Pax5 regulates contraction of the immunoglobulin heavy chain (Igh) locus-an essential step in V(D)J recombination-by promoting chromatin loop extrusion via repression ofWaplexpression. Nuclear processes, such as V(D)J recombination, are orchestrated by the three-dimensional organization of chromosomes at multiple levels, including compartments(1)and topologically associated domains (TADs)(2,3)consisting of chromatin loops(4). TADs are formed by chromatin-loop extrusion(5-7), which depends on the loop-extrusion function of the ring-shaped cohesin complex(8-12). Conversely, the cohesin-release factor Wapl(13,14)restricts loop extension(10,15). The generation of a diverse antibody repertoire, providing humoral immunity to pathogens, requires the participation of allVgenes in V(D)J recombination(16), which depends on contraction of the 2.8-Mb-long immunoglobulin heavy chain (Igh) locus by Pax5(17,18). However, how Pax5 controlsIghcontraction in pro-B cells remains unknown. Here we demonstrate that locus contraction is caused by loop extrusion across the entireIghlocus. Notably, the expression of Wapl is repressed by Pax5 specifically in pro-B and pre-B cells, facilitating extended loop extrusion by increasing the residence time of cohesin on chromatin. Pax5 mediates the transcriptional repression ofWaplthrough a single Pax5-binding site by recruiting the polycomb repressive complex 2 to induce bivalent chromatin at theWaplpromoter. Reduced Wapl expression causes global alterations in the chromosome architecture, indicating that the potential to recombine allVgenes entails structural changes of the entire genome in pro-B cells.