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Updated: Jan 28, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

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Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data

Nikolai Genov1,2, Alireza Basti3,4, Mónica Abreu5,6

  • 1Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Theoretical Biology, 10115 Berlin, Germany. nikolai.genov@zedat.fu-berlin.de.

International Journal of Molecular Sciences
|March 13, 2019
PubMed

Insights

Alternative splicing in cancer cells shows time-dependent changes, particularly in the tumor necrosis factor (TNF) pathway. These temporal isoform switches may affect cell behavior and cancer development.

Area of Science:

  • Molecular Biology
  • Cancer Research
  • Genomics

Background:

  • Alternative splicing is crucial for cellular processes, and its dysregulation is linked to cancer.
  • The temporal regulation of alternative splicing and its impact on cancer remain largely unexplored.

Purpose of the Study:

  • To investigate time-dependent isoform production in Hodgkin lymphoma cell lines.
  • To focus on alterations within the tumor necrosis factor (TNF) pathway.
  • To understand the functional consequences of temporal alternative splicing in tumorigenesis.

Main Methods:

  • Utilized time-course RNA-sequencing data from Hodgkin lymphoma and B lymphoblastoid cell lines.
  • Applied a computational pipeline to identify genes exhibiting isoform switching over time.
  • Analyzed temporal expression profiles and evaluated functional implications of isoform alterations.

Main Results:

  • Identified time-dependent variations in isoform production for elements within the TNF pathway.
  • Observed isoform switching in key genes including TRAF1, TNFRSF12A, and NFKB2.
  • Detected potential impacts on cell migration, proliferation, and apoptosis due to altered isoform expression.

Conclusions:

  • Temporal alternative splicing plays a role in isoform production within the TNF pathway.
  • These dynamic splicing events may influence pathway outcomes and contribute to cancer development.
  • The study highlights the significance of time-dependent alternative splicing in Hodgkin lymphoma.
Keywords:
RNA-sequencingTNF-pathwayalternative splicinganalysis of oscillating genescancercircadian clockhigh-throughput data analysispathway enrichmentsystems biology

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