Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy.

Genomic deletions provide a powerful loss-of-function model in noncoding regions to assess the role of purifying selection on genetic variation. Regulatory element function is characterized by nonuniform tissue and cell type activity, necessarily linking the study of fitness consequences from regulatory variants to their corresponding cellular activity. We generated a callset of deletions from genomes in the Alzheimer's Disease Neuroimaging Initiative (ADNI) and used deletions from The 1000 Genomes Project Consortium (1000GP) in order to examine whether purifying selection preserves noncoding sites of chromatin accessibility marked by DNase I hypersensitivity (DHS), histone modification (enhancer, transcribed, Polycomb-repressed, heterochromatin), and chromatin loop anchors. To examine this in a cellular activity-aware manner, we developed a statistical method, pleiotropy ratio score (PlyRS), which calculates a correlation-adjusted count of "cellular pleiotropy" for each noncoding base pair by analyzing shared regulatory annotations across tissues and cell types. By comparing real deletion PlyRS values to simulations in a length-matched framework and by using genomic covariates in analyses, we found that purifying selection acts to preserve both DHS and enhancer noncoding sites. However, we did not find evidence of purifying selection for noncoding transcribed, Polycomb-repressed, or heterochromatin sites beyond that of the noncoding background. Additionally, we found evidence that purifying selection is acting on chromatin loop integrity by preserving colocalized CTCF binding sites. At regions of DHS, enhancer, and CTCF within chromatin loop anchors, we found evidence that both sites of activity specific to a particular tissue or cell type and sites of cellularly pleiotropic activity are preserved by selection.

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.

In primates and other animals, reverse transcription of mRNA followed by genomic integration creates retroduplications. Expressed retroduplications are either "retrogenes" coding for functioning proteins, or expressed "processed pseudogenes," which can function as noncoding RNAs. To date, little is known about the variation in retroduplications in terms of their presence or absence across individuals in the human population. We have developed new methodologies that allow us to identify "novel" retroduplications (i.e., those not present in the reference genome), to find their insertion points, and to genotype them. Using these methods, we catalogued and analyzed 174 retroduplication variants in almost one thousand humans, which were sequenced as part of Phase 1 of The 1000 Genomes Project Consortium. The accuracy of our data set was corroborated by (1) multiple lines of sequencing evidence for retroduplication (e.g., depth of coverage in exons vs. introns), (2) experimental validation, and (3) the fact that we can reconstruct a correct phylogenetic tree of human subpopulations based solely on retroduplications. We also show that parent genes of retroduplication variants tend to be expressed at the M-to-G1 transition in the cell cycle and that M-to-G1 expressed genes have more copies of fixed retroduplications than genes expressed at other times. These findings suggest that cell division is coupled to retrotransposition and, perhaps, is even a requirement for it.

Adaptive potential of genomic structural variation in human and mammalian evolution.

Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.

Sea urchin coelomocyte arylsulfatase: a modulator of the echinoderm clotting pathway.

Sea urchin petalloid coelomocytes effectuate the clotting pathway by undergoing a rapid and dynamic cellular transformation that leads to cellular adhesion and wounds closure. We have identified high levels of activity of arylsulfatase (Ars) associated with coelomocytes of the sea urchin Lytechinus variegatus (Lamarck, 1816). Ars activity was extracted from clotted coelomocytes with EDTA and showed high levels of activity up to a 1:100 dilution. Clot formation from isolated coelomic fluid was significantly inhibited by the ARS inhibitor, p-nitrophenyl phosphate. Ars activity was collected by 80% ethanol precipitation, a diagnostic test previously used in Ars isolation. Cellular extraction studies in the presence and absence of the non-ionic detergent Triton X-100 indicated that some Ars activity was present intracellularly, possibly in intracellular membrane-bound compartments, however the majority of Ars activity was extracted from the extracellular coelomocyte membrane. Polyclonal anti-sea urchin embryo Ars antibodies recognized a single protein band with an approximate molecular weight of 75 kDa on western blots. Immunofluorescence using the anti-sea urchin Ars antibody revealed an intracellular and extracellular staining of Ars in both petalloid and filopodial coelomocytes. Taken together, these data indicate that coelomocyte Ars might be involved in cell-to-cell crosslinking of surface sulfated polysaccharides vital for clot formation.