Circadian Cell-Cycle Progression: Cracking Open the Gate

In cyanobacteria cell division is intimately linked with the circadian cycle. Dong et al. (2010) now identify components of the circadian clock that regulate the formation of the midcell ring for cytokinesis, revealing a critical link between the circadian cycle and the control of cell division

RNA, Genome Output and Input

RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation

RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome.

We have previously developed and described a method for measuring RNA co-locations within cells, called Proximity RNA-seq, which promises insights into RNA expression, processing, storage and translation. Here, we describe transcriptome-wide proximity RNA-seq datasets obtained from human neuroblastoma SH-SY5Y cell nuclei. To aid future users of this method, we also describe and release our analysis pipeline, CloseCall, which maps cDNA to a custom transcript annotation and allocates cDNA-linked barcodes to barcode groups. CloseCall then performs Monte Carlo simulations on the data to identify pairs of transcripts, which are co-barcoded more frequently than expected by chance. Furthermore, derived co-barcoding frequencies for individual transcripts, dubbed valency, serve as proxies for RNA density or connectivity for that given transcript. We outline how this pipeline was applied to these sequencing datasets and openly share the processed data outputs and access to a virtual machine that runs CloseCall. The resulting data specify the spatial organization of RNAs and builds hypotheses for potential regulatory relationships between RNAs

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Funder: FP7 Ideas: European Research Council; doi: http://dx.doi.org/10.13039/100011199; Grant(s): 259743Abstract: Background: Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized. Results: Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA binding sites for liver nuclear receptors and other transcription factors, some exclusively present in either rhythmic or stable contacts. Finally, by comparing the interaction profiles between core clock and output circadian genes, we show that core clock interactomes are more dynamic compared to output circadian genes. Conclusion: Our results identify chromatin conformation dynamics at different scales that parallel oscillatory gene expression and characterize the repertoire of regulatory elements that control circadian gene transcription through rhythmic or stable chromatin configurations

The cold-inducible RNA-binding protein CIRP regulates circadian gene expression

Virtually all light-sensitive organisms, ranging from bacteria to human, anticipate and adapt to daily changes in luminosity and/or temperature caused by the rotation of the earth around its own axis. Endogenous circadian clocks synchronize to such external cues and regulate many aspects of behavior and physiology. In mammals, the circadian timing system comprises the master clock in the suprachiasmatic nuclei (SCN) in the brain and subsidiary clocks in most cells of the body. The SCN is reset by light in a daily fashion and in turn ensures phase coherence of subsidiary oscillators in the periphery. The master clock synchronizes peripheral oscillators by diverse means. These include hormone secretion, neuronal cues, rest-activity and feeding-fasting cycles of the animal as well as circadian fluctuations in body temperature. In order to gain insights into how SCN-emitted cues are integrated into peripheral oscillators, we attempted to characterize the function of Cold-inducible RNA-binding protein (CIRP) and to examine its effect on circadian rhythms. CIRP belongs to a group of genes, which are expressed in a circadian manner in mouse liver irrespective of whether local hepatocyte clocks are functional or not. These genes must therefore be regulated by oscillating systemic signals under the direct control of the master clock in the SCN. Conversely, if systemically driven genes, such as Cirp, were involved in the regulation of peripheral core clock components, this would provide a plausible mechanism to relay cyclic SCN signals to the circadian clock circuitry. Indeed, loss-of-function experiments demonstrated that CIRP is required for high-amplitude circadian gene expression and thereby confers robustness to oscillators. We aimed at identifying the molecular interactions between CIRP and circadian clocks. For this purpose, we, purified CIRP–RNA complexes and analyzed CIRP-interacting RNAs through high-throughput sequencing (CLIP-seq). We furthermore deep-sequenced whole transcriptomes (RNA-seq) from control and CIRP-depleted cells, respectively. We thereby identified transcripts associated with and regulated by CIRP. These experiments revealed Clock and several additional core clock components as targets of CIRP and therefore established a molecular link between CIRP and the core clock. Using cultured fibroblasts, a clock model devoid of complex SCN signals, we were able to reconstitute the rhythmic expression of CIRP by imposed circadian temperature fluctuations, suggesting that body temperature cycles act as the systemic signal that regulates CIRP abundance. Thus, CIRP might participate in a pathway, which relays temperature cues to circadian oscillators

RNA, Genome Output and Input

RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation

Autonomous and self-sustained circadian oscillators displayed in human islet cells

Following on from the emerging importance of the pancreas circadian clock on islet function and the development of type 2 diabetes in rodent models, we aimed to examine circadian gene expression in human islets. The oscillator properties were assessed in intact islets as well as in beta cells

[Perspectives and Challenges of hand-held Ultrasound].

The use of handheld ultrasound devices from a technical and data protection point of view, device properties, functionality, documentation, indications, delegation of performance, applications by doctors, students and non-medical staff is examined and discussed