Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects

Wan, Lilin; Li, Wenchao; Meng, Yuan; Hou, Yue; Chen, Ming; Xu, Bin

doi:10.3389/fimmu.2022.849451

Cited by 9 publications

(9 citation statements)

References 203 publications

(273 reference statements)

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“…We used all read alignments with F to build an all all feature-associated count matrix . During this process, only alignments that are less than 4, 000 bases away from their nearest feature were used, corresponding to the reported length range of eRNAs and other lncRNAs [Wan et al, 2022].…”

Section: Methodsmentioning

confidence: 99%

scCensus: Off-target scRNA-seq reads reveal meaningful biology

He,

Mount,

Patro

2024

Preprint

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Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3′ end of polyadenylated RNAs, recent studies have shown that “off-target” reads can constitute a substantial portion of the read population. in this work, we introducedscCensus, a comprehensive analysis workflow for systematically evaluating and categorizing off-target reads in scRNA-seq. We appliedscCensusto seven scRNA-seq datasets. Our analysis of intergenic reads shows that these off-target reads contain information about chromatin structure and can be used to identify similar cells across modalities. Our analysis of antisense reads suggests that these reads can be used to improve gene detection and capture interesting transcriptional activities like antisense transcription. Furthermore, using splice-aware quantification, we find that spliced and unspliced reads provide distinct information about cell clusters and biomarkers, suggesting the utility of integrating signals from reads with different splicing statuses.Overall, our results suggest that off-target scRNA-seq reads contain underappreciated information about various transcriptional activities. These observations about yet-unexploited information in existing scRNA-seq data will help guide and motivate the community to improve current algorithms and analysis methods, and to develop novel approaches that utilize off-target reads to extend the reach and accuracy of single-cell data analysis pipelines.Data AvailabilityThe scripts for reproducing the results are available athttps://github.com/COMBINE-lab/sc-census. Supplementary files can be found athttps://doi.org/10.5281/zenodo.10520670.

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Section: Methodsmentioning

confidence: 99%

scCensus: Off-target scRNA-seq reads reveal meaningful biology

He,

Mount,

Patro

2024

Preprint

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“…Expression of eRNA is responsive to environmental stimuli. For instance, eRNAs are preferentially expressed at inflammation-related genes in response to inflammatory stimuli (Wan et al, 2022). Global run-on sequencing (GRO-seq) has demonstrated that expression of eRNA is altered in response to early-life undernutrition (Wang Y. et al, 2021).…”

Section: Regulation Of Erna Expressionmentioning

confidence: 99%

Natural antisense transcripts as drug targets

Khorkova

Stahl

Joji

et al. 2022

Front. Mol. Biosci.

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The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.

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“…Based on structure and transcription patterns, eRNAs (approximately from 0.1–9 Kb) [ 8 ] can be classified in two groups of short bidirectional, non-spliced, non-polyadenylated RNAs and long unidirectional, spliced, stable polyadenylated transcripts ( Figure 1 ). Since eRNAs are mainly non-polyadenylated and unstable, they are predominantly localized in the nucleus and chromatin-enriched fractions [ 9 , 10 , 11 , 12 ].…”

Section: Biogenesis and Function Of Ernamentioning

confidence: 99%

Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer

Panahi-Moghadam

Hassani

Farivar

et al. 2022

ncRNA

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Enhancers are distal cis-acting elements that are commonly recognized to regulate gene expression via cooperation with promoters. Along with regulating gene expression, enhancers can be transcribed and generate a class of non-coding RNAs called enhancer RNAs (eRNAs). The current discovery of abundant tissue-specific transcription of enhancers in various diseases such as cancers raises questions about the potential role of eRNAs in disease diagnosis and therapy. This review aimed to demonstrate the current understanding of eRNAs in cancer research with a focus on the potential roles of eRNAs as prognostic and diagnostic biomarkers in cancers.

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Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects

Cited by 9 publications

References 203 publications

scCensus: Off-target scRNA-seq reads reveal meaningful biology

scCensus: Off-target scRNA-seq reads reveal meaningful biology

Natural antisense transcripts as drug targets

Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer

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