Specific mammalian genes functionally and dynamically associate together within the nucleus. Yet, how an array of many genes along the chromosome sequence can be spatially organized and folded together is unknown. We investigated the 3D structure of a well-annotated, highly conserved 4.3-Mb region on mouse chromosome 14 that contains four clusters of genes separated by gene “deserts.” In nuclei, this region forms multiple, nonrandom “higher order” structures. These structures are based on the gene distribution pattern in primary sequence and are marked by preferential associations among multiple gene clusters. Associating gene clusters represent expressed chromatin, but their aggregation is not simply dependent on ongoing transcription. In chromosomes with aggregated gene clusters, gene deserts preferentially align with the nuclear periphery, providing evidence for chromosomal region architecture by specific associations with functional nuclear domains. Together, these data suggest dynamic, probabilistic 3D folding states for a contiguous megabase-scale chromosomal region, supporting the diverse activities of multiple genes and their conserved primary sequence organization.
Chloride-the most abundant ion in sea water 1 -a ects ocean salinity, and thereby seawater density and ocean circulation. Its lack of reactivity gives it an extremely long residence time 2 . Other halogens are known to be incorporated into marine organic matter 3-5 . However, evidence of similar transformations of seawater chloride is lacking, aside from emissions of volatile organochlorine by marine algae 6-8 . Here we report high organochlorine concentrations from 180 to 700 mg kg −1 in natural particulate organic matter that settled into sediment traps at depths between 800 and 3,200 m in the Arabian Sea, taken between 1994 and 1995. X-ray spectromicroscopic imaging of chlorine bonding reveals that this organochlorine exists primarily in concentrated aliphatic forms consistent with lipid chlorination, along with a more di use aromatic fraction. High aliphatic organochlorine in particulate material from cultured phytoplankton suggests that primary production is a source of chlorinated organic matter. We also found that particulate algal detritus can act as an organic substrate for abiotic reactions involving Fe 2+ , H 2 O 2 or light that incorporate chlorine into organic matter at levels up to several grams per kilogram. We conclude that transformations of marine chloride to non-volatile organochlorine through biological and abiotic pathways represent an oceanic sink for this relatively unreactive element.Settling biogenic particulates remove much material from the surface ocean, and in addition to carbon this 'biological pump' entrains many other elements 9,10 . This route is established for the halogens Br and I (refs 3-5), whose low oxidation potential makes them amenable to incorporation into organic molecules. Cl, with the highest electron affinity of any element, has never been shown to participate in this process. Organochlorines are known in the ocean, but primarily as volatile compounds emitted to the atmosphere 6-8 , anthropogenic contaminants with various fates 11-13 , and trace compounds in microbes or dissolved organic matter 14,15 with no significant recognized fluxes.Both enzymatic and abiotic pathways have recently been shown to incorporate Br into particulate organic matter (POM) in sea water 16 . We reasoned that similar reactions can incorporate Cl into marine organic particulates. We tested this hypothesis by first investigating whether settling organic particulates show significant organochlorine content. Second, we looked for biological production of particulate organochlorines by phytoplankton, the main progenitors of POM in the oceans. Third, we examined the potential of abiotic processes, including photochemical, peroxidative and Fenton-like mechanisms, to chlorinate algal detritus.In each of these tests, we used the analytical capability of X-ray absorption near-edge structure (XANES) spectroscopy to distinguish organic from inorganic forms of Cl ( Fig. 1 and Supplementary Fig. 1). Spectral features near 2,822 eV (the Cl 'K-edge') denote electronic transitions from the Cl-1s shell to e...
Although bromine (Br) is considered conservative in seawater, it exhibits a well established correlation with organic carbon in marine sediments. This carbon-bromine association was recently attributed to covalent bonding, with organobromine in sinking particulates providing a putative link between sedimentary organobromine and organic matter cycling in surface waters. We hypothesized that phytoplankton detritus, a major precursor of sedimentary organic matter, would be susceptible to bromination through oxidative attack. Through a series of model experiments, we demonstrate incorporation of Br into algal particulate detritus through peroxidative and photochemical mechanisms. Peroxidative bromination was enhanced by addition of exogenous bromoperoxidase, but the enzyme was not required for the reaction. Fenton-like reaction conditions also promoted bromination, especially under solar irradiation, implicating radical mechanisms in the euphotic zone as another abiotic source of brominated particulates. These reactions produced aliphatic and aromatic forms of organobromine, suggesting that lipid-and protein-rich components of algal membranes provide suitable substrates for bromination. Biogenic organobromines in
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