Statistical learning quantifies transposable element-mediated cis-regulation.

BACKGROUND: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryogenesis to innate immune responses. Because of their repetitive nature, TEs have the potential to form CRE platforms enabling the coordinated and genome-wide regulation of protein-coding genes by only a handful of trans-acting transcription factors (TFs). RESULTS: Here, we directly test this hypothesis through mathematical modeling and demonstrate that differences in expression at protein-coding genes alone are sufficient to estimate the magnitude and significance of TE-contributed cis-regulatory activities, even in contexts where TE-derived transcription fails to do so. We leverage hundreds of overexpression experiments and estimate that, overall, gene expression is influenced by TE-embedded CREs situated within approximately 500 kb of promoters. Focusing on the cis-regulatory potential of TEs within the gene regulatory network of human embryonic stem cells, we find that pluripotency-specific and evolutionarily young TE subfamilies can be reactivated by TFs involved in post-implantation embryogenesis. Finally, we show that TE subfamilies can be split into truly regulatorily active versus inactive fractions based on additional information such as matched epigenomic data, observing that TF binding may better predict TE cis-regulatory activity than differences in histone marks. CONCLUSION: Our results suggest that TE-embedded CREs contribute to gene regulation during and beyond gastrulation. On a methodological level, we provide a statistical tool that infers TE-dependent cis-regulation from RNA-seq data alone, thus facilitating the study of TEs in the next-generation sequencing era.

Primate-specific transposable elements shape transcriptional networks during human development.

The human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.

Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections.

Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development.

A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.

The human forebrain has expanded in size and complexity compared to chimpanzees despite limited changes in protein-coding genes, suggesting that gene expression regulation is an important driver of brain evolution. Here, we identify a KRAB-ZFP transcription factor, ZNF558, that is expressed in human but not chimpanzee forebrain neural progenitor cells. ZNF558 evolved as a suppressor of LINE-1 transposons but has been co-opted to regulate a single target, the mitophagy gene SPATA18. ZNF558 plays a role in mitochondrial homeostasis, and loss-of-function experiments in cerebral organoids suggests that ZNF558 influences developmental timing during early human brain development. Expression of ZNF558 is controlled by the size of a variable number tandem repeat that is longer in chimpanzees compared to humans, and variable in the human population. Thus, this work provides mechanistic insight into how a cis-acting structural variation establishes a regulatory network that affects human brain evolution.

Alleged Allergy to Penicillin and Isolation Issues: Toward New Practices for French Navy?

INTRODUCTION: According to the literature, 8% of the population claim to have an allergy to penicillin. Allergy tests show that 90% of these patients tolerate this molecule. Physicians working in the French Navy are faced with situations of real isolation and only have a limited number of antibiotics on board, the majority of which are penicillins. They must anticipate the risks linked to the prescription of antibiotics before the mission. However, there is no French recommendation, either military or civilian, intended for general practitioners clarifying the management and allergy assessments of patients alleging a history of allergy to penicillin. This study is the first to evaluate the professional practices of French military practitioners taking care of these patients. The main objective was to evaluate the proportion of sailors who reported an allergy to penicillin and who have never been referred for a consultation with an allergist, by studying the medical files of all the submariners working on the submersible ballistic nuclear submarines squadron in Brest. The secondary objective was to compare these data with the practices of Navy doctors by means of questionnaires. MATERIAL AND METHODS: Our work is composed of two parts: monocentric study of the digital and paper medical files of Brest submariners (n = 814) looking for allergist consultation reports in cases alleging an allergy to penicillin, then comparison with a multicentric collection of all Navy doctors' practices collected by an anonymized questionnaire (n = 37 out of 53 practicing at the time of the study). RESULTS: Forty-seven subjects out of 814 alleged an allergy to penicillin (5.8%). Among them, only 12 (25.5%) had undergone allergy tests, of which 3 (6.4%) were confirmed to be allergic, with no cross-reaction between ß-lactam antibiotics. Yet, according to the questionnaire, 25 doctors (67%) report referring their patients to an allergist and 16 (43%) report having had difficulties at sea in connection with the prescription of antibiotics for these patients. CONCLUSIONS: A study of medical records shows that the allergic risk is not anticipated for 74.5% of patients labeled allergic, despite the difficulties encountered at sea. Standardization of practices within the French Navy is necessary to avoid the prescription of second-line antibiotics, less effective and sometimes unavailable on board, and to improve patient safety in isolation situations. In agreement with French military allergists, we propose, in this article, guidelines for a systematic exploration of allegations of allergy to penicillin in the French Navy.

