TY - JOUR
TI - A comprehensive nanopore sequencing methodology deciphers the complete
transcriptional landscape of cyclin-dependent kinase 4 (CDK4) in human
malignancies
AU - Adamopoulos, Panagiotis G.
AU - Athanasopoulou, Konstantina and
AU - Tsiakanikas, Panagiotis
AU - Scorilas, Andreas
JO - FEBS Journal
PY - 2022
VL - 289
TODO - 3
SP - 712-729
PB - Wiley
SN - 1742-464X, 1742-4658
TODO - 10.1111/febs.16201
TODO - alternative splicing; CDK4; cyclin-dependent kinases; long-read
sequencing; nanopore sequencing
TODO - Cyclin-dependent kinase 4 (CDK4) is a member of the cyclin-dependent
kinases, a family of protein kinases with outstanding roles in signaling
pathways, transcription regulation, and cell division. Defective or
overactivated CDK4/cyclin D1 pathway leads to enhanced cellular
proliferation, thus being implicated in human cancers. Although the
biological role of CDK4 has been extensively studied, its pre-mRNA
processing mechanism under normal or pathological conditions is
neglected. Thus, the identification of novel CDK4 mRNA transcripts,
especially protein-coding ones, could lead to the identification of new
diagnostic and/or prognostic biomarkers or new therapeutic targets. In
the present study, instead of using the `gold standard' direct RNA
sequencing application, we designed and employed a targeted nanopore
sequencing approach, which offers higher sequencing depth and enables
the thorough investigation of new mRNAs of any target gene. Our study
elucidates for the first time the complex transcriptional landscape of
the human CDK4 gene, highlighting the existence of previously unknown
CDK4 transcripts with new alternative splicing events and protein-coding
capacities. The relative expression levels of each novel CDK4 transcript
in human malignancies were elucidated with custom qPCR-based assays. The
presented wide spectrum of CDK4 transcripts (CDK4 v.2-v.42) is only the
first step to distinguish and assemble the missing pieces regarding the
exact functions and implications of this fundamental kinase in cellular
homeostasis and pathophysiology.
ER -