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Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within theDrosophila simulansclade—D.simulans,D.sechellia, andD.mauritiana—and their relative,D.melanogaster. Using chromatin profiling combined with high-resolution fluorescence in situ hybridization on stretched chromatin fibers, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timescales. We also reveal the recent origin (<240 Kya) of telocentric chromosomes inD.sechellia, where the X and fourth centromeres now sit on telomere-specific retroelements. Finally, the Y chromosome centromeres, which are the only chromosomes that do not experience female meiosis, do not show dynamic cycling between satDNA and TEs. The patterns of rapid centromere turnover in these species are consistent with genetic conflicts in the female germline and have implications for centromeric DNA function and karyotype evolution. Regardless of the evolutionary forces driving this turnover, the rapid reorganization of centromeric sequences over short evolutionary timescales highlights their potential as hotspots for evolutionary innovation. 

Advances in genomic technology led to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag. 

Abstract. Salinity is one of the most common water quality threats in riverbasins and irrigated regions worldwide. However, no available numericalmodels simulate all major processes affecting salt ion fate and transport at the watershed scale. This study presents a new salinity module for the SWAT model that simulates the fate and transport of eight major salt ions(SO42-, Ca2+, Mg2+, Na+, K+, Cl−,CO32-, HCO3-) in a watershed system. The module accountsfor salt transport in surface runoff, soil percolation, lateral flow,groundwater, and streams, and equilibrium chemistry reactions in soil layersand the aquifer. The module consists of several new subroutines that areimbedded within the SWAT modelling code and one input file containing soilsalinity and aquifer salinity data for the watershed. The model is appliedto a 732 km2 salinity-impaired irrigated region within the ArkansasRiver Valley in southeastern Colorado and tested against root zone soilsalinity, groundwater salt ion concentration, groundwater salt loadings tothe river network, and in-stream salt ion concentration. The model can be auseful tool in simulating baseline salinity transport and investigatingsalinity best management practices in watersheds of varying spatial scales.