A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS

Author Summary The cohesin complex is crucial for chromosome segregation during cell divisions but was recently also implicated in transcriptional regulation and chromatin architecture. Cohesin's binding to chromatin depends on NIPBL, a factor that was found to be mutated in 50% of the cases of the human developmental disorder Cornelia de Lange Syndrome (CdLS). To understand the role of NIPBL for cohesin, we need to know when and where the cohesin is loaded onto DNA. Our experiments have identified high-affinity NIPBL binding sites in different cells lines which do not overlap with cohesin-binding, but colocalize with specific transcription factors at active promoters. The activity of the respective genes depends on NIPBL but not cohesin. This is in contrast with other published data showing colocalization of NIPBL and cohesin, and we reveal the existence of different types of NIPBL binding sites that are detected differently by the antibodies used in the different studies. Our observations reveal a dual role for NIPBL in cohesin loading and as potential transcription co-factor, which yields novel insights into how NIPBL defects could cause Cornelia de Lange Syndrome since NIPBL mutations might directly influence developmentally important genes. The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of cohesin onto chromatin, but how and where cohesin is loaded in vertebrate cells is unclear. Heterozygous mutations of NIPBL were found in 50% of the cases of Cornelia de Lange Syndrome (CdLS), a human developmental syndrome with a complex phenotype. However, no defects in the mitotic function of cohesin have been observed so far and the links between NIPBL mutations and the observed developmental defects are unclear. We show that NIPBL binds to chromatin in somatic cells with a different timing than cohesin. Further, we observe that high-affinity NIPBL binding sites localize to different regions than cohesin and almost exclusively to the promoters of active genes. NIPBL or cohesin knockdown reduce transcription of these genes differently, suggesting a cohesin-independent role of NIPBL for transcription. Motif analysis and comparison to published data show that NIPBL co-localizes with a specific set of other transcription factors. In cells derived from CdLS patients NIPBL binding levels are reduced and several of the NIPBL-bound genes have previously been observed to be mis-expressed in CdLS. In summary, our observations indicate that NIPBL mutations might cause developmental defects in different ways. First, defects of NIPBL might lead to cohesin-loading defects and thereby alter gene expression and second, NIPBL deficiency might affect genes directly via its role at the respective promoters.