Biology subjects

Mu, X.

Publications and source records attributed to Mu, X..

33 records · Page 2Linked to original sources

bioRxiv2021

Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Proper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the RIG-I-like receptors (RLRs), which recognize viral dsRNA and initiate antiviral innate immune responses with the potential of triggering systemic inflammation and immunopathology. Here we show that stress granules (SGs), molecular condensates that form in response to various stresses including viral dsRNA, play key roles in controlled activation of RLR signaling. Without the SG nucleators G3BP1/2 and UBAP2L, dsRNA triggers excessive inflammation and immune-mediated apoptosis. In addition to exogenous dsRNA, we find that host-derived dsRNA generated in response to ADAR1 deficiency is also controlled by SG biology. Intriguingly, SGs can function beyond immune control by suppressing viral replication independent of the RLR pathway. These observations thus highlight the multi-functional nature of SGs as cellular "shock absorbers" that converge on protecting cell homeostasis-by dampening both toxic immune response and viral replication.

immunology↗

bioRxiv2021

Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes

De novo mutations in POGZ, which encodes the chromatin regulator Pogo Transposable Element with ZNF Domain protein, are strongly associated with autism spectrum disorder (ASD). Here we find that in the developing mouse and human brain POGZ binds predominantly euchromatic loci and these are enriched for human neurodevelopmental disorder genes and transposable elements. We profile chromatin accessibility and gene expression in Pogz-/- mice and find that POGZ promotes chromatin accessibility of candidate regulatory elements (REs) and the expression of clustered synaptic genes. We further demonstrate that POGZ forms a nuclear complex and co-occupies loci with HP1{gamma} and ADNP, another high-confidence ASD risk gene. In Pogz+/- mice, Adnp expression is reduced. We postulate that reduced POGZ dosage disrupts cortical function through alterations in the POGZ-ADNP balance which modifies neuronal gene expression.

neuroscience↗

bioRxiv2021

Comparative genomics reveals evolutionary drivers of sessile life and left-right shell asymmetry in bivalves

Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Evidence from comparative transcriptomics shows that the left-right asymmetrical C. hongkongensis plausibly diverged from the symmetrical Pinctada fucata in expression profiles marked by elevated activities of orthologous transcription factors and lineage-specific shell-related gene families including tyrosinases, which may cooperatively govern asymmetrical shell formation in Ostreoida oysters.

genomics↗

bioRxiv2020

Honeybee gut microbiota modulates host behaviors and neurological processes

Honeybee is a highly social insect with a reach behavioral repertoire and is a versatile model for neurobiological research. The honeybee gut microbiota is composed of a limited number of bacterial phylotypes that play an important role in host health. However, it remains unclear whether the microbiota can shape brain profiles and behaviors. Here, we revealed that the gut microbiota is requisite for the olfactory learning and memory ability of honeybees and alters the level of neurotransmitters in the brain. Transcriptomic and proteomic analysis showed distinctive gene expression and protein signatures for gnotobiotic bees associated with different gut bacteria. Specifically, genes related to olfactory functions and labor division are most upregulated. Moreover, differentially spliced genes in the brains of colonized bees largely overlapped with the datasets for human autism. The circulating metabolome profiles identified that different gut species regulated specific module of metabolites in the host hemolymph. Most altered metabolites are involved in the amino acid and glycerophospholipid metabolism pathways for the production of neuroactive compounds. Finally, antibiotic treatment disturbed the gut community and the nursing behavior of worker bees under field conditions. The brain transcripts and gut metabolism was also greatly interfered in treated bees. Collectively, we demonstrate that the gut microbiota regulates honeybee behaviors, brain gene transcription, and the circulating metabolism. Our findings highlight the contributions of honeybee gut microbes in the neurological processes with striking parallels to those found in other animals, thus providing a promising model to understand the host-microbe interactions via the gut-brain axis.

microbiology↗

bioRxiv2020

Honeybee genetics shape the strain-level structure of gut microbiota in social transmission

Honeybee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honeybees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of queen, we hypothesize that the microbiota structure can be shaped by host genetics. We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of individuals from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and "sequence-discrete population"-level. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. A genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene that is specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the expression and alternative splicing of the gluR-B gene, which is associated with an altered circulating metabolomic profile. Our results indicated that host genetics influence the bee gut composition, and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honeybees have been used extensively as a model organism for social behaviors, genetics, and gut microbiome. Further identification of host genetic function as shaping force of microbial structure will advance our understanding of the host-microbe interactions.

microbiology↗

bioRxiv2020

Zfp36l1 and Zfp36l2 balances proliferation and differentiation in the developing retina

