Mammalian genomes contain several billion base pairs of DNA that are packaged in chromatin fibres. At selected gene loci, cohesin complexes have been proposed to arrange these fibres into higher-order structures, but how important this function is for determining overall chromosome architecture and how the process is regulated are not well understood. Using conditional mutagenesis in the mouse, here we show that depletion of the cohesin-associated protein Wapl stably locks cohesin on DNA, leads to clustering of cohesin in axial structures, and causes chromatin condensation in interphase chromosomes. These findings reveal that the stability of cohesin-DNA interactions is an important determinant of chromatin structure, and indicate that cohesin has an architectural role in interphase chromosome territories. Furthermore, we show that regulation of cohesin-DNA interactions by Wapl is important for embryonic development, expression of genes such as c-myc (also known as Myc), and cell cycle progression. In mitosis, Wapl-mediated release of cohesin from DNA is essential for proper chromosome segregation and protects cohesin from cleavage by the protease separase, thus enabling mitotic exit in the presence of functional cohesin complexes.

Blimp1 is an essential regulator of plasma cells. Here we studied its functions in plasmablast differentiation by identifying regulated Blimp1 target genes. Blimp1 promoted plasmablast migration and adhesion. It repressed several transcription factor genes and Aicda, thus silencing Bcell-specific gene expression, antigen presentation and class switch recombination in plasmablasts. It directly activated genes, leading to increased expression of the plasma cell regulator IRF4 and proteins involved in immunoglobulin secretion. Blimp1 induced immunoglobulin gene transcription by controlling Igh and Igk 3' enhancers and regulated the posttranscriptional expression switch from the membrane-bound to secreted immunoglobulin heavy-chain by activating Ell2. Notably, Blimp1 recruited chromatin-remodeling and histone-modifying complexes to regulate its target genes. Hence, many essential functions of plasma cells are under Blimp1 control.

Polycomb complexes establish chromatin modifications for maintaining gene repression and are essential for embryonic development in mice. Here we use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb-repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas simultaneous loss of PRC1 and PRC2 abrogates differentiation. On the molecular level, the differentiation defect is caused by the derepression of a set of genes that is redundantly repressed by PRC1 and PRC2 in ES cells. Furthermore, we find that genomic repeats are Polycomb targets and show that, in the absence of Polycomb complexes, endogenous murine leukemia virus elements can mobilize. This indicates a contribution of the Polycomb group system to the defense against parasitic DNA, and a potential role of genomic repeats in Polycomb-mediated gene regulation.[Keywords: Polycomb; histone modification; chromatin; embryonic stem cells; tumor; retrovirus] Supplemental material is available at http://www.genesdev.org.

Pax5 controls the identity and development of B cells by repressing lineage-inappropriate genes and activating B-cell-specific genes. Here, we used genome-wide approaches to identify Pax5 target genes in pro-B and mature B cells. In these cell types, Pax5 bound to 40% of the cisregulatory elements defined by mapping DNase I hypersensitive (DHS) sites, transcription start sites and histone modifications. Although Pax5 bound to 8000 target genes, it regulated only 4% of them in pro-B and mature B cells by inducing enhancers at activated genes and eliminating DHS sites at repressed genes. Pax5-regulated genes in pro-B cells account for 23% of all expression changes occurring between common lymphoid progenitors and committed pro-B cells, which identifies Pax5 as an important regulator of this developmental transition. Regulated Pax5 target genes minimally overlap in pro-B and mature B cells, which reflects massive expression changes between these cell types. Hence, Pax5 controls B-cell identity and function by regulating distinct target genes in early and late B lymphopoiesis. The EMBO Journal (2012) (Nutt and Kee, 2007). The helix-loop-helix protein E2A and the early B-cell factor EBF1 specify the B-cell lineage by activating the expression of B-lymphoid genes in pre-pro-B cells Treiber et al, 2010). Pax5 subsequently controls B-cell commitment at the transition to the pro-B cell stage by restricting the developmental potential of lymphoid progenitors to the B-cell lineage, as shown by the fact that Pax5-deficient pro-B cells are still able to differentiate into most hematopoietic cell types in vitro and in vivo (Nutt et al, 1999;Medvedovic et al, 2011). At the molecular level, Pax5 fulfills a dual role by repressing B-lineage-inappropriate genes to suppress alternative lineage options and by simultaneously activating B-cell-specific genes to promote B-cell development (Nutt et al, 1999;Medvedovic et al, 2011). Gene expression analyses of wild-type and Pax5-deficient pro-B cells identified 110 Pax5-repressed and 170 Pax5-activated genes, which code for key regulatory and structural proteins involved in transcriptional control, receptor signalling, adhesion, migration and immune function (Delogu et al, 2006;Schebesta et al, 2007;Pridans et al, 2008). Pax5 regulates these gene expression changes by inducing active chromatin at activated target genes and eliminating active chromatin at repressed genes in pro-B cells . Notably, Pax5 induces these chromatin and transcription changes by recruiting chromatin-remodelling, histone-modifying and basal transcription factor complexes to its target genes, which identifies Pax5 as an epigenetic regulator of B-cell commitment .Pax5 is expressed throughout B-cell development from pro-B cells in the bone marrow to mature B cells in peripheral lymphoid organs (Fuxa and Busslinger, 2007), where it plays an important role in the generation and function of distinct mature B-cell types (Horcher et al, 2001;Medvedovic et al, 2011). Pax5 is essential for maintaining the B-cell gene exp...