Related Experiment Video

Updated: Jun 16, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

6.6K

Nuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role

Dimitrios G Anastasakis1, Maria Apostolidi2, Khalid A Garman3

  • 1RNA Molecular Biology Laboratory, NIAMS/NIH, Bethesda, MD, USA.

Molecular Cell
|August 17, 2024
PubMed

Insights

Nuclear PKM2 binds RNA G-quadruplexes, promoting cancer gene expression. Inhibiting PKM2 reduced cancer cell invasion, suggesting a therapeutic target for cancer progression.

Area of Science:

  • Molecular Biology
  • Cancer Biology
  • RNA Biology

Background:

  • Nuclear localization of pyruvate kinase M2 (PKM2) is common in cancers.
  • PKM2's role beyond metabolism is increasingly recognized.

Purpose of the Study:

  • To investigate the non-canonical functions of nuclear PKM2.
  • To determine PKM2's interaction with RNA structures and its role in gene expression.

Main Methods:

  • Identifying PKM2 as an RNA-binding protein (RBP).
  • Analyzing PKM2's interaction with RNA G-quadruplex (rG4) structures in pre-mRNAs.
  • Assessing the impact of PKM2 on the expression of rG4-containing pre-mRNAs (the "rG4ome").
  • Evaluating the role of PKM2 and the rG4ome in cancer progression, including epithelial-to-mesenchymal transition (EMT) and patient survival.
  • Investigating the therapeutic potential of inhibiting nuclear PKM2 accumulation in triple-negative breast cancer (TNBC) models.

Main Results:

  • Nuclear PKM2 functions as an RBP that specifically binds to folded RNA G-quadruplex (rG4) structures in pre-mRNAs.
  • PKM2 binding to rG4s displaces repressive RBPs (e.g., HNRNPF), thereby promoting the expression of rG4-containing pre-mRNAs (the "rG4ome").
  • The rG4ome is upregulated during EMT, and higher rG4 abundance correlates with poorer patient survival across various cancer types.
  • Inhibition of nuclear PKM2 accumulation suppressed the rG4ome in TNBC cells, reducing cancer cell migration and invasion in vitro and in vivo.

Conclusions:

  • Nuclear PKM2 is a key regulator of the rG4ome, influencing gene expression during tumor progression.
  • The balance between folded and unfolded rG4 structures, modulated by RBPs like PKM2, is critical for cancer development.
  • Targeting nuclear PKM2 offers a potential therapeutic strategy to combat cancer by repressing the rG4ome and inhibiting cancer cell invasion.
Keywords:
G-quadruplexG4PAR-CLIPPKM2RNA-binding proteinscrosslinking and immunoprecipitationposttranscriptional gene regulation

More Related Videos

mRNA Interactome Capture from Plant Protoplasts12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

9.1K
CD Spectroscopy to Study DNA-Protein Interactions06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

6.7K

Related Concept Videos

Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
7.0K
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
22.6K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
876
Regulation of Nuclear Protein Sorting01:45

Regulation of Nuclear Protein Sorting

Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
2.4K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.1K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.4K