RNA transcribed from heterochromatic simple-tandem repeats are required for male fertility and histone-protamine exchange in Drosophila melanogaster, bioRxiv, 2019-04-25

AbstractLong arrays of simple, tandemly repeated DNA sequences (known as satellites) are enriched in centromeres1 and pericentromeric regions2, and contribute to chromosome segregation and other heterochromatin functions3,4. Surprisingly, satellite DNAs are expressed in many multicellular eukaryotes, and their aberrant transcription may contribute to carcinogenesis and cellular toxicity5-7. Satellite transcription andor RNAs may also promote centromere and heterochromatin activities 8-12. However, we lack direct evidence that satellite DNA transcripts are required for normal cell or organismal functions. Here, we show that satellite RNAs derived from AAGAG tandem repeats are transcribed in many cell types throughout Drosophila melanogaster development, enriched in neuronal tissues and testes, localized within heterochromatic regions, and important for viability. Strikingly, we find that AAGAG transcripts are necessary for male fertility and are specifically required for normal histone-protamine exchange and sperm chromatin organization. Since AAGAG RNA-dependent events happen late in spermatogenesis when the transcripts are not detected, we speculate that AAGAG RNA functions in primary spermatocytes to ‘prime’ post-meiosis steps in sperm maturation. In addition to demonstrating specific essential functions for AAGAG RNAs, comparisons between closely related Drosophila species suggest that satellite repeats and their transcription evolve quickly to generate new functions.

biorxiv cell-biology 100-200-users 2019

The gut microbiota influences how circulating immune cells in humans change from one day to the next, bioRxiv, 2019-04-25

ABSTRACTThe gut microbiota influences the development and homeostasis of the mammalian immune system1–3, can alter immune cell compositions in mice4–7, and is associated with responses to immunotherapy that rely on the activity of peripheral immune cells8–12. Still, our understanding of how the microbiota modulates circulatory immune cells remains limited, particularly in humans where a lack of manipulative experiments makes inference challenging. Here we overcome this challenge by studying hundreds of hospitalized—and closely monitored—bone marrow transplantation patients as they recover from chemotherapy-induced immune ablation. This aggressive treatment causes large shifts in both circulatory immune cell and microbiota populations, allowing the relationships between the two to be studied simultaneously over time with unprecedented resolution. We analyzed daily changes in white blood cell counts from 2,235 patients, and 10,680 longitudinal fecal microbiota samples to identify bacterial genera consistently associated with those changes. Bayesian inference and validation across different patient cohorts revealed consistent associations between intestinal bacteria and peripheral immune cell dynamics in the context of immunomodulatory medications, clinical metadata and homeostatic feedbacks between peripheral immune cells. The quantification of validated microbiota associations enabled us to contrast the potency of fermentatively active, obligate anaerobic bacteria with that of medications with known immunomodulatory mechanism, and this way estimate the microbiota potential to alter peripheral immune cell dynamics directly in patients. Our analysis establishes and quantifies the link between the intestinal microbiota and immune cell dynamics in humans, with implications for microbiota-driven modulation of immunity and immunotherapies that rely on circulatory immune cells.

biorxiv microbiology 100-200-users 2019

Alzheimer’s patient brain myeloid cells exhibit enhanced aging and unique transcriptional activation, bioRxiv, 2019-04-19

AbstractGene expression changes in brain microglia from mouse models of Alzheimer’s disease (AD) are highly characterized and reflect specific myeloid cell activation states that could modulate AD risk or progression. While some groups have produced valuable expression profiles for human brain cells1–4, the cellular clarity with which we now view transcriptional responses in mouse AD models has not yet been realized for human AD tissues due to limited availability of fresh tissue samples and technological hurdles of recovering transcriptomic data with cell-type resolution from frozen samples. We developed a novel method for isolating multiple cell types from frozen post-mortem specimens of superior frontal gyrus for RNA-Seq and identified 66 genes differentially expressed between AD and control subjects in the myeloid cell compartment. Myeloid cells sorted from fusiform gyrus of the same subjects showed similar changes, and whole tissue RNA analyses further corroborated our findings. The changes we observed did not resemble the “damage-associated microglia” (DAM) profile described in mouse AD models5, or other known activation states from other disease models. Instead, roughly half of the changes were consistent with an “enhanced human aging” phenotype, whereas the other half, including the AD risk gene APOE, were altered in AD myeloid cells but not differentially expressed with age. We refer to this novel profile in human Alzheimer’s microgliamyeloid cells as the HAM signature. These results, which can be browsed at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpresearch-pub.gene.comBrainMyeloidLandscapereviewVersion>research-pub.gene.comBrainMyeloidLandscapereviewVersion<jatsext-link>, highlight considerable differences between myeloid activation in mouse models and human disease, and provide a genome-wide picture of brain myeloid activation in human AD.

biorxiv neuroscience 100-200-users 2019

Diversity begets diversity in microbiomes, bioRxiv, 2019-04-19

AbstractMicrobes are embedded in complex microbiomes where they engage in a wide array of inter- and intra-specific interactions1–4. However, whether these interactions are a significant driver of natural biodiversity is not well understood. Two contrasting hypotheses have been put forward to explain how species interactions could influence diversification. ‘Ecological Controls’ (EC) predicts a negative diversity-diversification relationship, where the evolution of novel types becomes constrained as available niches become filled5. In contrast, ‘Diversity Begets Diversity’ (DBD) predicts a positive relationship, with diversity promoting diversification via niche construction and other species interactions6. Using the Earth Microbiome Project, the largest standardized survey of global biodiversity to date7, we provide support for DBD as the dominant driver of microbiome diversity. Only in the most diverse microbiomes does DBD reach a plateau, consistent with increasingly saturated niche space. Genera that are strongly associated with a particular biome show a stronger DBD relationship than non-residents, consistent with prolonged evolutionary interactions driving diversification. Genera with larger genomes also experience a stronger DBD response, which could be due to a higher potential for metabolic interactions and niche construction offered by more diverse gene repertoires. Our results demonstrate that the rate at which microbiomes accumulate diversity is crucially dependent on resident diversity. This fits a scenario in which species interactions are important drivers of microbiome diversity. Further (population genomic or metagenomic) data are needed to elucidate the nature of these biotic interactions in order to more fully inform predictive models of biodiversity and ecosystem stability4,5.

biorxiv evolutionary-biology 100-200-users 2019

 

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