Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases

Area of Science:

• Molecular Biology
• Biochemistry
• Cell Biology

Background:

• Nuclear speckles contain pre-mRNA processing factors, including serine/arginine-rich splicing factors (SRSFs) and transactive response DNA binding protein (TDP)-43.
• These proteins possess RNA recognition motifs (RRMs) and disordered regions, acting as unique block copolymers.

Purpose of the Study:

• To investigate the role of inter-domain interactions in driving microphase separation and assembly formation of nuclear speckle proteins.
• To understand how RNA molecules, specifically MALAT1, influence these protein microphases.

Main Methods:

• Analysis of protein structure-function relationships, focusing on block copolymer characteristics.
• Observation and characterization of microphase formation and assembly dynamics in vitro and in cellular contexts.
• Investigation of specific RNA-protein interactions, particularly MALAT1 with SRSF1 and TDP-43 microphases.

Main Results:

• SRSFs and TDP-43 form distinct microphases (23-45 nm) driven by homotypic and heterotypic attractions/repulsions.
• Sub-micron SRSF assemblies are consistent with clusters of these microphases.
• Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) lncRNA binds SRSF1 microphases and destabilizes TDP-43 microphases.
• Protein mixtures form micron-scale core-shell structures via microphase interactions.

Conclusions:

• Interactions within copolymers featuring folded and disordered regions are crucial for driving microphase formation.
• These microphase behaviors contribute to the organization of nuclear speckles and influence RNA processing.
• Specific lncRNAs can modulate the behavior of distinct protein microphases, highlighting a regulatory mechanism.