Chromosome-level organization of the regulatory genome in the Drosophila nervous system

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Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

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Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models

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The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains

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HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia

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Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions

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Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism

X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is characterized by aggressive growth hormone (GH)-secreting pituitary tumors that occur in early childhood. X-LAG is associated with chromosome Xq26.3 duplications (the X-LAG locus typically includes VGLL1, CD40LG, ARHGEF6, RBMX, and GPR101) that lead to massive pituitary tumoral expression of GPR101, a novel regulator of GH secretion. The mechanism by which the duplications lead to marked pituitary misexpression of GPR101 alone was previously unclear. Using Hi-C and 4C-seq, we characterized the normal chromatin structure at the X-LAG locus. We showed that GPR101 is located within a topologically associating domain (TAD) delineated by a tissue-invariant border that separates it from centromeric genes and regulatory sequences. Next, using 4C-seq with GPR101, RBMX, and VGLL1 viewpoints, we showed that the duplications in multiple X-LAG-affected individuals led to ectopic interactions that crossed the invariant TAD border, indicating the existence of a similar and consistent mechanism of neo-TAD formation in X-LAG. We then identified several pituitary active cis-regulatory elements (CREs) within the neo-TAD and demonstrated in vitro that one of them significantly enhanced reporter gene expression. At the same time, we showed that the GPR101 promoter permits the incorporation of new regulatory information. Our results indicate that X-LAG is a TADopathy of the endocrine system in which Xq26.3 duplications disrupt the local chromatin architecture forming a neo-TAD. Rewiring GPR101-enhancer interaction within the new regulatory unit is likely to cause the high levels of aberrant expression of GPR101 in pituitary tumors caused by X-LAG.     

Proton-induced X-ray emission (PIXE) analysis of trace elements of total atmospheric deposit (TAD) around a smelting industry: Aerial pollution monitor

This study monitored total atmospheric deposit (TAD) around a smelting plant in Ile-Ife, Nigeria to assess the contributions of the industry to Nigeria's air-shed pollution. Samples were collected for 12 consecutive months using an Australian model gauge, harvested after 30 d of exposure, filtered and dried to constant weights using oven. Monthly deposition rates were determined and elemental characterizations of the TAD samples were done using proton-induced X-ray emission technique. Results revealed that the monthly deposition rates ranged from 0.69 to 4.62 gm^?3 and was more pronounced in Harmattan. Twenty-three elements were detected; their total elemental concentrations ranged from 1.23 to 13.63 mg m^?3 with Fe having the highest concentrations, while Na has the least. Pearson correlation indicated that some elements have common sources and/or similar chemical properties; enrichment factor showed that Fe, Zn, Pb, Mn were extremely enriched in the study area, modified degree of contamination (3.75) and pollution load intensity (1.21) showed that the neighborhoods could be exposed to high air pollution related impacts. Positive matrix factorization model revealed three distinct sources: Smelting emission (63%), biomass burning (17%), and suspended input material emissions (21%). The study concluded that the smelting activities posed a great hazard to receptors around the smelting industry.