Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

A large-scale comparative gene expression study reveals the different ways in which the chromosome-wide gene dosage reductions resulting from sex chromosome differentiation events were compensated during mammalian and avian evolution

The leak channel NALCN controls tonic firing and glycolytic sensitivity of substantia nigra pars reticulata neurons

Certain neuron types fire spontaneously at high rates, an ability that is crucial for their function in brain circuits. The spontaneously active GABAergic neurons of the substantia nigra pars reticulata (SNr), a major output of the basal ganglia, provide tonic inhibition of downstream brain areas. A depolarizing 'leak' current supports this firing pattern, but its molecular basis remains poorly understood. To understand how SNr neurons maintain tonic activity, we used single-cell RNA sequencing to determine the transcriptome of individual mouse SNr neurons. We discovered that SNr neurons express the sodium leak channel, NALCN, and that SNr neurons lacking NALCN have impaired spontaneous firing. In addition, NALCN is involved in the modulation of excitability by changes in glycolysis and by activation of muscarinic acetylcholine receptors. Our findings suggest that disruption of NALCN could impair the basal ganglia circuit, which may underlie the severe motor deficits in humans carrying mutations in NALCN. DOI: http://dx.doi.org/10.7554/eLife.15271.00

Specificity of the coxsackievirus B4 VP4 capsid protein investigated in silico.

International audienceThe Enterovirus genus encompasses several species and various serotypes, like coxsackievirus-B1 (CV-B1) to CV-B6, and many variants. The role of these viruses, especially CV-B4, in the pathogenesis of type 1 diabetes is strongly suspected. It has been reported that antibodies directed towards the region of amino acids 11-30 of the VP4 capsid protein enhance the infection of human peripheral blood mononuclear cells with CV-B4. In order to predict the inter- and intra-serotype specificity of the region 11-30 of CV-B4 VP4, 362 available protein sequences of CV-B1 to -B6, CV-A9, and swine vesicular disease virus (SVDV) have been aligned and levels of homology have been calculated. Serine residue substitutions in this region of VP4 were observed without predictable subsequent modification of conformation or charge. The amino acids 16-24 region was the most variable. The sequence of amino acids 16-24 of the CV-B4E2 VP4 protein was highly homologous to those of other CV-B4 (64.4%) whereas there was no homology with CV-B3 and B5 and very low levels of homology with CV-B1 and B2 (3.3% and 9.9%, respectively). In conclusion, the bioinformatic analysis suggests that the region 16-24 of the VP4 capsid protein is the feature of the specificity of the target of infection-enhancing antibodies directed towards CV-B

Light-activated cell identification and sorting (LACIS) for selection of edited clones on a nanofluidic device.

Despite improvements in the CRISPR molecular toolbox, identifying and purifying properly edited clones remains slow, laborious, and low-yield. Here, we establish a method to enable clonal isolation, selection, and expansion of properly edited cells, using OptoElectroPositioning technology for single-cell manipulation on a nanofluidic device. Briefly, after electroporation of primary T cells with CXCR4-targeting Cas9 ribonucleoproteins, single T cells are isolated on a chip and expanded into colonies. Phenotypic consequences of editing are rapidly assessed on-chip with cell-surface staining for CXCR4. Furthermore, individual colonies are identified based on their specific genotype. Each colony is split and sequentially exported for on-target sequencing and further off-chip clonal expansion of the validated clones. Using this method, single-clone editing efficiencies, including the rate of mono- and bi-allelic indels or precise nucleotide replacements, can be assessed within 10 days from Cas9 ribonucleoprotein introduction in cells

Distributions of current and inferred ancestral expression levels of genes on the marsupial (proto) X chromosomes and autosomes.

<p>Distributions of expression levels of (proto) X-linked genes (blue line) and (proto) autosomal genes (red line) are shown for cerebellum and liver from opossum. Expression levels in the comparison of the current X and proto-X (right plots) are normalized by the respective autosomal expression levels. In all cases, the two plotted distributions are not significantly different from each other (Benjamini-Hochberg corrected <i>p</i>>0.05; Komolgorov-Smirnov test). See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s019" target="_blank">Table S1</a> for all tests of differences between X and autosomal expression distributions (all tissues).</p

Expression levels of therian genes in the X-conserved region and their autosomal counterparts in platypus and chicken.

<p>Left: Global expression levels (based on third quartiles of the RPKM distribution) of genes in the therian XCR (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio-1001328-g003" target="_blank">Figure 3B</a> legend for details) and their autosomal orthologs in outgroup species with different sex chromosome systems (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s010" target="_blank">Figure S10</a> for all five somatic tissues). Error bars represent the range containing 90% of the third quartiles of individual resampling sets (80% of 90 orthologous genes were resampled 100 times). Right: Expression levels of resampled sets of 90 genes that are autosomal in all ten species. The central value is the median of the third quartiles of resampled sets (error bars represent the central 90% of the distribution of those third quartiles).</p

Concerted downregulation of X-linked and autosomal genes in the brain of placental and marsupial (i.e., therian) mammals.

<p>Modules with specific expression states in the therian brain (module 563; 330 genes) or eutherian brain/cerebellum (module 634; 313 genes) are shown. Bars represent the weighted average expression of all genes in a module, for each sample (horizontal grey line, average bar height). The horizontal red line represents the cutoff of the biclustering algorithm; samples above the red line are considered to have a distinct expression state. Note that the modules shown are highly enriched for X-linked genes (module 563: 25 observed versus 8.5 expected, <i>p</i><10⁻³; module 634: 28 observed versus 8.3 expected, <i>p</i><10⁻⁴), as are modules 421, 507, 521, and 618, which display transcriptional downregulations in therians or eutherians and were all considered in the protein–protein interaction analyses (see main text and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#s3" target="_blank">Methods</a>). All modules can be explored in a searchable database: <a href="http://www.unil.ch/cbg/ISA/species" target="_blank">http://www.unil.ch/cbg/ISA/species</a>.</p