Towards a complete map of the human long non-coding RNA transcriptome

Abstract

Gene maps, or annotations, enable us to navigate the functional landscape of our genome. They are a resource upon which virtually all studies depend, from single-gene to genome-wide scales and from basic molecular biology to medical genetics. Yet present-day annotations suffer from trade-offs between quality and size, with serious but often unappreciated consequences for downstream studies. This is particularly true for long non-coding RNAs (lncRNAs), which are poorly characterized compared to protein-coding genes. Long-read sequencing technologies promise to improve current annotations, paving the way towards a complete annotation of lncRNAs expressed throughout a human lifetime.

Long non‐coding RNA THRIL predicts increased acute respiratory distress syndrome risk and positively correlates with disease severity, inflammation, and mortality in sepsis patients

“…LncRNAs are diverse and abundant in each component of human life with the total number exceeding that of protein‐coding genes . The biological complexity of lncRNAs enables them to participate in various biological processes such as gene transcription, cell state coordination, and disease progression, while only a small proportion of lncRNAs are studied . As one of the novel lncRNAs, lnc‐THRIL is initially disclosed to regulate the expression of TNF‐α, which is a key mediator of inflammation and immune response by forming a complex with hnRNPL and then binding to the promoter region of TNF‐α, and it influences the expression of inflammatory cytokines such as IL‐1β, IL‐6, and IL‐8 .…”

“…The biological complexity of lncRNAs enables them to participate in various biological processes such as gene transcription, cell state coordination, and disease progression, while only a small proportion of lncRNAs are studied. 6 As one of the novel lncRNAs, lnc-THRIL is initially disclosed to regulate the expression of TNF-α, which is a key mediator of inflammation and immune response by forming a complex with hnRNPL and then binding to the promoter region of TNF-α, and it influences the expression of inflammatory cytokines such as IL-1β, IL-6, and IL-8. 9,11 Additionally, lnc-THRIL is reported to influence inflammation-related cell injuries in inflammatory diseases, and cell injury, especially alveolar epithelial cells injury that is one of the main contributors for the development of ARDS in sepsis.…”

“…Long non‐coding RNA (lncRNA) is a class of RNAs longer than 200 nucleotides and does not contain protein‐coding sequences . Accumulating studies reveal that a number of lncRNAs are implicated in regulating gene transcription as well as etiology of immune or inflammatory diseases .…”

“…Long non-coding RNA (lncRNA) is a class of RNAs longer than 200 nucleotides and does not contain protein-coding sequences. 6 Accumulating studies reveal that a number of lncRNAs are implicated in regulating gene transcription as well as etiology of immune or inflammatory diseases. 7,8 Tumor necrosis factor (TNF)-related and heterogeneous nuclear ribonucleoprotein L (hnRNPL)-related immunoregulatory lncRNA (lnc-THRIL) is responsible for the transcription of TNF-α.…”

ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow

“…Recent advances in micro-array and sequencing technologies have revealed that large amounts of non-coding RNAs exist in cells. For example, in human cells, tens of thousands of long non-coding RNAs have been identified [1]. The functions of non-coding RNAs have been studied extensively, and relationships between mutations in non-coding RNAs and diseases have been investigated [2][3][4].…”