The single-cell chromatin landscape in gonadal cell lineage specification.

Gonad development includes sex determination and divergent maturation of the testes and ovaries. Recent advances in measuring gene expression in single cells are providing new insights into this complex process. However, the underlying epigenetic regulatory mechanisms remain unclear. Here, we profiled chromatin accessibility in mouse gonadal cells of both sexes from embryonic day 11.5 to 14.5 using single-cell assay for transposase accessible chromatin by sequencing (scATAC-seq). Our results showed that individual cell types can be inferred by the chromatin landscape, and that cells can be temporally ordered along developmental trajectories. Integrative analysis of transcriptomic and chromatin-accessibility maps identified multiple putative regulatory elements proximal to key gonadal genes Nr5a1, Sox9 and Wt1. We also uncover cell type-specific regulatory factors underlying cell type specification. Overall, our results provide a better understanding of the epigenetic landscape associated with the progressive restriction of cell fates in the gonad.

Genome-wide 5-hydroxymethylcytosine (5hmC) reassigned in Pten-depleted mESCs along neural differentiation.

DNA methylation and hydroxymethylation have been implicated in the regulatory dynamics of gene expression in normal development and differentiation. 5-Hydroxymethylcytosine (5hmC), created by the ten-eleven translocation (TET) protein-catalyzed oxidation of 5-methylcytosine (5mC), is abundant in the brain, but the genome-wide distribution and impact of 5hmC during diverse neuronal differentiation remain unknown. Here, we used an in vitro model to differentiate mouse embryonic stem cells (mESCs) into ventral midbrain and hindbrain neural progenitors, followed by characterizing global 5hmC distribution using a nano-5hmC-seal approach. The 5hmC pattern was dynamic in promoter, exon, and enhancer regions, associated with gene activation and repression. For example, ventral midbrain markers (Lmx1a, Otx2, and Th) and hindbrain markers (Hoxa1, Zic1, and Tph1) acquire 5hmC and are upregulated during differentiation. Among the differentially expressed genes involved in both midbrain and hindbrain lineage commitment, phosphatase and tensin homolog (Pten) was identified as a key regulator for neuronal development. We confirmed that Pten knockout disrupted the normal differentiation of midbrain/hindbrain neural progenitors, resulting in immature neurons. In addition, 5421 and 4624 differentially hydroxymethylated regions (DhMRs) were identified in the differentiation of Pten-/- mESC into ventral midbrain and hindbrain progenitors, respectively. Gene ontology analysis showed that the majority of these DhMRs were associated with neurogenesis, ectoderm development, and signal transduction. Moreover, further combinational analysis of the 5hmC pattern and transcriptomic profile in the midbrain progenitor cells demonstrated Pten as a toggle to modulate mitochondrial associated pathways. Therefore, our findings elucidated the molecular mechanisms underlying lineage-specific differentiation of pluripotent stem cells to the midbrain/hindbrain progenitors, where Pten participates as one key regulator.

Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil.

Two aerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated as DHOA06T and 4 M-K27T, were isolated from soil samples collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E 23° 10' N). Strains DHOA06T and 4 M-K27T grew at pH 4.5-7.0 (optimum, pH 5.0-6.0) and pH 4.5-6.5 (pH 6.0), respectively. Both strains grew at 12-37 °C (optimum, 28 °C) and NaCl levels up to 1.0 % (optimum 0 %, w/v). Phylogenetic analysis based on both 16S rRNA gene sequences and the concatenated partial atpD, gyrB andlepA gene sequences showed that strains DHOA06T and 4 M-K27T formed two isolated clades with members of the genus Dyella, but they each occupied a distinctive position within the genus. Strains DHOA06T and 4 M-K27T showed the highest 16S rRNA gene sequence similarities to Dyellacaseinilytica DHOB09T (98.7 %) and Dyellaacidisoli 4M-Z03T (98.8 %), respectively. DNA-DNA hybridization values of strains DHOA06T/DHOB09T and 4 M-K27T/4M-Z03T were 27.4±2.4 % and 38.8±1.0 %, respectively. Ubiquinone-8 was the only respiratory quinone detected in both strains. Their major fatty acids consisted of iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c, and strain DHOA06T had iso-C17 : 0 in addition. Their polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified aminolipids, and strain DHOA06T had phosphatidylmethylethanolamine and one unidentified lipid in addition. The DNA G+C contents of strains DHOA06T and 4 M-K27T were 59.1 and 61.7 mol%, respectively. Based on the above results, we propose that strains DHOA06T and 4 M-K27T represent two novel species of the genus Dyella, namely Dyelladinghuensis sp. nov. (type strain DHOA06T = KCTC 52129T=NBRC 111978T) and Dyellachoica sp. nov. (type strain 4 M-K27T=GDMCC 1.1189T=LMG 30267T).

Aliidongia dinghuensis gen. nov., sp. nov., a poly-ß-hydroxybutyrate-producing bacterium isolated from Pinus massoniana forest soil.

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated 7M-Z19T, was isolated from a soil sample collected from a Pinus massoniana forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain 7M-Z19T grew at pH 4.5-7.5 (optimum pH 6.0-6.5), 10 to 37 °C (optimum 28 °C) and NaCl concentration up to 2.0 % (optimum 0 %, w/v). iso-C17 : 0, C18 : 1ω7c and C19 : 0ω8c cyclo were the major fatty acids (>10 %) while ubiquinone-10 was the only respiratory quinone detected in 7M-Z19T. The polar lipids of the strain consisted of phosphatidylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, six unidentified aminophospholipids, three unidentified phospholipids, six unidentified lipids and a glycolipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate formed a distinct lineage with Dongia mobilis and Dongia rigui within the family Rhodospirillaceae, but with a low sequence similarity of 92.7 and 92.0 %, respectively. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain 7M-Z19T should be placed in the family Rhodospirillaceae as a representative of a novel genus and species, for which the name Aliidongia dinghuensis gen. nov., sp. nov., is proposed. The type strain of the type species is 7M-Z19T (=NBRC 112240T=KCTC 52134T=CGMCC 1.15725T).