Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.

The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.

The differential expression of PilY1 proteins by the HsfBA phosphorelay allows twitching motility in the absence of exopolysaccharides.

Type Four Pili (T4P) are extracellular appendages mediating several bacterial functions such as motility, biofilm formation and infection. The ability to adhere to substrates is essential for all these functions. In Myxococcus xanthus, during twitching motility, the binding of polar T4P to exopolysaccharides (EPS), induces pilus retraction and the forward cell movement. EPS are produced, secreted and weakly associated to the M. xanthus cell surface or deposited on the substrate. In this study, a genetic screen allowed us to identify two factors involved in EPS-independent T4P-dependent twitching motility: the PilY1.1 protein and the HsfBA phosphorelay. Transcriptomic analyses show that HsfBA differentially regulates the expression of PilY1 proteins and that the down-regulation of pilY1.1 together with the accumulation of its homologue pilY1.3, allows twitching motility in the absence of EPS. The genetic and bioinformatic dissection of the PilY1.1 domains shows that PilY1.1 might be a bi-functional protein with a role in priming T4P extension mediated by its conserved N-terminal domain and roles in EPS-dependent motility mediated by an N-terminal DUF4114 domain activated upon binding to Ca2+. We speculate that the differential transcriptional regulation of PilY1 homologs by HsfBA in response to unknown signals, might allow accessorizing T4P tips with different modules allowing twitching motility in the presence of alternative substrates and environmental conditions.

Coordination of symbiosis and cell cycle functions in Sinorhizobium meliloti.

The symbiotic nitrogen fixing species Sinorhizobium meliloti represents a remarkable model system for the class Alphaproteobacteria, which includes genera such as Caulobacter, Agrobacterium and Brucella. It is capable of living free in the soil, and is also able to establish a complex symbiosis with leguminous plants, during which its cell cycle program is completely rewired presumably due, at least in part, to the action of peptides secreted by the plant. Here we will discuss how the cell cycle regulation works in S. meliloti and the kinds of molecular mechanisms that take place during the infection. We will focus on the complex regulation of the master regulator of the S. meliloti cell cycle, the response regulator CtrA, discussing its implication in symbiosis.

Real-time detection of hypochlorite in tap water and biological samples by a colorimetric, ratiometric and near-infrared fluorescent turn-on probe.

In this paper, we report a highly selective and sensitive ratiometric NIR fluorescent probe that can be used for real-time detection of the biologically important hypochlorite with colorimetric and significant NIR fluorescent turn-on signal changes at NIR excitation wavelength. In addition, experiments showed that this probe can be applied to detect hypochlorite in tap water, serum samples, and living cells with low cytotoxicity.

A readily available colorimetric and near-infrared fluorescent turn-on probe for rapid and selective detection of cysteine in living cells.

A readily available naphthofluorescein-based near-infrared (NIR) fluorescent probe was reported for rapid, colorimetric and NIR fluorescent turn-on detection of cysteine (Cys) with high selectivity and sensitivity over various analytes including the similar structured homocysteine (Hcy) and glutathione (GSH). This probe was successfully applied to bioimage intracellular Cys in living cells with low cytotoxicity.