Subsurface Confinement: Evidence from Submariners of the Benefits of Mindfulness.

OBJECTIVES: The subsurface ballistic missile nuclear submarine (SSBN) is an extreme professional environment in which personnel are both isolated and confined during patrols, which can last longer than 2 months. This environment is known to degrade submariners' mood and cognition. METHODS: This exploratory, empirical study followed a cohort of 24 volunteer submariners. Dispositional mindfulness was assessed with the Freiburg Mindfulness Inventory, in order to identify two groups (mindful and non-mindful) and compare change in emotional state, interoception, and health behaviors during the patrol. RESULTS: Overall, psychological health deteriorated during the patrol. However, mindful submariners demonstrated better psychological adaptation and interoception than the non-mindful group. This was associated with better subjective health behaviors (sleeping and eating). CONCLUSIONS: Dispositional mindfulness appears to protect against the negative effects of long-term containment in a professional environment, such as a submarine patrol. Our work highlights that mindfulness may help individuals to cope with stress in such situations. Developing mindfulness could also be an important preventive healthcare measure during quarantine imposed by the outbreak of a serious infectious disease.

Is Regular Physical Activity Practice During a Submarine Patrol an Efficient Coping Strategy?

Introduction: A nuclear-powered ballistic missile submarine (SSBN) is a singular professional environment, exposing personnel to isolation and confinement amidst sophisticated technology for the duration of a mission. Submariners see their mood and cognition deteriorate as their mission progresses. With regard to the benefits of physical activity (PA) on mental health, this study evaluates the impact of regular PA on the maintenance of thymia and sensory functioning during patrols. Method: This pragmatic exploratory cohort follow-up study included 29 volunteer submariners before, during and 1 month after return from patrol. PA practice was evaluated by a daily self-questionnaire. This allowed submariners to be classified into two groups according to the median of the total duration in minutes of a sport practiced during the patrol (PA practicing submariners and non-practicing). Changes in mood and psychological activation, health (including sleep), unipodal stability, and accommodation distances were compared between the two groups over the period of the patrol. Results: Overall thymic functioning deteriorated during the patrol. Submariners who practice PA maintain a stable level of activation unlike non-practicing PA submariners, but they exhibited both worse general health and sleep at recovery. For these personnel, postural control is better at the end of the patrol and far visual accommodation tends to be preserved. Conclusion: PA during patrol alone is not sufficient to compensate for the thymic dysregulation induced by the SSBN environment. Nevertheless, it seems to help in maintaining an exteroceptive functioning. This exploratory study suggests directions for possible future research on physical activity associated with sensory stimulation amongst submariners, and more generally amongst people working in isolated and confined environments.

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons.

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influence this process is largely unknown. We identify ZNF417 and ZNF587 as primate-specific KZFPs repressing HERVK (human endogenous retrovirus K) and SVA (SINE-VNTR-Alu) integrants in human embryonic stem cells (ESCs). Expressed in specific regions of the human developing and adult brain, ZNF417/587 keep controlling TEeRS in ESC-derived neurons and brain organoids, secondarily influencing the differentiation and neurotransmission profile of neurons and preventing the induction of neurotoxic retroviral proteins and an interferon-like response. Thus, evolutionarily recent KZFPs and their TE targets partner up to influence human neuronal differentiation and physiology.

The H3K9 Methylation Writer SETDB1 and its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells.

SETDB1 (SET Domain Bifurcated histone lysine methyltransferase 1) is a key lysine methyltransferase (KMT) required in embryonic stem cells (ESCs), where it silences transposable elements and DNA repeats via histone H3 lysine 9 tri-methylation (H3K9me3), independently of DNA methylation. The H3K9 methylation reader M-Phase Phosphoprotein 8 (MPP8) is highly expressed in ESCs and germline cells. Although evidence of a cooperation between H3K9 KMTs and MPP8 in committed cells has emerged, the interplay between H3K9 methylation writers and MPP8 in ESCs remains elusive. Here, we show that MPP8 interacts physically and functionally with SETDB1 in ESCs. Indeed, combining biochemical, transcriptomic and genomic analyses, we found that MPP8 and SETDB1 co-regulate a significant number of common genomic targets, especially the DNA satellite repeats. Together, our data point to a model in which the silencing of a class of repeated sequences in ESCs involves the cooperation between the H3K9 methylation writer SETDB1 and its reader MPP8.

