lncRNA Functions (Mattick et al., 2023): Beyond acting as a scaffold, describe how lncRNAs like NEAT1 contribute to the formation of biomolecular condensates (or PSDs) in the nucleus.

What role do lncRNAs like NEAT1 play beyond acting as a simple scaffold?

They serve as "architectural" molecules that actively nucleate and organize the internal structure of biomolecular condensates (phase-separated domains or PSDs).

What are paraspeckles?

Mammal-specific nuclear organelles.

What lncRNA is essential for paraspeckle assembly?

NEAT1.

How does NEAT1 trigger paraspeckle formation?

It triggers phase separation, creating dynamic, membraneless assemblies with high local concentrations of macromolecules.

What specific internal architecture does NEAT1 dictate within the paraspeckle?

A core-shell spheroidal organization based on the RNA's own modular domains.

What localizes to the centre (core) of the paraspeckle?

The middle region of the NEAT1 transcript.

Which proteins are embedded in the core of the paraspeckle?

FUS, NONO, and SFPQ.

What forms the shell of the paraspeckle?

The 5' and 3' ends of the NEAT1 transcript.

Which protein is recruited to the shell of the paraspeckle?

RBM14.

What are intrinsically disordered regions (IDRs)?

Flexible protein segments that lack a stable 3D structure.

How do IDRs interact with lncRNAs?

They interact with the negatively charged backbone of lncRNAs to form condensed liquid-like droplets called coacervates.

What biochemical property do IDRs give lncRNAs regarding condensates?

They allow lncRNAs to "tune" the size and composition of the condensate.

How do lncRNA-nucleated condensates contribute to nuclear compartmentalization beyond structure?

They sequester factors, organize chromosome territories, and regulate enhancer action.

Give an example of a lncRNA that sequesters a splicing factor.

PNCTR.

What splicing factor does PNCTR sequester, and what does this suppress?

It sequesters PTBP1 to suppress its activity elsewhere in the nucleoplasm.

How do repeat-rich lncRNAs help organize chromosome territories?

Their collective presence bound to chromatin helps organize chromosome territories and prevents excessive chromatin condensation.

What role is increasingly attributed to lncRNA-driven phase separation regarding enhancers?

It is seen as a requirement for enhancer and super-enhancer action, helping stabilize interactions between distal regulatory elements and target gene promote