRNA transcription elongation (purple arrows) could have independent roles in deposition of histone methylation .
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... Enhancers generate eRNAs by recruiting RNA polymerase II (Pol II) and binding to multiple TFs and cofactors, including the histone acetyltransferase p300 and cAMP response element-binding protein (CBP) (Rada-Iglesias et al. 2011;Wang et al. 2011). Most eRNAs are produced in a bidirectional manner without polyadenylation (Li et al. 2014a;Natoli and Andrau 2012), while a small portion of eRNAs are polyadenylated, generated through unidirectional transcription on enhancers (Li et al. 2014a). In this way, eRNAs can be roughly divided into two groups: the first group are bidirectional eRNAs (2D eRNAs), short (0.5-2 kb), and not polyadenylated; the other group are unidirectional eRNAs (1D eRNAs), comparatively long (> 3-4 kb), and polyadenylated (Natoli and Andrau 2012). ...
... Enhancers generate eRNAs by recruiting RNA polymerase II (Pol II) and binding to multiple TFs and cofactors, including the histone acetyltransferase p300 and cAMP response element-binding protein (CBP) (Rada-Iglesias et al. 2011;Wang et al. 2011). Most eRNAs are produced in a bidirectional manner without polyadenylation (Li et al. 2014a;Natoli and Andrau 2012), while a small portion of eRNAs are polyadenylated, generated through unidirectional transcription on enhancers (Li et al. 2014a). In this way, eRNAs can be roughly divided into two groups: the first group are bidirectional eRNAs (2D eRNAs), short (0.5-2 kb), and not polyadenylated; the other group are unidirectional eRNAs (1D eRNAs), comparatively long (> 3-4 kb), and polyadenylated (Natoli and Andrau 2012). ...
Purpose
Enhancer RNAs (eRNAs) are non-coding RNAs, which are characterized as transcripts without protein coding functions. Increasing evidence indicates that eRNAs play important roles in gene regulation and cancer progression. Furthermore, various roles of eRNAs in sex hormone-induced signaling pathways are emerging, indicating the important roles of eRNAs in the development of sex hormone-dependent cancers. The aim of this study is to summarize the current knowledge about eRNAs in several typical sex hormone-dependent cancers, mainly involving their roles in sex hormones mediated pathways and cancer progression.
Methods
We reviewed all the published articles concerning eRNAs in sex hormone-dependent cancers, and summarized the roles of eRNAs in these cancers.
Results
In cancer development, elevated expression of some eRNAs could promote the progression of cancer cells. In gene regulation, eRNAs not only regulate gene activation but also participate in gene repression. Additionally, in androgen receptor signaling, eRNAs were found to play a role at cis and trans loci, and both sense and antisense strands of eRNAs are both important.
Conclusion
Abnormal overexpression of eRNAs is mostly oncogenic, leading to cancer progression, and both strands of eRNAs play multiple and complex roles at cis and trans loci in sex hormones mediated pathways, which are tightly associated with sex hormone-dependent tumorigenesis.
... Several roles have been proposed for eRNAs. These include promoting the formation of chromatin loops between the enhancers and their target promoters (Hsieh et al. 2014;Li, Lam, and Notani 2014), or acting to increase transcription at promoters after such loops have been formed, for example by remodeling chromatin or promoting Pol II elongation (Mousavi et al. 2013;Schaukowitch et al. 2014). It has also been suggested that the act of eRNA transcription at enhancers, rather than the mature RNA product, might be important for enhancer function (Natoli and Andrau 2012). ...
Active enhancers in mammals produce enhancer RNAs (eRNAs), that are bidirectionally transcribed, unspliced, and unstable noncoding RNAs. Enhancer regions are also enriched with long noncoding RNA (lncRNA) genes, which are typically spliced and are longer and substantially more stable than eRNAs. In order to explore the relationship between these two classes of RNAs and the implications of lncRNA transcription on enhancer functionality, we analyzed DNAse hypersensitive sites with evidence of bidirectional transcription, which we termed eRNA producing centers (EPCs). A subset of EPCs, which are found very close to the transcription start site of lncRNA genes, exhibit attributes of both enhancers and promoters, including distinctive DNA motifs and a characteristic landscape of bound proteins. These EPCs are associated with a subset of relatively highly active enhancers. This stronger enhancer activity is driven, at least in part, by the presence of evolutionary conserved, directional splicing signals that promote lncRNA production, pointing at a causal role of lncRNA processing in enhancer activity. Together, our results suggest a model whereby the ability of some enhancers to produce lncRNAs, which is conserved in evolution, enhances their activity in a manner likely mediated through maturation of the associated lncRNA.
