Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation

Defective silencing of retrotransposable elements has been linked to inflammageing, cancer and autoimmune diseases. However, the underlying mechanisms are only partially understood. Here we implicate the histone H3.3 chaperone Daxx, a retrotransposable element repressor inactivated in myeloid leukaemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx alters the chromatin landscape, H3.3 distribution and histone marks of haematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional programme for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to develop an autoinflammatory skin disease. While these molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx, haematopoietic progenitors in these mice show unique chromatin and transcriptome alterations, suggesting an interaction between these two pathways. Overall, our findings implicate retrotransposable element silencing in haematopoiesis and suggest a cross-talk between the H3.3 loading machinery and the pioneer transcription factor Pu.1.

Grafting vigour is associated with DNA de-methylation in eggplant

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.

New insights into the functional role of retrotransposon dynamics in mammalian somatic cells

Retrotransposons are genetic elements present across all eukaryotic genomes. While their role in evolution is considered as a potentially beneficial natural source of genetic variation, their activity is classically considered detrimental due to their potentially harmful effects on genome stability. However, studies are increasingly shedding light on the regulatory function and beneficial role of somatic retroelement reactivation in non-pathological contexts. Here, we review recent findings unveiling the regulatory potential of retrotransposons, including their role in noncoding RNA transcription, as modulators of mammalian transcriptional and epigenome landscapes. We also discuss technical challenges in deciphering the multifaceted activity of retrotransposable elements, highlighting an unforeseen central role of this neglected portion of the genome both in early development and in adult life.

Global DNA methylation analysis in relapsed Pre-B cell acute lymphoblastic leukemia

Reliable biomarkers for relapsed acute lymphoblastic leukemia are scarce. Currently, minimal residual disease (MRD) is the best method in predicting a relapse event, but is invasive to the patient. In addition, high quantity amount of cells are needed for flow-MRD and PCR-MRD requires stable IG-TCR rearrangements. An alternative MRD strategy may involve DNA based technologies involving mass spectrometry that have the potential to monitor the progression of ALL. There are also many recurrent karyotypes that stratify patients into either low-standard risk or high-risk of relapsing. However, many patients with favorable karyotypes (e.g. highhyperdiploidy, ETV6/RUNX1) still experience one or more relapse events. DNA methylation has the potential to serve as a biomarker throughout the course of the disease in several aspects. DNA methylation associated microarrays have demonstrated the ability to stratify patients into their recurrent cytogenetic subtype. Further, others have identified CpG loci that have the potential to stratify patients at diagnosis that are at risk of relapsing. This dissertation identified differential DNA methylation between matched diagnosis and relapsed patients by creating a methylome profile (MIRA-seq) for each patient. We are the first to report global hypomethylation that occurs at relapse, predominately within retrotransposable elements. In addition, genes that exhibited 5' regulatory aberrant methylation from diagnosis to relapse were identified. Some of the genes harboring epigenetic lesions may be considered an "epidriver" of ALL. A "driver" mutation can be defined as a mutation that can directly or indirectly offer a Darwinian advantage in terms of growth for leukemic blasts. The "epi" component refers to the nature of the mutation as epigenetic in origin and in the context of this study is synonymous with deviant or aberrant methylation. Further, our MIRA-seq study in canine acute leukemia observed epigenetic lesions of epidriver genes that were also present at diagnosis and relapse in human ALL. Lastly, MIRA-seq profiles from ALL patients at diagnosis who either did or did not go on to relapse were compared against each other in order to identify individual CpGs using pyrosequencing that were associated with relapse (prognostic). These combined efforts were done with the foresight of identifying potential novel targets that exist as epidrivers of ALL or loci that hold prognostic power at diagnosis. This dissertation builds upon others who have previously identified relapse-associated biomarkers with implications of improved patient care and risk stratification.

Cytogenetic Characterization of Two Metynnis Species (Characiformes, Serrasalmidae) Reveals B Chromosomes Restricted to the Females

Karyotypes and chromosomal characteristics with focus on B chromosomes of 2 species of the serrasalmid genus Metynnis, namely M. lippincottianus and M. maculatus, were examined using conventional (C-banding) and molecular (FISH mapping of minor and major rDNAs and Rex1, Rex3, and Rex6 retrotransposable elements) protocols. Both species possessed a diploid chromosome number of 2n = 62 and karyotypes composed of 32 metacentric + 28 submetacentric + 2 subtelocentric and 32 metacentric + 26 submetacentric + 4 subtelocentric, respectively; one small B element was found in the female genome of M. lippincottianus. C-banding revealed heterochromatin in the pericentromeric and terminal portions of all chromosomes of both species; the B chromosome was entirely heterochromatic. FISH showed 18S rDNA sites in 2 chromosome pairs in both species (pairs 19 and 22), and a large block in the B chromosome, while 5S rDNA signals were detected in the first pair of subtelocentric chromosomes in both species, moreover in M. maculatus an additional labeled pair 4 was observed. Mapping of the Rex1, Rex3, and Rex6 retrotransposable elements in the genomes of M. lippincottianus and M. maculatus indicated that they were dispersed throughout nearly all the chromosomes of the complement, except for the B chromosome of M. lippincottianus.

A nematode retrotransposon in the common shrew: horizontal transfer between parasite and host

Reports of horizontal transposon and gene transfers involving metazoan species has increased with the sequencing of their genomes. Horizontal transfer could be facilitated by the intimate relationship between a parasite and its hosts. To date, two studies have identified horizontal transfer of RTEs, a class of retrotransposable elements, involving parasites: ticks might act as vector for BovB between ruminants and squamates, and AviRTE was transferred between birds and parasitic nematodes. We wanted to know if parasitic nematodes are involved in other cases of horizontal transfer of RTEs. We searched 33 mSammalian RTEs in 81 nematode assemblies, and 10 nematode RTEs in 98 mammalian assemblies. We identified RTE1õ Sar from Sorex araneus, the common shrew, in parasitic nematodes and show that it originates from nematodes. To exclude contamination of the S. araneus assembly, we developed an approach that uses long reads and paired-end reads. With phylogenetic analysis and copy age estimation, we show that RTE1_Sar was horizontally transferred from nematodes to S. araneus. We confirm horizontal transfer of RTEs in host-parasite interactions, and we present a new method to distinguish between contamination and horizontal transfer.