Search

International audience; The lack of a consensus DNA sequence defining replication origins in mammals has led researchers to consider chromatin as a means to specify these regions. However, to date, there is no mechanistic understanding of how this could be achieved and maintained given that nucleosome disruption occurs with each fork passage and with transcription. Here, by genome-wide mapping of the de novo deposition of the histone variants H3.1 and H3.3 in human cells during S phase, we identified how their dual deposition mode ensures a stable marking with H3.3 flanked on both sides by H3.1. These H3.1/H3.3 boundaries correspond to the initiation zones of early origins. Loss of the H3.3 chaperone HIRA leads to the concomitant disruption of H3.1/H3.3 boundaries and initiation zones. We propose that the HIRA-dependent deposition of H3.3 preserves H3.1/H3.3 boundaries by protecting them from H3.1 invasion linked to fork progression, contributing to a chromatin-based definition of early replication zones.; L'absence d'une séquence d'ADN consensuelle définissant les origines de réplication chez les mammifères a conduit les chercheurs à considérer la chromatine comme un moyen de spécifier ces régions. Cependant, à ce jour, il n'y a pas de compréhension mécaniste de la façon dont cela pourrait être réalisé et maintenu étant donné que la rupture des nucléosomes se produit à chaque passage de fourche et avec la transcription. Ici, en cartographiant à l'échelle du génome le dépôt de novo des variants d'histone H3.1 et H3.3 dans les cellules humaines pendant la phase S, nous avons identifié comment leur mode de dépôt double assure un marquage stable avec H3.3 flanqué des deux côtés par H3.1. Ces frontières H3.1/H3.3 correspondent aux zones d'initiation des origines précoces. La perte du chaperon H3.3 HIRA conduit à la perturbation concomitante des frontières H3.1/H3.3 et des zones d'initiation. Nous proposons que le dépôt de H3.3 dépendant de HIRA préserve les frontières H3.1/H3.3 en les protégeant de l'invasion de H3.1 liée à la progression des fourches, contribuant ainsi à une définition chromatinienne des zones de réplication précoce.

Stormwater from urban, industrial and rural areas is very often discharged into recipient water bodies without any treatment. This is now changing in many parts of the word, especially in Europe due to The EU Water Framework Directive (European Union, 2000). According to the new policy, will probably stormwater that has often small concentrations but complex mix of different organic and inorganic pollutants has to be treated. Many different systems have been used, such as wetlands and soil infiltration trenches, among others. Sawdust has many times been reported as a good sorbent used for removing mostly toxic metals from wastewaters. However, in most cases, studies have been carried out with distilled water spiked with, for instance, 1-2 different toxic metals. Very few studies have used real wastewater and even less have studied removal of metals from stormwater using sorbent such as sawdust. Sawdust has also drawbacks, since it may release potentially hazardous substances as tannins: lignin, phenolic compounds, resin acids and overall high COD concentrations which results in oxygen depletion in the recipient water bodies. In this paper, the results of using sawdust as sorbent for removal of heavy metal from stormwater with different pollutants are presented.

Acute myeloid leukemias (AMLs) result from a series of genetic events occurring in a stem or progenitor hematopoietic cell that gives rise to their clonal expansion and an impaired capacity to differentiate. To circumvent the genetic heterogeneity of AML patient cohorts, we have developed a model system, driven by the MLL-AF9 (MA9) oncogene, to generate multiple human leukemias using progenitor cells from a single healthy donor. Through stepwise RNA-sequencing data generated using this model and AML patients, we have identified consistent changes associated with MA9-driven leukemogenesis and demonstrate that no recurrent secondary mutations are required. We identify 39 biomarkers whose high expression level is specific to this genetic subtype of AML and validate that many of these have diagnostic utility. We further examined one biomarker, the receptor tyrosine kinase (RTK) RET, and show through shRNA knockdowns that its expression is essential for in vivo and in vitro growth of MA9-AML. These results highlight the value of novel human models of AML derived from single donors using specific oncogenic fusions to understand their biology and to uncover potential therapeutic targets.

Next generation DNA sequencing has provided significant insights into the genetic determinants of acute myeloid leukemia (AML). Large scale sequencing studies of AML patient cohorts have revealed a remarkable level of genetic heterogeneity between patients who nevertheless have the same disease phenotype. As a solution to the problem of extensive genetic diversity between patients, we have modified a previously published model system in order to generate multiple human leukemias from CD34+ cord blood cells from a single healthy donor. A human MLL-AF9 (MA9) fusion gene is retrovirally introduced into the donor cells which are then cultured for 30 days before being transplanted into immunocompromised (NSG) mice that subsequently develop either AML or acute B-cell lymphoblastic leukemia (B-ALL) after ~24 weeks. We have now generated 22 leukemias from 4 single donors and have performed RNA-seq on the samples during their step-wise leukemic transformation (i.e. CD34+ cells, CD34+ cells with MA9, and the resulting leukemias). We have compared these data to RNA-seq data we have generated for several pediatric AML patients with MA9 translocations, as well as normal blood cells and other tissues. This analysis has revealed 39 candidate genes with an expression pattern highly specific for MA9 AMLs. Interestingly, we can find no evidence for secondary mutations acquired by the human leukemias in our model system, suggesting the human MA9 translocation is sufficient to generate leukemias in this context. To understand the epigenetic impact of the MA9 fusion gene, we have examined the DNA methylation changes at each stage in our model system using a capture survey approach (e.g. Human Methyl-Seq; Agilent) and used this same approach for several primary patient samples with MLL translocations. These data have been correlated with gene expression changes within the model system and have revealed a number of specific changes with relevance for the process of transformation. Lastly, functional assessment of specific candidate genes through shRNA knock-down experiments has shown that at least some of these candidate genes, which are known oncogenes in other tumor types, are essential for MA9 AML. In summary, the combination of RNA-seq data from patient and single donor model AMLs has highlighted consistent genetic changes associated with this AML sub-group, and has also revealed novel potential therapeutic targets. Citation Format: Frederic Barabe, Magalie Celton, Audrey Forest, Anne Bergeron, Radia Johnson, Laurine Gil, Angélique Bellemare-Pelletier, Sonia Cellot, Josee Hebert, Etienne Gagnon, Brian T. Wilhelm. Integrated genetic and epigenetic analysis of model and patient acute myeloid leukemias. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-14.