... These weak interactions would explain the ability of enhancers to activate non-cognate promoters when moved close to them (when J is high), as in enhancer trap assays (33). An ability to interact with nearby basal promoters probably also underlies the weak transcription and RNAP localization often found near enhancers (34). ...
Genes are frequently regulated by interactions between proteins that bind to the DNA near the gene and proteins that bind to DNA sites located far away, with the intervening DNA looped out. But it is not understood how efficient looping can occur when the sites are very far apart. We develop a simple theoretical framework that relates looping efficiency to the energetic cost and benefit of looping, allowing prediction of the efficiency of single or multiple nested loops at different distances. Measurements of absolute loop efficiencies for Lac repressor and λ CI using gene expression reporters in Escherichia coli cells show that, as predicted by the model, long-range DNA looping between a pair of sites can be strongly enhanced by the use of nested DNA loops or by the use of additional protein-binding sequences. A combination of these approaches was able to generate efficient DNA looping at a 200 kb distance.
... On average, however, eRNA transcription is a good predictor of enhancer activity [12]. For further discussion of the potential functions of eRNAs see Li et al [17]. ...
A new paradigm has emerged in recent years characterizing transcription initiation as a bidirectional process encompassing a larger proportion of the genome than previously thought. Past concepts of coding genes thinly scattered among a vast background of transcriptionally inert noncoding DNA have been abandoned. A richer picture has taken shape, integrating transcription of coding genes, enhancer RNAs (eRNAs), and various other noncoding transcriptional events. In this review we give an overview of recent studies detailing the mechanisms of RNA polymerase II (RNA Pol II)-based transcriptional initiation and discuss the ways in which transcriptional direction is established as well as its functional implications.
Background
Medullary thyroid carcinoma (MTC) is a rare but aggressive endocrine malignancy that originates from the parafollicular C cells of the thyroid gland. Enhancer RNAs (eRNAs) are non-coding RNAs transcribed from enhancer regions, which are critical regulators of tumorigenesis. However, the roles and regulatory mechanisms of eRNAs in MTC remain poorly understood. This study aims to identify key eRNAs regulating the malignant phenotype of MTC and to uncover transcription factors involved in the regulation of key eRNAs.
Methods
GSE32662 and GSE114068 were used for the identification of differentially expressed genes, eRNAs, enhancers and enhancer-regulated genes in MTC. Metascape and the transcription factor affinity prediction method were used for gene function enrichment and transcription factor prediction, respectively. qRT-PCR was used to detect gene transcription levels. ChIP-qPCR was used to assess the binding of histone H3 lysine 27 acetylation (H3K27ac)-enriched regions to anti- H3K27ac. RIP-qPCR was used to detect the binding between FOXQ1 and LINC00887. CCK8 and Transwell were performed to measure the proliferation and invasion of MTC cells, respectively. Intracellular reactive oxygen species (ROS) levels were quantified using a ROS assay kit.
Results
Four eRNAs (H1FX-AS1, LINC00887, MCM3AP-AS1 and A1BG-AS1) were screened, among which LINC00887 was the key eRNA promoting the proliferation and invasion of MTC cells. A total of 135 genes controlled by LINC00887-regulated enhancers were identified; among them, BCL2, PRDX1, SFTPD, TPO, GSS, RAD52, ZNF580, and ZFP36L1 were significantly enriched in the “ROS metabolic process” term. As a transcription factor regulating genes enriched in the “ROS metabolic process” term, FOXQ1 could recruit LINC00887. Overexpression of FOXQ1 restored LINC00887 knockdown-induced downregulation of GSS and ZFP36L1 transcription in MTC cells. Additionally, FOXQ1 overexpression counteracted the inhibitory effects of LINC00887 knockdown on the proliferation and invasion of MTC cells and the promotion of intracellular ROS accumulation induced by LINC00887 knockdown.
Conclusion
LINC00887 was identified as a key eRNA promoting the malignant phenotype of MTC cells. The involvement of FOXQ1 was essential for LINC00887 to play a pro-tumorigenic role in MTC. Our findings suggest that the FOXQ1/LINC00887 axis is a potential therapeutic target for MTC.
Acute kidney injury (AKI) is a condition characterized by a rapid decline in kidney function within a span of 48 hours. It is influenced by various factors including inflammation, oxidative stress, excessive calcium levels within cells, activation of the renin-angiotensin system, and dysfunction in microcirculation. Ischemia-reperfusion injury (IRI) is recognized as a major cause of AKI; however, the precise mechanisms behind this process are not yet fully understood and effective treatments are still needed. To enhance the accuracy of diagnosing AKI during its early stages, the utilization of innovative markers is crucial. Numerous studies suggest that certain noncoding RNAs (ncRNAs), such as long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), play a central role in regulating gene expression and protein synthesis. These ncRNAs are closely associated with the development and recovery of AKI and have been detected in both kidney tissue and bodily fluids. Furthermore, specific ncRNAs may serve as diagnostic markers and potential targets for therapeutic interventions in AKI. This review aims to summarize the functional roles and changes observed in noncoding RNAs during ischemic AKI, as well as explore their therapeutic potential.
