Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

A subset of highly active chromosomal "hot zones" reproducibly positions adjacent to nuclear speckles (NS). Genes within these regions amplify their expression with NS proximity. However, gene expression changes inversely correlate with changes in NS distance genome-wide. We hypothesized the existence of additional gene expression "niches" away from but spatially correlated with NS. Here we report the identification of two dynamic perispeckle patterns of protein concentrations extending outwards from nuclear speckles and persisting even after NS are eliminated. Highly active chromosome regions which weakly associate with NS instead show close, NS-independent association with these perispeckle patterns. Additionally, transcripts from model intron-containing versus intronless genes associate differentially with these two patterns. While genes within speckle-associated genomic regions predominately are downregulated upon nuclear speckle depletion, genes associated with perispeckle patterns are biased towards upregulation. We suggest the interchromatin space (ICS) is partitioned into additional gene expression “niches”- surrounding and extending from nuclear speckles- that may be involved in mRNA and gene dynamics. Total 44 samples generated using TSA-seq in Homo sapiens on HCT116 (with anti-THRAP3 or anti-DDX39B or anti-SON treated with Auxin or DMSO) and U2OS (with anti-DDX39B, anti-THRAP3, anti-SON) cell lines.