bims-lorfki Biomed News
on Long non-coding RNA functions in the kidney
Issue of 2021–04–04
two papers selected by
Nikita Dewani, Max Delbrück Centre for Molecular Medicine
  1. CALINCA-A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease.
  2. Alternative splicing of lncRNAs in human diseases.
  1. Cells. 2021 Mar 20. pii: 692. [Epub ahead of print]10(3):
    CALINCA-A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease.
    Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, K Johanna R Hoyer-Allo, Felix C Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman-Ulrich Müller, Christoph Dieterich.
      Diseases of the renal filtration unit-the glomerulus-are the most common cause of chronic kidney disease. Podocytes are the pivotal cell type for the function of this filter and focal-segmental glomerulosclerosis (FSGS) is a classic example of a podocytopathy leading to proteinuria and glomerular scarring. Currently, no targeted treatment of FSGS is available. This lack of therapeutic strategies is explained by a limited understanding of the defects in podocyte cell biology leading to FSGS. To date, most studies in the field have focused on protein-coding genes and their gene products. However, more than 80% of all transcripts produced by mammalian cells are actually non-coding. Here, long non-coding RNAs (lncRNAs) are a relatively novel class of transcripts and have not been systematically studied in FSGS to date. The appropriate tools to facilitate lncRNA research for the renal scientific community are urgently required due to a row of challenges compared to classical analysis pipelines optimized for coding RNA expression analysis. Here, we present the bioinformatic pipeline CALINCA as a solution for this problem. CALINCA automatically analyzes datasets from murine FSGS models and quantifies both annotated and de novo assembled lncRNAs. In addition, the tool provides in-depth information on podocyte specificity of these lncRNAs, as well as evolutionary conservation and expression in human datasets making this pipeline a crucial basis to lncRNA studies in FSGS.
    Keywords:  FSGS; RNAscope; focal-segmental glomerulosclerosis; glomerulus; kidney; lncRNA; long non-coding RNA; podocyte
    DOI:  https://doi.org/10.3390/cells10030692
  2. Am J Cancer Res. 2021 ;11(3): 624-639
    Alternative splicing of lncRNAs in human diseases.
    Jiaxi Chen, Yawen Liu, Jingyu Min, Huizhi Wang, Feifan Li, Chunhui Xu, Aihua Gong, Min Xu.
      Alternative splicing (AS), a vital post-transcription process for eukaryote gene expression regulating, can efficiently improve gene utilization and increase the variety of RNA transcripts and proteins. However, AS of non-coding RNAs (ncRNAs) has not been paid enough attention to compared with that of protein-coding RNAs (mRNAs) for a long time. In fact, AS of ncRNAs, especially long noncoding RNAs (lncRNAs), also plays a significant regulatory role in the human disease. Recently, some bifunctional genes transcribed into both mRNA and lncRNA transcripts by AS have been observed. Here, we focus on the AS of lncRNAs and bifunctional genes producing lncRNA transcripts and propose a strategy for the future research of lncRNA AS.
    Keywords:  Alternative splicing; bifunctional genes; lncRNAs
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