Illumina Infinium DNA Methylation (5mC) arrays are a popular technology for low-cost, high-throughput, genome-scale measurement of 5mC distribution, especially in cancer and other complex diseases. After the success of its HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers. Despite the widespread use of 850k, analysis of the corresponding data remains suboptimal: it still relies mostly on Illumina’s default annotation, which underestimates enhancerss and long noncoding RNAs. Results: We have thus developed an approach, based on the ENCODE and LNCipedia databases, which greatly improves upon Illumina’s default annotation of enhancers and long noncoding transcripts. We compared the re-annotated 850k with both 450k and reduced-representation bisulphite sequencing (RRBS), another high-throughput 5mC profiling technology. We found 850k to cover at least three times as many enhancers and long noncoding RNAs as either 450k or RRBS. We further investigated the reproducibility of the three technologies, applying various normalization methods to the 850k data. Most of these methods reduced variability to a level below that of RRBS data. We then used 850k with our new annotation and normalization to profile 5mC changes in breast cancer biopsies. 850k highlighted aberrant enhancer methylation as the predominant feature, in agreement with previous reports. Our study provides an updated processing approach for 850k data, based on refined probe annotation and normalization, allowing for improved analysis of methylation at enhancers and long noncoding RNA genes. Our findings will help to further advance understanding of the DNA methylome in health and disease.
Enhancers are cis-acting elements that control the transcription of target genes and are transcribed into a class of noncoding RNAs (ncRNAs) termed enhancer RNAs (eRNAs). eRNAs have shorter half-lives than mRNAs and long noncoding RNAs; however, the frequency of transcription of eRNAs is close to that of mRNAs. eRNA expression is associated with a high level of histone mark H3K27ac and a low level of H3K27me3. Although eRNAs only account for a small proportion of ncRNAs, their functions are important. eRNAs can not only increase enhancer activity by promoting the formation of enhancer-promoter loops but also regulate transcriptional activation. Increasing numbers of studies have found that eRNAs play an important role in the occurrence and development of brain diseases; however, further research into eRNAs is required. This review discusses the concept, characteristics, classification, function, and potential roles of eRNAs in brain diseases.
Examining neural etiologic factors’role in the decline of neuromuscular function with aging is essential to our understanding of the mechanisms underlying sarcopenia, the age-dependent decline in muscle mass, force and power. Innervation of the skeletal muscle by both motor and sympathetic axons has been established, igniting interest in determining how the sympathetic nervous system (SNS) affect skeletal muscle composition and function throughout the lifetime. Selective expression of the heart and neural crest derivative 2 gene in peripheral SNs increases muscle mass and force regulating skeletal muscle sympathetic and motor innervation; improving acetylcholine receptor stability and NMJ transmission; preventing inflammation and myofibrillar protein degradation; increasing autophagy; and probably enhancing protein synthesis. Elucidating the role of central SNs will help to define the coordinated response of the visceral and neuromuscular system to physiological and pathological challenges across ages.
This review discusses the following questions: (1) Does the SNS regulate skeletal muscle motor innervation? (2) Does the SNS regulate presynaptic and postsynaptic neuromuscular junction (NMJ) structure and function? (3) Does sympathetic neuron (SN) regulation of NMJ transmission decline with aging? (4) Does maintenance of SNs attenuate aging sarcopenia? and (5) Do central SN group relays influence sympathetic and motor muscle innervation?
Enhancers are cis-acting elements with many sites bound by transcription factors and activate transcription over long distance. Histone modifications are critical for enhancer activity and utilized as hallmarks for the identification of putative enhancers. Monomethylation of histone H3 lysine 4 (H3K4me1) is the mark for enhancer priming; acetylation of histone H3 lysine 27 (H3K27ac) for active enhancers and trimethylation of histone H3 lysine 27 (H3K27me3) for silent enhancers. Recent studies from multiple groups have provided evidence that enhancer reprogramming, especially gain of enhancer activity, is closely related to tumorigenesis and cancer development. In this review, we will summarize the recent discoveries about enhancer regulation and the mechanisms of enhancer reprogramming in tumorigenesis, and discuss the potential application of enhancer manipulation in precision medicine.