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification.

Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin-inducing KAP1 as repressors of transposable elements (TEs) during early embryogenesis. Yet, their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. Here, we characterized the protein interactome of 101 of the ~350 human KZFPs. Consistent with their targeting of TEs, most KZFPs conserved up to placental mammals essentially recruit KAP1 and associated effectors. In contrast, a subset of more ancient KZFPs rather interacts with factors related to functions such as genome architecture or RNA processing. Nevertheless, KZFPs from coelacanth, our most distant KZFP-encoding relative, bind the cognate KAP1. These results support a hypothetical model whereby KZFPs first emerged as TE-controlling repressors, were continuously renewed by turnover of their hosts' TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions.

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs.

Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation.

KAP1 facilitates reinstatement of heterochromatin after DNA replication.

During cell division, maintenance of chromatin features from the parental genome requires their proper establishment on its newly synthetized copy. The loss of epigenetic marks within heterochromatin, typically enriched in repetitive elements, endangers genome stability and permits chromosomal rearrangements via recombination. However, how histone modifications associated with heterochromatin are maintained across mitosis remains poorly understood. KAP1 is known to act as a scaffold for a repressor complex that mediates local heterochromatin formation, and was previously demonstrated to play an important role during DNA repair. Accordingly, we investigated a putative role for this protein in the replication of heterochromatic regions. We first found that KAP1 associates with several DNA replication factors including PCNA, MCM3 and MCM6. We then observed that these interactions are promoted by KAP1 phosphorylation on serine 473 during S phase. Finally, we could demonstrate that KAP1 forms a complex with PCNA and the histone-lysine methyltransferase Suv39h1 to reinstate heterochromatin after DNA replication.

Impact of Minor Surgery Emergencies in Isolated Sea-Based Environment: The French Navy Experience.

INTRODUCTION: The aim of this article is to determine whether some of the urgent (<24 hours) medical evacuations (MEDEVACs) (from French Navy surface ships in isolated situations but with an embarked medical officer) of patients suffering from minor surgical emergencies could have been avoided, and if so, which ones. MATERIALS AND METHODS: This was a retrospective descriptive study of all MEDEVAC's performed between 2009 and 2014. This was done by an analysis of the records held at the French Naval Medical Headquarters that included both MEDEVAC signals and anonymized files called "Patient Movement Request." RESULTS: 560 MEDEVACs were performed from French Navy surface ships which most had an embarked medical officer but which were in isolated situations. Only 34 (6.1%) of the total evacuations were suffering from minor surgical emergencies. The majority of these were nonurgent MEDEVAC's of whom 17 (50%) had no surgical procedure attempted on board. Seven (20%) underwent urgent MEDEVAC and only 2 of them had undergone the indicated therapeutic procedure on board. The most common pathology was displaced fracture of the fifth metacarpal (29.4%) before deep abscess (17.6%). CONCLUSION: Contrary to our initial expectation, the operational impact of minor surgical emergencies remains low, which might suggest that a French naval medical doctor's training is sufficient in this particular field. However, 50% of the overall evacuated patients and 71% of the "urgent" MEDEVACs (<24 hours) did not undergo the indicated, simple surgical procedure before evacuation. The idea of introducing a specific training program for these procedures may therefore still have value.

Erratum: Roche, J. et al. Global Decrease of Histone H3K27 Acetylation in ZEB1-Induced Epithelial to Mesenchymal Transition in Lung Cancer Cells. Cancers, 2013, 5, 334-356.

n/a.

Erratum: Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation.

[This corrects the article DOI: 10.1038/celldisc.2016.37.].

Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation.