Transcription by RNA polymerase II (RNAPII) is coupled to mRNA processing and chromatin modifications via the C-terminal domain (CTD) of its largest subunit, consisting of multiple repeats of the heptapeptide YSPTSPS. Pioneering studies showed that CTD serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Genome-wide analyses challenged this idea, suggesting that this cycle is not uniform among different genes. Moreover, the respective role of enzymes responsible for CTD modifications remains controversial. Here, we systematically profiled the location of the RNAPII phosphoisoforms in wild-type cells and mutants for most CTD modifying enzymes. Together with results of in vitro assays, these data reveal a complex interplay between the modifying enzymes, and provide evidence that the CTD cycle is uniform across genes. We also identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes.

Acute myeloid leukemia (AML) occurs when hematopoietic progenitor cells acquire genetic defects blocking the regulation of normal growth and differentiation. Although recurrent translocations have been identified in AML, almost half of adult AML patients present with a normal karyotype (NK-AML). While cell line models exist to study AML, they frequently have abnormal/unstable karyotypes, while primary cells from NK-AML patients are difficult to maintain in vitro. Here we provide a thorough molecular characterization of a recently established cell line, CG-SH, which has normal cytogenetics, representing a useful new model for NK-AML. Using high-throughput DNA sequencing, we first defined the genetic background of this cell line. In addition to identifying potentially deleterious SNVs in genes relevant to AML, we also found insertions in both GATA2 and EZH2, two genes previously linked to AML. We further characterized the growth of this model system in vitro with a cytokine mix that promotes faster cell growth. We assessed gene expression changes after the addition of cytokines to the culture media and found differential expression in genes implicated in proliferation, apoptosis and differentiation. Our results provide a detailed molecular characterization of genetic defects in this cell line derived from an NK-AML patient.

Adenoviral gene transfer into human B lymphocytes and haematopoietic progenitors would allow the characterization of their function on cellular growth, differentiation and survival. Efficient gene expression is however strongly dependent on the promoter used. In this study, we investigated the relative strength of various promoters by following and measuring the expression of the reporter gene EYFP in human peripheral B lymphocytes, cord blood CD34(+) cells and the megakaryocytic cell line M-07e. The murine PGK promoter provided the best level of transgene expression in CD34(+) cells among the four promoters tested, followed closely by the CMV promoter, and to a lesser extend by a CMV promoter with a beta-globin/IgG chimeric intron, whereas the human CD40 promoter provided the lowest levels of expression. In contrast, the strongest promoters in B lymphocytes were the two CMV promoters. Surprisingly, even the best promoters were unable to induce transgene expression in more than 75-80% of the primary B and CD34(+) cells, even though 100% of the cells were infected. Finally and in contrast to retroviruses, only a minority of B lymphocytes and CD34(+) cells were able to induce the transcription of IRES-containing bicistronic expression cassettes from adenovirus.

A role for variant histone H2A.Z in gene expression is now well established but little is known about the mechanisms by which it operates. Using a combination of ChIP–chip, knockdown and expression profiling experiments, we show that upon gene induction, human H2A.Z associates with gene promoters and helps in recruiting the transcriptional machinery. Surprisingly, we also found that H2A.Z is randomly incorporated in the genome at low levels and that active transcription antagonizes this incorporation in transcribed regions. After cessation of transcription, random H2A.Z quickly reappears on genes, demonstrating that this incorporation utilizes an active mechanism. Within facultative heterochromatin, we observe a hyper accumulation of the variant histone, which might be due to the lack of transcription in these regions. These results show how chromatin structure and transcription can antagonize each other, therefore shaping chromatin and controlling gene expression., Author Summary DNA in living cells is packaged into chromatin by histones and non-histone proteins. This packaging is very dynamic, allowing the controlled access of regulatory proteins such as transcription factors to DNA. Most chromatin is packaged with so-called canonical histones; namely H2A, H2B, H3, and H4. In some regions, however, variant histones replace canonical histones, creating special chromatin regions. Here we show that the variant histone H2A.Z is dynamically recruited to promoter regions where it helps in the recruitment of RNA polymerase II, the enzyme responsible for the first step of gene expression. In addition, we show that H2A.Z also associates randomly in the genome, but these molecules are removed during the passage of RNA polymerase II. In non-transcribed regions, H2A.Z accumulates in large domains called heterochromatin. We propose that a battle between random H2A.Z deposition and RNAPII-dependent H2A.Z eviction shapes the chromatin landscape.