Mammalian DNA replication initiates at multiple sites along chromosomes at different times, following a temporal replication program. Homologous alleles typically replicate synchronously; however, mono-allelically expressed genes such as imprinted genes, allelically excluded genes and genes on the female X chromosome replicate asynchronously. We have used a chromosome engineering strategy to identify a human autosomal locus that controls this replication timing program in cis. We show that Cre/loxP-mediated rearrangements at a discrete locus at 6q16.1 result in delayed replication of the entire chromosome. This locus displays asynchronous replication timing that is coordinated with other mono-allelically expressed genes on chromosome 6. Characterization of this locus revealed mono-allelic expression of a large intergenic non-coding RNA, which we have named asynchronous replication and autosomal RNA on chromosome 6, ASAR6. Finally, disruption of this locus results in the activation of the previously silent alleles of linked mono-allelically expressed genes. We previously found that chromosome rearrangements involving eight different autosomes display delayed replication timing, and that cells containing chromosomes with delayed replication timing have a 30-80-fold increase in the rate at which new gross chromosomal rearrangements occurred. Taken together, these observations indicate that human autosomes contain discrete cis-acting loci that control chromosome-wide replication timing, mono-allelic expression and the stability of entire chromosomes.

Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes.

DNA replication initiates at multiple sites along each mammalian chromosome at different times during each S phase, following a temporal replication program. We have used a Cre/loxP-based strategy to identify cis-acting elements that control this replication-timing program on individual human chromosomes. In this report, we show that rearrangements at a complex locus at chromosome 15q24.3 result in delayed replication and structural instability of human chromosome 15. Characterization of this locus identified long, RNA transcripts that are retained in the nucleus and form a “cloud” on one homolog of chromosome 15. We also found that this locus displays asynchronous replication that is coordinated with other random monoallelic genes on chromosome 15. We have named this locus ASynchronous replication and Autosomal RNA on chromosome 15, or ASAR15. Previously, we found that disruption of the ASAR6 lincRNA gene results in delayed replication, delayed mitotic condensation and structural instability of human chromosome 6. Previous studies in the mouse found that deletion of the Xist gene, from the X chromosome in adult somatic cells, results in a delayed replication and instability phenotype that is indistinguishable from the phenotype caused by disruption of either ASAR6 or ASAR15. In addition, delayed replication and chromosome instability were detected following structural rearrangement of many different human or mouse chromosomes. These observations suggest that all mammalian chromosomes contain similar cis-acting loci. Thus, under this scenario, all mammalian chromosomes contain four distinct types of essential cis-acting elements: origins, telomeres, centromeres and “inactivation/stability centers”, all functioning to promote proper replication, segregation and structural stability of each chromosome.

Background The United States of America (USA), European Union (EU), Brazil and China are four of the largest agricultural producers and users of agricultural pesticides in the world. Comparing the inclination and ability of different regulatory agencies to ban or eliminate pesticides that have the most potential for harm to humans and the environment can provide a glimpse into the effectiveness of each nation’s pesticide regulatory laws and oversight. Methods The approval status of more than 500 agricultural pesticides was identified in the USA, EU, Brazil and China and compared between nations. The amount of pesticides that were used in the USA and banned in these other nations was compiled and linear regression was used to identify trends in use. Results There are 72, 17, and 11 pesticides approved for outdoor agricultural applications in the USA that are banned or in the process of complete phase out in the EU, Brazil, and China, respectively. Of the pesticides used in USA agriculture in 2016, 322 million pounds were of pesticides banned in the EU, 26 million pounds were of pesticides banned in Brazil and 40 million pounds were of pesticides banned in China. Pesticides banned in the EU account for more than a quarter of all agricultural pesticide use in the USA. The majority of pesticides banned in at least two of these three nations have not appreciably decreased in the USA over the last 25 years and almost all have stayed constant or increased over the last 10 years. Conclusions Many pesticides still widely used in the USA, at the level of tens to hundreds of millions of pounds annually, have been banned or are being phased out in the EU, China and Brazil. Of the pesticides banned in at least two of these nations, many have been implicated in acute pesticide poisonings in the USA and some are further restricted by individual states. The United States Environmental Protection Agency (US EPA) has all but abandoned its use of non-voluntary cancellations in recent years, making pesticide cancellation in the USA largely an exercise that requires consent by the regulated industry. Electronic supplementary material The online version of this article (10.1186/s12940-019-0488-0) contains supplementary material, which is available to authorized users.

Agricultural pesticide use and its associated environmental harms is widespread throughout much of the world. Efforts to mitigate this harm have largely been focused on reducing pesticide contamination of the water and air, as runoff and pesticide drift are the most significant sources of offsite pesticide movement. Yet pesticide contamination of the soil can also result in environmental harm. Pesticides are often applied directly to soil as drenches and granules and increasingly in the form of seed coatings, making it important to understand how pesticides impact soil ecosystems. Soils contain an abundance of biologically diverse organisms that perform many important functions such as nutrient cycling, soil structure maintenance, carbon transformation, and the regulation of pests and diseases. Many terrestrial invertebrates have declined in recent decades. Habitat loss and agrichemical pollution due to agricultural intensification have been identified as major driving factors. Here, we review nearly 400 studies on the effects of pesticides on non-target invertebrates that have egg, larval, or immature development in the soil. This review encompasses 275 unique species, taxa or combined taxa of soil organisms and 284 different pesticide active ingredients or unique mixtures of active ingredients. We identified and extracted relevant data in relation to the following endpoints: mortality, abundance, biomass, behavior, reproduction, biochemical biomarkers, growth, richness and diversity, and structural changes. This resulted in an analysis of over 2,800 separate “tested parameters,” measured as a change in a specific endpoint following exposure of a specific organism to a specific pesticide. We found that 70.5% of tested parameters showed negative effects, whereas 1.4% and 28.1% of tested parameters showed positive or no significant effects from pesticide exposure, respectively. In addition, we discuss general effect trends among pesticide classes, taxa, and endpoints, as well as data gaps. Our review indicates that pesticides of all types pose a clear hazard to soil invertebrates. Negative effects are evident in both lab and field studies, across all studied pesticide classes, and in a wide variety of soil organisms and endpoints. The prevalence of negative effects in our results underscores the need for soil organisms to be represented in any risk analysis of a pesticide that has the potential to contaminate soil, and for any significant risk to be mitigated in a way that will specifically reduce harm to soil organisms and to the many important ecosystem services they provide.