LAUSR

Significance Transcription occurs at chromosomal sites known as active transcription sites (ATS). We report that ATS can exist in two classes when assessed at key regulatory genes in their natural context: these “iATS” and “cATS” possess incomplete and complete nascent transcripts, respectively. Frequencies of the two classes are patterned within the developing tissue in a gene-, developmental stage-, and sex-specific manner, revealing ATS class regulation. Moreover, cATS frequency, not iATS frequency, corresponds to mRNA abundance, indicating that regulation of ATS class impacts gene expression. The iATS signature—presence of a long first intron but lacking exons—suggests slowing or pausing of transcriptional progression midway through the gene. We suggest that ATS class regulation can pattern gene expression during development. The expression of genes encoding powerful developmental regulators is exquisitely controlled, often at multiple levels. Here, we investigate developmental expression of three conserved genes, Caenorhabditis elegans mpk-1, lag-1, and lag-3/sel-8, which encode homologs of ERK/MAPK and core components of the Notch-dependent transcription complex, respectively. We use single-molecule FISH (smFISH) and MATLAB to visualize and quantify nuclear nascent transcripts and cytoplasmic mRNAs as a function of position along the germline developmental axis. Using differentially labeled probes, one spanning an exceptionally long first intron and the other spanning exons, we identify two classes of active transcription sites (ATS). The iATS class, for “incomplete” ATS, harbors only partial nascent transcripts; the cATS class, for “complete” ATS, harbors full-length nascent transcripts. Remarkably, the frequencies of iATS and cATS are patterned along the germline axis. For example, most mpk-1 ATS are iATS in hermaphrodite germline stem cells, but most are cATS in differentiating stem cell daughters. Thus, mpk-1 ATS class frequencies switch in a graded manner as stem cell daughters begin differentiation. Importantly, the patterns of ATS class frequency are gene-, stage-, and sex-specific, and cATS frequency strongly correlates with transcriptional output. Although the molecular mechanism underlying ATS classes is not understood, their primary difference is the extent of transcriptional progression. To generate only partial nascent transcripts in iATS, progression must be slowed, paused, or aborted midway through the gene. We propose that regulation of ATS class can be a critical mode of developmental gene regulation.