FISH-eyed and genome-wide views on the spatial organisation of gene expression

AbstractEukaryotic cells store their genome inside a nucleus, a dedicated organelle shielded by a double lipid membrane. Pores in these membranes allow the exchange of molecules between the nucleus and cytoplasm. Inside the mammalian cell nucleus, roughly 2 m of DNA, divided over several tens of chromosomes is packed. In addition, protein and RNA molecules functioning in DNA-metabolic processes such as transcription, replication, repair and the processing of RNA fill the nuclear space. While many of the nuclear proteins freely diffuse and display a more or less homogeneous distribution across the nuclear interior, some appear to preferentially cluster and form foci or bodies. A non-random structure is also observed for DNA: increasing evidence shows that selected parts of the genome preferentially contact each other, sometimes even at specific sites in the nucleus. Currently a lot of research is dedicated to understanding the functional significance of nuclear architecture, in particular with respect to the regulation of gene expression. Here we will evaluate evidence implying that the folding of DNA is important for transcriptional control in mammals and we will discuss novel high-throughput techniques expected to further boost our knowledge on nuclear organisation

Chromosome Conformation Capture on Chip (4C): Meeting genomic neighbors

__Abstract__ The eukaryotic genome is extensively folded to fit in the small volume of the cell nucleus. Several lines of evidence have suggested a functional relationship between the structural folding of chromosomes and gene expression; however methods to systematically analyze chromosome folding were missing. This thesis describes the development and application of a novel method, chromosome conformation capture on chip (4C). In 4C one genomic fragment is selected (e.g. a gene promoter), and for this viewpoint fragment all the DNA that is found in spatial proximity is captured and analyzed. We applied 4C to analyze the nuclear surroundings of the beta globin locus in two tissues, one in which the locus is active and one in which it is silent. We found that the beta globin locus contacts other active parts of the genome when it is active and silent genomic regions in the tissue in which it is not expressed. A second application of 4C is the detection of genomic rearrangements. Any given fragment in the genome will always be surrounded by the parts of the genome that flank it on the linear genome map, therefore these sequences will always appear most strongly in the 4C data. This allows the identification of new genomic neighbors in case of a rearrangement.4C uniquely allows the detection of genomic breakpoints rapidly and at high resolution. To optimize the technique further, 4C was adapted from a microarray based to a sequencing based method

Justice and the Human Alarm System: The Impact of Exclamation Points and Flashing Lights on the Justice Judgment Process

Extending theory within the justice domain and work on the human alarm system, the current paper argues that the process by which justice judgments are formed may be influenced reliably by the activation of psychological systems that people use to detect and handle alarming situations. Building on this analysis, it is further proposed that if this line of reasoning is true then presenting alarm-related stimuli, such as exclamation points and flashing lights, to people should lead to more extreme judgments about subsequent justice-related events than not presenting these alarming stimuli. Findings collected using different experimental paradigms provide evidence supporting these predictions both inside and outside the psychology lab. Implications for the social psychology of justice and the human alarm system literature are discussed

Genomic landscape of rat strain and substrain variation

Background: Since the completion of the rat reference genome in 2003, whole-genome sequencing data from more than 40 rat strains have become available. These data represent the broad range of strains that are used in rat research including commonly used substrains. Currently, this wealth of information cannot be used to its full extent, because the variety of different variant calling algorithms employed by different groups impairs comparison between strains. In addition, all rat whole genome sequencing studies to date used an outdated reference genome for analysis (RGSC3.4 released in 2004). Results: Here we present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains. We reanalyzed all primary data using a recent version of the rat reference assembly (RGSC5.0 released in 2012) and identified over 12 million genomic variants (SNVs, indels and structural variants) among the 40 strains. 28,318 SNVs are specific to individual substrains, which may be explained by introgression from other unsequenced strains and ongoing evolution by genetic drift. Substrain SNVs may have a larger predicted functional impact compared to older shared SNVs. Conclusions: In summary we present a comprehensive catalog of uniformly analyzed genetic variants among 40 widely used rat inbred strains based on the RGSC5.0 assembly. This represents a valuable resource, which will facilitate rat functional genomic research. In line with previous observations, our genome-wide analyses do not show evidence for contribution of multiple ancestral founder rat subspecies to the currently used rat inbred strains, as is the case for mouse. In addition, we find that the degree of substrain variation is highly variable between strains, which is of importance for the correct interpretation of experimental data from different labs

Three-dimensional organization of gene expression in erythroid cells

The history of globin research is marked by a series of contributions seminal to our understanding of the genome, its function, and its relation to disease. For example, based on studies on hemoglobinopathies, it was understood that gene expression can be under the control of DNA elements that locate away from the genes on the linear chromosome template. Recent technological developments have allowed the demonstration that these regulatory DNA elements communicate with the genes through physical interaction, which loops out the intervening chromatin fiber. Subsequent studies showed that the spatial organization of the beta-globin locus dynamically changes in relation to differences in gene expression. Moreover, it was shown that the beta-globin locus adopts a different position in the nucleus during development and erythroid maturation. Here, we discuss the most recent insight into the three-dimensional organization of gene expression