title: Nipbl and mediator cooperatively regulate gene expression to control limb development.
abstract: Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de Lange Syndrome (CdLS), the most common "cohesinopathy". It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements. Here we use zebrafish and mouse models of CdLS to examine how transcriptional changes caused by Nipbl deficiency give rise to limb defects, a common condition in individuals with CdLS. In the zebrafish pectoral fin (forelimb), knockdown of Nipbl expression led to size reductions and patterning defects that were preceded by dysregulated expression of key early limb development genes, including fgfs, shha, hand2 and multiple hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis revealed many similar gene expression changes, as well as altered expression of additional classes of genes that play roles in limb development. In both species, the pattern of dysregulation of hox-gene expression depended on genomic location within the Hox clusters. In view of studies suggesting that Nipbl colocalizes with the mediator complex, which facilitates enhancer-promoter communication, we also examined zebrafish deficient for the Med12 Mediator subunit, and found they resembled Nipbl-deficient fish in both morphology and gene expression. Moreover, combined partial reduction of both Nipbl and Med12 had a strongly synergistic effect, consistent with both molecules acting in a common pathway. In addition, three-dimensional fluorescent in situ hybridization revealed that Nipbl and Med12 are required to bring regions containing long-range enhancers into close proximity with the zebrafish hoxda cluster. These data demonstrate a crucial role for Nipbl in limb development, and support the view that its actions on multiple gene pathways result from its influence, together with Mediator, on regulation of long-range chromosomal interactions.
authors.affiliation: Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America; Center for Complex Biological Systems, University of California, Irvine, Irvine California; Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
authors.forename: Akihiko
authors.initials: A
authors.lastname: Muto
authors.affiliation: Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Ikeda
authors.affiliation: Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America; Center for Complex Biological Systems, University of California, Irvine, Irvine California.
authors.forename: Martha E
authors.initials: ME
authors.lastname: Lopez-Burks
authors.affiliation: Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kikuchi
authors.affiliation: Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan; Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, California, United States of America.
authors.forename: Anne L
authors.initials: AL
authors.lastname: Calof
authors.affiliation: Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America; Center for Complex Biological Systems, University of California, Irvine, Irvine California.
authors.forename: Arthur D
authors.initials: AD
authors.lastname: Lander
authors.affiliation: Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America; Center for Complex Biological Systems, University of California, Irvine, Irvine California.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Schilling
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D018797:Cell Cycle Proteins; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D005121:Extremities / Q000196:embryology*; D018507:Gene Expression Regulation, Developmental; D005801:Genes, Homeobox; D057895:Haploinsufficiency / Q000235:genetics; D051379:Mice; D018345:Mice, Knockout; D038081:Organogenesis / Q000235:genetics*; D010641:Phenotype; D011485:Protein Binding; D014157:Transcription Factors / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism*; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism*; D000097722:Cohesins
chemical_list: D018797:Cell Cycle Proteins; D002843:Chromatin; D014157:Transcription Factors; D029961:Zebrafish Proteins; C546088:Nipbl protein, mouse; C570219:nipblb protein, zebrafish; D000097722:Cohesins