The cohesin complex is at the heart of many chromosomal activities, including sister chromatid cohesion and transcriptional regulation1-3. Cohesin loading onto chromosomes depends on the Scc2/Scc4 cohesin loader complex4-6, but the chromatin features that form cohesin loading sites remain poorly understood. Here, we show that the RSC chromatin remodeling complex recruits budding yeast Scc2/Scc4 to broad nucleosome-free regions, that the cohesin loader itself helps to maintain. Consequently, inactivation of the cohesin loader or RSC complex have similar effects on nucleosome positioning, gene expression and sister chromatid cohesion. These results reveal an intimate link between local chromatin structure and higher order chromosome architecture. Our findings pertain to the similarities between two severe human disorders, Cornelia de Lange syndrome, caused by mutations in the human cohesin loader, and Coffin-Siris syndrome, resulting from mutations in human RSC complex components7-9. Both could arise from gene misregulation due to related changes in the nucleosome landscape.

Lymphomas are assumed to originate at different stages of lymphocyte development through chromosomal aberrations. Thus, different lymphomas resemble lymphocytes at distinct differentiation stages and show characteristic morphologic, genetic, and transcriptional features. Here, we have performed a microarray-based DNA methylation profiling of 83 mature aggressive B-cell non-Hodgkin lymphomas (maB-NHLs) characterized for their morphologic, genetic, and transcriptional features, including molecular Burkitt lymphomas and diffuse large B-cell lymphomas. Hierarchic clustering indicated that methylation patterns in maB-NHLs were not strictly associated with morphologic, genetic, or transcriptional features. By supervised analyses, we identified 56 genes de novo methylated in all lymphoma subtypes studied and 22 methylated in a lymphoma subtype-specific manner. Remarkably, the group of genes de novo methylated in all lymphoma subtypes was significantly enriched for polycomb targets in embryonic stem cells. De novo methylated genes in all maB-NHLs studied were expressed at low levels in lymphomas and normal hematopoietic tissues but not in nonhematopoietic tissues. These findings, especially the enrichment for polycomb targets in stem cells, indicate that maB-NHLs with different morphologic, genetic, and transcriptional background share a similar stem cell-like epigenetic pattern. This suggests that maB-NHLs originate from cells with stem cell features or that stemness was acquired during lymphomagenesis by epigenetic remodeling. (Blood. 2009; 113:2488-2497 IntroductionAberrant DNA methylation is a hallmark of cancer. Virtually all cancer types are associated with alterations of the methylome. These include global DNA hypomethylation, mostly targeting DNA repeats, and hypermethylation of CpG islands located in the promoter regions of tumor suppressor genes. [1][2][3][4] It is widely accepted that tumor suppressor gene inactivation by DNA hypermethylation allows the tumor clone to obtain a selective (eg, proliferative) advantage. However, recent reports have provided evidence for an instructive mechanism behind aberrant DNA methylation in cancer, which might indicate that specific sequences are predisposed to acquire epigenetic alterations. [5][6][7][8][9] Remarkably, 3 independent reports have recently shown that a highly significant proportion of genes becoming hypermethylated in cancer were already repressed at the embryonic stem cell (ESC) stage by polycomb group (PcG) marks. 7-9 These findings are considered to support the "cancer stem cell theory" in which The online version of this article contains a data supplement.The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked ''advertisement'' in accordance with 18 USC section 1734. For personal use only. on May 13, 2018. by guest www.bloodjournal.org From aberrant epigenetic changes of PcG target genes occurring in a cell with stem cell features might represent the ...

The establishment of stable sister chromatid cohesion during DNA replication requires acetylation of the chromosomal cohesin complex by the replication fork-associated acetyltransferase Eco1. Cohesin acetylation is thought to facilitate replication fork progression by counteracting an as yet ill-defined cohesion "antiestablishment" activity imposed by the Wapl protein. Here, using budding yeast, we find no evidence that cohesin acetylation must overcome Wapl during replication fork progression. Instead, Wapl emerges as a negative regulator of cohesion maintenance in G2, a function that it likely exerts through its role as destabilizer of unacetylated, chromosome-bound cohesin. Our results suggest that acetylation renders cohesin Wapl-resistant from S phase onward until mitosis. In the absence of Wapl, sister chromatid cohesion functions well, suggesting that Wapl partakes in a cohesin function outside of sister chromatid cohesion. We find that Wapl is not required for cohesin's known role in transcriptional regulation. Rather, cells lacking Wapl display increased chromosome condensation in both interphase and mitosis. Thus, as a conserved regulator of cohesin dynamics on chromosomes, Wapl controls cohesion maintenance after its establishment in S phase and adjusts the chromosome condensation status.

DNA methylation and the machinery involved in epigenetic regulation are key elements in the maintenance of cellular homeostasis. Epigenetic mechanisms are involved in embryonic development and the establishment of tissue-specific expression, X-chromosome inactivation and imprinting patterns, and maintenance of chromosome stability. The balance between all the enzymes and factors involved in DNA methylation and its interpretation by different groups of nuclear factors is crucial for normal cell behaviour. In cancer and other diseases, misregulation of epigenetic marks is a common feature, also including DNA methylation and histone posttranslational modifications. In this scenario, it is worth mentioning a family of proteins characterized by the presence of a methyl-CpGbinding domain (MBDs) that are involved in interpreting the information encoded by DNA methylation and the recruitment of the enzymes responsible for establishing a silenced state of the chromatin. The generation of novel aberrantly hypermethylated regions during cancer development and progression makes MBD proteins interesting targets for their biological and clinical implications. British Journal of Cancer (2008) DNA METHYLATION AND ITS MEDIATORSDNA methylation is one of the most important mechanisms for epigenetic silencing in mammals. It is a key element in heterochromatin formation and maintenance, and is involved in processes such as X-chromosome inactivation and gene imprinting. DNA methylation also occurs at repetitive sequences to ensure chromosome stability. DNA methylation is developed by a family of DNA methyltransferase enzymes (DNMTs) that add a methyl group to the fifth carbon position of cytosine when followed by a guanine nucleotide. Methylation of DNA is accompanied by histone post-translational modifications that modulate DNA function, regulating chromatin structure and determining the transcriptional state of the DNA wrapped around it.The crosstalk between DNA methylation and histone modifications is established by different nuclear factors. Among them, it is particularly remarkable a family of proteins that contain a MethylCpG-binding domain commonly known as MBD proteins that recognises single methylated CpG dinucleotide (Hendrich and Bird, 1998). MBD family members recruit histone modifying and chromatin remodeling complexes to methylated sites. The MBD family of proteins is composed by five members namely MeCP2, MBD1, MBD2, MBD3 and MBD4. MeCP2 was the first characterised member and its 70 amino acids region corresponding to the MBD was used for database identification of the remaining MBD containing proteins. The binding affinity of MBD proteins differs between them, as was demonstrated that MBD2 is the MBD protein with higher methylated DNA-binding affinity in vitro .