Nuclear Speckles

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Hello,

Some recent published literature has detailed pathophysiology of nuclear speckles aka ‘nuclear dots’

I will list the primary articles for your reading and learning:
original study in 2000 that used intrinsic mutation in osteogenesis imperfecta to look at role of splicing with respect to nuclear structure Tracking Col1a1 RNA in Osteogenesis Imperfecta: Splice-Defective Transcripts Initiate Transport from the Gene but Are Retained within the Sc35 Domain - PMC

Primary scaffolding genes observed: SON and SRRM2 are essential for nuclear speckle formation | eLife

study of SON-dependent nuclear speckle rehabilitation in protieinopathies SON-dependent nuclear speckle rehabilitation alleviates proteinopathies | Nature Communications → this is followed by a recent clinical trial using a pinworm therapy which affects nuclear speckle spherical surface tension for disease modification

spatialtemporal resolution of nuclear speckle periphery and introns centered on RNA and mitosis The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis | Nature Cell Biology

https://www.cell.com/neuron/fulltext/S0896-6273(21)00196-3 Tau

GC https://www.cell.com/cell/fulltext/S0092-8674(26)00098-X

HSV activation https://www.pnas.org/doi/10.1073/pnas.2511555123

Renal cell carcinoma https://www.pnas.org/doi/10.1073/pnas.2511555123

Review https://www.cell.com/trends/cell-biology/fulltext/S0962-8924(26)00059-0

while early nuclear speckle studies used electron microscopy and antibodies/SDS-page to profile these structures, whole genome profiling has enabled investigators to identify critical genes that are expressed with nuclear speckles; additionally literature has implicated the presence of high GC content and introns in said structures as well as alternative splicing

differential splicing software that can be coupled with splicing aware: Differential Alternative Splicing Analysis with rMATS - BTEP Coding Club

als and ftd https://www.cell.com/neuron/fulltext/S0896-6273(24)00570-1

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Interesting!

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@mgebre256 thanks for pulling these together. Are you planning an analysis with OSDR data on this? Intron retention and alternative splicing in the spaceflight RNA-seq would be a good angle. If so, add the question and datasets here and I’ll link it from the master table. If it’s more of a reading list for now, I can move it to AWG Discussions so more people see it.

-Ryan