Talyan, Sweta ORCID: 0000-0002-7160-6742, Filipow, Samantha ORCID: 0000-0002-9290-1273, Ignarski, Michael ORCID: 0000-0001-6057-7694, Smieszek, Magdalena, Chen, He ORCID: 0000-0002-7616-8438, Kuehne, Lucas, Butt, Linus, Gobel, Heike, Hoyer-Allo, K. Johanna R., Koehler, Felix C., Altmuller, Janine ORCID: 0000-0003-4372-1521, Brinkkoeter, Paul, Schermer, Bernhard, Benzing, Thomas, Kann, Martin ORCID: 0000-0003-2956-1699, Mueller, Roman-Ulrich and Dieterich, Christoph (2021). CALINCA-A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease. Cells, 10 (3). BASEL: MDPI. ISSN 2073-4409

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Abstract

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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Talyan, SwetaUNSPECIFIEDorcid.org/0000-0002-7160-6742UNSPECIFIED
Filipow, SamanthaUNSPECIFIEDorcid.org/0000-0002-9290-1273UNSPECIFIED
Ignarski, MichaelUNSPECIFIEDorcid.org/0000-0001-6057-7694UNSPECIFIED
Smieszek, MagdalenaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, HeUNSPECIFIEDorcid.org/0000-0002-7616-8438UNSPECIFIED
Kuehne, LucasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Butt, LinusUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gobel, HeikeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hoyer-Allo, K. Johanna R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Koehler, Felix C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Altmuller, JanineUNSPECIFIEDorcid.org/0000-0003-4372-1521UNSPECIFIED
Brinkkoeter, PaulUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schermer, BernhardUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Benzing, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kann, MartinUNSPECIFIEDorcid.org/0000-0003-2956-1699UNSPECIFIED
Mueller, Roman-UlrichUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dieterich, ChristophUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-583174
DOI: 10.3390/cells10030692
Journal or Publication Title: Cells
Volume: 10
Number: 3
Date: 2021
Publisher: MDPI
Place of Publication: BASEL
ISSN: 2073-4409
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
Cell BiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/58317

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