Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function.

We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.

Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts.

Eukaryotic genomes vary in terms of size, chromosome number, and genetic complexity. Their temporal organization is complex, reflecting coordination between DNA folding and function. Here, we used fused karyotypes of budding yeast to characterize the effects of chromosome length on nuclear architecture. We found that size-matched megachromosomes expand to occupy a larger fraction of the enlarged nucleus. Hi-C maps reveal changes in the three-dimensional structure corresponding to inactivated centromeres and telomeres. De-clustering of inactive centromeres results in their loss of early replication, highlighting a functional correlation between genome organization and replication timing. Repositioning of former telomere-proximal regions on chromosome arms exposed a subset of contacts between flocculin genes. Chromatin reorganization of megachromosomes during cell division remained unperturbed, and it revealed that centromere-rDNA contacts in anaphase, extending over 0.3 Mb on wild-type chromosome, cannot exceed ∼1.7 Mb. Our results highlight the relevance of engineered karyotypes to unveiling relationships between genome organization and function.

Frontal lobe functions in schizophrenia: Interest of the Stuss approach.

OBJECTIVE: The term Executive Functions (EFs) refers to the higher-level skills we use every day to control and coordinate our cognitive abilities and behaviours. EFs are mainly supported by the frontal lobes and its connections. EFs are frequently impaired in schizophrenia, but the profiles of executive deficits accompanying schizophrenia remains unclear. The use of specific EFs models might help to shed new light on this issue. Stuss (Stuss & Alexander, 2007; Stuss, 2008, 2011, 2017) proposed an integrative and operant model of EFs which has never been used to explore and characterize deficits in schizophrenia. The aim of this study is to further examine EFs in schizophrenia in the light of the frontal lobe functional approach developed by Stuss (2008, 2011, 2017) in order to question EFs impairment homogeneity and heterogeneity in schizophrenia. METHODS: Forty-five patients with schizophrenia and fifty-five healthy controls were recruited. They all completed a series of neuropsychological tests selected and adapted to measure the five majors' functions of the frontal lobe described by Stuss (2017). RESULTS: Patients showed deficits in almost all the frontal functions. Inside each frontal lobe function, correlations were observed between all the corresponding measures. The study of profiles highlighted a heterogeneous functioning in schizophrenia. CONCLUSIONS: The model of Stuss (Stuss & Alexander, 2007; Stuss, 2008, 2011, 2017) allows accurate and specific measures of the frontal functions and observation. Beyond "cold" or "hot" EFs division, this integrative approach is helpful to understand links within neurocognition.

Adult-onset Still's disease or systemic-onset juvenile idiopathic arthritis and spondyloarthritis: overlapping syndrome or phenotype shift?

OBJECTIVES: Systemic-onset JIA (SJIA) and adult-onset Still's disease (AOSD) are the same sporadic systemic auto-inflammatory disease. SpA is a group of inflammatory non-autoimmune disorders. We report the observations of eight patients with SJIA/AOSD who also presented features of SpA during their disease evolution and estimate the prevalence of SpA in SJIA/AOSD. METHODS: This was a retrospective national survey of departments of paediatric and adult rheumatology and internal medicine. To be included, SJIA patients had to fulfil the ILAR criteria, AOSD patients the Yamaguchi or Fautrel criteria, and all patients the Assessment of SpondyloArthritis International Society (ASAS) classification criteria for axial or peripheral SpA, ESSG criteria for SpA or Classification Criteria for Psoriatic Arthritis (CASPAR) criteria for PsA. The data were collected with a standardized form. RESULTS: Eight patients (five adults) were identified in one paediatric and two adult departments. In all but one patient, SpA manifestations occurred several years after SJIA/AOSD onset [mean (s.d.) delay 6.2 (3.8) years]. Two patients had peripheral and three axial SpA, and four later exhibited PsA and one SAPHO syndrome. The prevalence of SpA in an adult cohort of 76 patients with AOSD was 6.58% (95% CI 2.17, 14.69), greater than the prevalence of SpA in the French general population (0.3%; 95% CI 0.17, 0.46). The prevalence of SpA in an SJIA cohort of 30 patients was 10% (95% CI 2.11, 26.53), more than that reported in the general population of industrialized countries, estimated at 0.016-0.15%. CONCLUSION: While the temporal disassociation between SpA and AOSD in most cases might suggest a coincidental finding, our work raises the possibility of an SpA/AOSD spectrum overlap that needs further study.

