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An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation

Philipp Raffeiner1, Jonathan R Hart1, Daniel García-Caballero1

  • 1Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037.

Proceedings of the National Academy of Sciences of the United States of America
|March 12, 2020
PubMed

Insights

Researchers identified 320 long noncoding RNAs (lncRNAs) crucial for MYC-driven cell proliferation using CRISPR interference. Repressing these MYC-regulated lncRNAs significantly reduces cancer cell growth, highlighting their oncogenic role.

Area of Science:

  • Oncology
  • Molecular Biology
  • Genetics

Background:

  • The MYC oncoprotein regulates numerous long noncoding RNAs (lncRNAs), some of which are implicated in cancer development.
  • Understanding the functional role of MYC-regulated lncRNAs is crucial for identifying novel cancer therapeutic targets.

Purpose of the Study:

  • To identify MYC-regulated lncRNAs essential for cell proliferation in human lymphoid cancer cell lines.
  • To evaluate the efficacy of the SIN3-interacting domain (SID) repressor in CRISPR interference (CRISPRi) screening.

Main Methods:

  • CRISPR interference (CRISPRi) screening was employed in P493-6 and RAMOS cells to identify growth-promoting lncRNAs.
  • Quantitative real-time PCR (RT-qPCR), CRISPRi competition assays, and chromatin immunoprecipitation (ChIP) were used for validation.
  • The effectiveness of the SID repressor domain was compared against the KRAB repressor domain in CRISPRi.

Main Results:

  • 320 noncoding loci were identified as positively regulating cell growth; repression of these lncRNAs decreased cell proliferation.
  • MYC binding to the promoters of two candidate genes was confirmed via ChIP.
  • The SID repressor domain demonstrated superior efficiency in transcriptional repression and guide depletion compared to KRAB in the tested cell lines.

Conclusions:

  • MYC-driven cell proliferation is dependent on a specific set of lncRNAs.
  • The SID repressor domain offers an effective tool for doxycycline-inducible CRISPRi, facilitating the functional study of growth-promoting lncRNAs.
  • These findings provide a foundation for targeting MYC-regulated lncRNAs in cancer therapy.
Keywords:
CRISPRiMYClncRNAsoncogenesistranscriptional regulation

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