In vivo BMAL1 occupancy mapping using MACS-Calling Cards reveals disease-associated retargeting in Cln3Δex7/8 astrocytes

BMAL1 binding was extensively redistributed, with comparable numbers of wild-type-specific and disease-specific sites. Wild-type-specific BMAL1 binding was enriched near genes involved in circadian regulation and astrocyte differentiation, whereas disease-specific sites lacked coherent functional enrichment. Consistent with these changes, RNA-seq of sorted astrocytes revealed reduced expression of mature astrocyte markers in Cln3Δex7/8 mice.

To define the mechanisms underlying BMAL1 retargeting in Cln3Δex7/8 astrocytes, we tested whether changes in chromatin accessibility could explain disease-associated gains and losses of BMAL1 binding. Although chromatin accessibility was broadly remodeled, differential accessibility did not predict BMAL1 binding gains or losses. Instead, motif analyses supported a model in which loss of normal cooperative transcription factor partnerships contributes to BMAL1 retargeting.

Together, these findings demonstrate that MACS-CC enables in vivo transcription factor occupancy mapping in astrocytes and reveals the mechanisms behind early rewiring of circadian regulatory programs within a model of progressive pathology leading to neurodegeneration. Our data also shed new light on astrocyte dysfunction in CLN3 disease.