The use of the French Dimensional Apathy Scale (f-DAS) to assess apathy in schizophrenia: Properties and profiles.

BACKGROUND: Apathy can be defined as a quantitative reduction of self-generated voluntary and purposeful (or goal-directed) behaviour. The literature underlines the triadic dimensional nature of apathy, but in schizophrenia there are inconsistencies due to difficulty in assessment. The Dimensional Apathy Scale (DAS) and its validation into French (f-DAS) provide measurement of three neurobehavioral apathy subtypes: Executive, Emotional and Initiation, but these subtypes have never been explored in schizophrenia. OBJECTIVE: The aims of this study are to assess apathy in schizophrenia with a tri-dimensional tool (the f-DAS), to examine its psychometric properties in schizophrenia and the apathetic profiles of patients with schizophrenia. METHODS: One hundred and ten subjects were recruited. Forty-five belonged to the patients' group and fifty-five to the control group. They all completed the Mini-International Neuropsychiatric Interview (M.I.N.I), the French National Reading Test (f-NART), the French Dimensional Apathy Scale (f-DAS), the Lille Apathy Rating Scale (LARS) and the Beck Depression Inventory (BDI II). RESULTS: Regarding the total score of the f-DAS and the subscores for each dimension, patients appeared significantly more apathetic than healthy controls. Consistency, validity, concurrent and divergent validity were good. In the patient group, several profiles of apathy were identified. CONCLUSIONS: The f-DAS has good psychometric properties and provides reliable and valid dimensional assessment of apathy in schizophrenia. From a dimensional point of view, using the f-DAS we demonstrated that prevalence of apathy could be underestimated in schizophrenia. Patients with schizophrenia are more impaired on the Executive and Initiative dimensions of apathy.

MRI and muscle imaging for idiopathic inflammatory myopathies.

Although idiopathic inflammatory myopathies (IIM) are a heterogeneous group of diseases nearly all patients display muscle inflammation. Originally, muscle biopsy was considered as the gold standard for IIM diagnosis. The development of muscle imaging led to revisiting not only the IIM diagnosis strategy but also the patients' follow-up. Different techniques have been tested or are in development for IIM including positron emission tomography, ultrasound imaging, ultrasound shear wave elastography, though magnetic resonance imaging (MRI) remains the most widely used technique in routine. Whereas guidelines on muscle imaging in myositis are lacking here we reviewed the relevance of muscle imaging for both diagnosis and myositis patients' follow-up. We propose recommendations about when and how to perform MRI on myositis patients, and we describe new techniques that are under development.

Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer.

We investigate the kinetics of a polymer collapse due to the formation of irreversible cross-links between its monomers. Using the contact probability P(s) as a scale-dependent order parameter depending on the chemical distance s, our simulations show the emergence of a cooperative pearling instability. Namely, the polymer undergoes a sharp conformational transition to a set of absorbing states characterized by a length scale ξ corresponding to the mean pearl size. This length and the transition time depend on the polymer equilibrium dynamics and the cross-linking rate. We confirm experimentally this transition using a DNA conformation capture experiment in yeast.

Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C.

In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn-HiC design). In the Syn-HiC region, Hi-C signal-to-noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact frequencies, allowing to propose a robust definition of a Hi-C experiment resolution. The redesigned region is also distinguishable from its native homologous counterpart in an otherwise isogenic diploid strain. As a proof of principle, we tracked homologous chromosomes during meiotic prophase in synchronized and pachytene-arrested cells and captured important features of their spatial reorganization, such as chromatin restructuration into arrays of Rec8-delimited loops, centromere declustering, individualization, and pairing. Overall, we illustrate the promises held by redesigning genomic regions to explore complex biological questions.

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle.

Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions. During replication, cohesion establishment promotes numerous long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle. Formation of a condensin-dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin-mediated forces may also directly facilitate segregation. This work therefore comprehensively recapitulates cell cycle-dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division.

3D organization of synthetic and scrambled chromosomes.

Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.