The human genome contains approximately one million Alu repetitive elements comprising 10% of the genome, yet their functions are not well understood. Here, we show that Alu elements resemble enhancers. Alu elements are bound by two well-phased nucleosomes that contain histones bearing marks of active chromatin, and they show tissue-specific enrichment for the enhancer mark H3K4me1. A proportion of Alu elements were experimentally validated as bona fide active enhancers with an in vitro reporter assay. In addition, Hi-C data indicate that Alus show long-range interactions with gene promoters. We also find that Alus are generally more conserved when located in the proximal upstream region of genes. Their similarity to enhancers becomes more prominent with their age in the human genome, following a clear evolutionary continuum reminiscent of the evolutionary pattern of proto-genes. Therefore, we conclude that some Alu elements can function as enhancers and propose that many more may be proto-enhancers that serve as a repertoire for the de novo birth of enhancers.

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a b s t r a c tSpatial variations in phytoplankton community within a large mesotrophic reservoir (Miyun reservoir, North China) were investigated in relation to variations in physico-chemical properties, nutrient concentrations, temperature and light conditions over a 5 month period in 2009. The dynamics of phytoplankton community was represented by the dominance of cyanobacteria through summer and fall, following with a short term dominance of chlorophyta in late fall, and a relatively high abundance of diatom in October; on the other hand, maximum phytoplankton biomass was recorded in the north shallow region of Miyun reservoir with a higher nutrients level. Particular attention was paid to the impacts of environmental conditions on the growth of two cyanobacteria genera, the toxin-producing Microcystis and the taste & odor-producing Oscillatoria. Microcystis biomass was in general greatly affected by water temperature and mixing depth/local water depth ratio in this reservoir, while the Oscillatoria biomass in the surface and middle layers was greatly affected by total dissolved phosphorus, and that in the bottom layer was related with the Secchi depth/local water depth ratio. Abundant Oscillatoria biomass was observed only in late September when Microcystis biomass decreased and allowed sufficient light go through.

Many physical, chemical, and biological processes in lakes depend on lake water temperature. However, attribution of the warming rate in a shallow lake is not well understood yet. Here, we evaluated a one-dimensional lake model FLake by observed daily lake surface water temperature (LSWT) at four typical lakes in the Middle and Lower Yangtze River basin and then attributed LSWT warming to climate variables during the period 1979–2017. We found that FLake could capture well the seasonal/interannual variation of observed LSWT. During the 39-year study period, LSWT significantly warms at a rate of 0.26–0.28 °C per decade, 24–35% slower than the air temperature. Increased solar radiation and air temperature contributed to most (>80%) of the LSWT warming. The warming trend of LSWT in the spring is the largest among the four seasons, 2–4 times the warming rate of the other seasons. Brightening in the spring contributes 50–64% of the largest spring warming. The future air warming plus the brightening trend with the Clean Air Act in China would amplify LSWT warming and, thus, advance and/or deteriorate algae blooms, especially in spring.