Cohesin is a protein complex important for chromatin structural organization. NIPBL is required for cohesin loading onto chromatin. Cornelia de Lange syndrome (CdLS) is a developmental disorder caused by heterozygous <italic>NIPBL<italic> (60% of CdLS) or cohesin (∼5–6%) mutations. How the mutations lead to developmental abnormalities was not well understood. We used the the <italic> Nipbl<italic> +/− mouse cells to investigate how <italic> Nipbl<italic> reduction affects cohesin–mediated gene regulation. We found that development–related genes bound by cohesin preferentially changed expression in <italic> Nipbl<italic> mutant cells, suggesting that dysregulation of cohesin target genes directly contributes to the CdLS pathogenesis. We also found that a sub–population of Nipbl localizes in the nucleolus, which is compromised in <italic> Nipbl<italic> heterozygous mutant cells. Nipbl binds to both ribosomal RNA and DNA (rRNA and rDNA) and stimulates pre–rRNA synthesis. Interestingly, binding of Nipbl to rDNA is dependent on RNA, suggesting that the active rRNA synthesis promotes Nipbl recruitment resulting in further stimulation of rRNA transcription. Nucleolar Nipbl dissociates from rDNA and relocalizes to the nucleolar cap structure in response to stress, suggesting that Nipbl is involved in stress–induced rRNA gene repression. Our results raise the possibility that defective ribosome biogenesis may also contribute to the CdLS phenotypes. Fascioscapulohumeral muscular dystrophy (FSHD) is associated with locus–restricted dysregulation of cohesin binding at D4Z4 macrosatellite repeat sequences on chromosome 4. The upregulation of the D4Z4–encoded <italic>DUX4<italic> retrogene is associated with FSHD. D4Z4 repeats contraction caused FSHD1 while FSHD2 has no repeat contraction. We previously found that H3K9me3, HP1γ and cohesin form a heterochromatin structure at D4Z4, which is lost in both FSHD1 and FSHD2. How this contributes to the disease, however, was unknown. We found that reducing H3K9me3 at D4Z4 results in <italic>DUX4<italic> upregulation accompanied with diminished binding of SMCHD1. SMCHD1 is an SMC homolog frequently mutated in FSHD2 and was shown to repress <italic>DUX4<italic> . Thus, the loss of H3K9me3 at D4Z4 contributes to dissociation of SMCHD1 and <italic>DUX4<italic> expression. My thesis research provided insights into the mechanisms of two cohesin–related developmental disorders, CdLS and FSHD, and may lead to development of new therapeutic strategies.