The histone 3 lysine 9 methyltransferase Setdb1 is essential for both stem cell pluripotency and terminal differentiation of different cell types. To shed light on the roles of Setdb1 in these mutually exclusive processes, we used mouse skeletal myoblasts as a model of terminal differentiation. Ex vivo studies on isolated single myofibres showed that Setdb1 is required for adult muscle stem cells expansion following activation. In vitro studies in skeletal myoblasts confirmed that Setdb1 suppresses terminal differentiation. Genomic binding analyses showed a release of Setdb1 from selected target genes upon myoblast terminal differentiation, concomitant to a nuclear export of Setdb1 to the cytoplasm. Both genomic release and cytoplasmic Setdb1 relocalisation during differentiation were dependent on canonical Wnt signalling. Transcriptomic assays in myoblasts unravelled a significant overlap between Setdb1 and Wnt3a regulated genetic programmes. Together, our findings revealed Wnt-dependent subcellular relocalisation of Setdb1 as a novel mechanism regulating Setdb1 functions and myogenesis.

Molecular Criteria for Defining the Naive Human Pluripotent State.

Recent studies have aimed to convert cultured human pluripotent cells to a naive state, but it remains unclear to what extent the resulting cells recapitulate in vivo naive pluripotency. Here we propose a set of molecular criteria for evaluating the naive human pluripotent state by comparing it to the human embryo. We show that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. We also show that induction of the naive state is accompanied by genome-wide DNA hypomethylation, which is reversible except at imprinted genes, and that the X chromosome status resembles that of the human preimplantation embryo. However, we did not see efficient incorporation of naive human cells into mouse embryos. Overall, the different naive conditions we tested showed varied relationships to human embryonic states based on molecular criteria, providing a backdrop for future analysis of naive human pluripotency.

Unexpected Distinct Roles of the Related Histone H3 Lysine 9 Methyltransferases G9a and G9a-Like Protein in Myoblasts.

Lysine methyltransferases G9a and GLP (G9a-like protein) are highly homologous and form functional heterodimeric complexes that establish mono- and dimethylation on histone H3 lysine 9 (H3K9me1, H3K9me2) in euchromatin. Here, we describe unexpected distinct roles for G9a and GLP in skeletal muscle terminal differentiation. Indeed, gain- or loss-of-function assays in myoblasts showed, in agreement with previous reports, that G9a inhibits terminal differentiation. While GLP plays a more intricate role in muscle differentiation,in one hand, both GLP gain and loss of function inhibit late steps of differentiation; on the other hand, in contrast to G9a, GLP overexpression promotes abnormal precocious expression of muscle differentiation-specific genes already in proliferating myoblasts. In agreement, transcriptomic analysis indicates that G9a and GLP regulate different sets of genes. Thus, GLP, but not G9a, inhibits proteasome subunit-encoding genes expression, resulting in an inhibition of the proteasome activities. Subsequently, GLP, but not G9a, overexpression stabilizes MyoD that is likely to be responsible for muscle markers expression in proliferating myoblasts.

Sound of silence: the properties and functions of repressive Lys methyltransferases.

The methylation of histone Lys residues by Lys methyltransferases (KMTs) regulates chromatin organization and either activates or represses gene expression, depending on the residue that is targeted. KMTs are emerging as key components in several cellular processes, and their deregulation is often associated with pathogenesis. Here, we review the current knowledge on the main KMTs that are associated with gene silencing: namely, those responsible for methylating histone H3 Lys 9 (H3K9), H3K27 and H4K20. We discuss their biochemical properties and the various mechanisms by which they are targeted to the chromatin and regulate gene expression, as well as new data on the interplay between them and other chromatin modifiers.

The downregulation of BAP1 expression by BCR-ABL reduces the stability of BRCA1 in chronic myeloid leukemia.

BCR-ABL induces an intrinsic genetic instability in chronic myeloid leukemia (CML). The protein breast cancer 1, early onset (BRCA1)-associated protein 1 (BAP1) is a deubiquitinase interacting with the DNA repair regulator BRCA1 and is frequently inactivated in many cancers. Here, we report that BAP1 mRNA and protein levels are downregulated in a BCR-ABL1-expressing hematopoietic cell line (UT-7/11). A decrease of BAP1 transcripts is also observed in newly diagnosed CML patients. Moreover, BAP1 protein levels are low or undetectable in CD34(+) cells from CML patients at diagnosis as compared with CD34(+) cells from normal donors. In addition, BRCA1 protein level is reduced in BCR-ABL1-expressing UT-7/11 cells. Finally, the enforced expression of BAP1 is associated with BRCA1 protein deubiquitination and restoration. These results demonstrate BAP1 as a major link with the BCR-ABL-induced downregulation of BRCA1 in CML.