Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription

Chromatin structure and dynamics are crucial for eukaryotic nuclear functions. Hi-C and related genomic assays have revealed chromatin conformations, such as A/B compartments, in fixed cells, but the dynamic motion of such structures is not well understood. Moreover, elucidating the relationship between the motion of chromatin and transcriptional activity is hampered by a lack of tools for specifically measuring the mobility of active euchromatin. Here, we introduce a CRISPR-based strategy for live imaging of the gene-rich A compartment by labeling Alu elements — a retrotransposon family enriched within the transcriptionally active A compartment. Surprisingly, within euchromatin, microscopy analysis reveals that Alu-rich regions do not correlate with lower local H2B density, and form irregular foci of a few hundred nanometers in diameter, underscoring the heterogeneity of euchromatin organization. Alu-rich (gene-rich) chromatin is also more mobile than Alu-poor (gene-poor) chromatin, and transcription inhibition by actinomycin D results in decreased chromatin mobility of Alu-rich regions. These observations highlight the complexity of chromatin organization and dynamics and connect them to transcriptional activity on a genome-wide scale.