Both transcriptional and post-transcriptional regulation of gene expression play significant roles in diverse biological processes, but little is known about how post-transcriptional regulation impacts retinal development. Here we report our study of the function of two members of the TTP (tristetraprolin) mRNA binding protein family, Zfp36l1 and Zfp36l2, in the developing retina. TTP proteins are highly conserved CCCH zinc finger proteins, which carry out their functions by promoting target mRNA decay and modulating translation. We found that Zfp36l1 and Zfp36l2 were expressed in retinal progenitor cells (RPCs) during development and Muller glial cells and photoreceptors in the mature retina. Our analysis of the mutant retinas showed that, whereas the single knockout retinas were largely normal, the double knockout (DKO) retina showed decreased RPC proliferation and increased differentiation of multiple retinal cell types. RNA-seq analysis confirmed the imbalance of proliferation and differentiation in the DKO retina. Gene ontology and in silico target gene analysis indicates that Zfp36l1 and Zfp36l2 exert their function by directly regulating multiple classes of proteins, including components of multiple signaling pathways such as the sonic hedgehog pathway and the Notch pathway, cell cycle regulators, and most interestingly transcription factors directly involved in retinal differentiation. These results reveal a new tier of gene regulation controlling retinal development.

developmental biology↗

bioRxiv2020

Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases

RNA helicases and ubiquitin E3 ligases mediate many critical functions within cells, but their actions have been studied largely in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryo-electron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity-driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass-spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses thus reveal not only conserved substrates for TRIM proteins but also unexpectedly deep evolutionary connections between TRIM proteins and RNA helicases, thereby linking ubiquitin and RNA biology throughout animal evolution.

biochemistry↗

bioRxiv2020

Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury

Key roles of the gut-brain axis in brain injury development have been suggested in various mouse models; however, little is known about its functional significance in human mild traumatic brain injury (TBI). Here, we decipher this axis by profiling the gut microbiota in 98 acute mild TBI patients and 62 matched controls, and subgroup of them also measured circulating mediators and applied neuroimaging. Mild TBI patients had increased -diversity and different overall microbial compositions compared with controls. 25-microbial genus classifiers distinguish patients from controls with an area under the receiver operating characteristic curve (AUC) of 0.889, while adding serum mediators and neuroimaging features further improved performance even in a small sample size (AUC = 0.969). Numerous correlations existed between gut bacteria, aberrant cortical thickness and cerebrovascular injury. Co-occurrence network analysis revealed two unique gut-brain axes in patients: 1) altered intestinal Lachnospiraceae_NK4A136_group and Eubacterium_ruminantium_group-increased serum GDNF-subcallosal hypertrophy and cerebrovascular injury; 2) decreased intestinal Eubacterium_xylanophilum_group-upregulated IL-6-thinned anterior insula. Our findings provide a new integrated mechanistic understanding and diagnostic model of mild TBI.

microbiology↗

bioRxiv2020

Chromosome-autonomous feedback downregulates meiotic DSB competence upon synaptonemal complex formation

The number of DNA double-strand breaks (DSBs) initiating meiotic recombination is elevated in Saccharomyces cerevisiae mutants that are globally defective in forming crossovers and synaptonemal complex (SC), a protein scaffold juxtaposing homologous chromosomes. These mutants thus appear to lack a negative feedback loop that inhibits DSB formation when homologs engage one another. This feedback is predicted to be chromosome autonomous, but this has not been tested. Moreover, what chromosomal process is recognized as "homolog engagement" remains unclear. To address these questions, we evaluated effects of homolog engagement defects restricted to small portions of the genome using karyotypically abnormal yeast strains with a homeologous chromosome V pair, monosomic V, or trisomy XV. We found that homolog-engagement-defective chromosomes incurred more DSBs, concomitant with prolonged retention of the DSB-promoting protein Rec114, while the rest of the genome remained unaffected. SC-deficient, crossover-proficient mutants ecm11 and gmc2 experienced increased DSB numbers diagnostic of homolog engagement defects. These findings support the hypothesis that SC formation provokes DSB protein dissociation, leading in turn to loss of a DSB competent state. Our findings show that DSB number is regulated in a chromosome-autonomous fashion and provide insight into how homeostatic DSB controls respond to aneuploidy during meiosis. bioRxiv version 2 (September 2020) We added one bioRxiv citation in the discussion section which shows increased breaks in gmc2 and ecm11 mutants. This work was done independently by Keun Kim, Miki Shinohara and colleagues. The pulse gel electrophoresis result shown in Figure 1D has been re-quantified. The conclusion remains that homeologous and monosomic chromosome V generate more DSBs compared to internally controlled chromosome III. One zip3 map included in PCA (Figure 6C) and hierarchical clustering analysis (Figure S5B) has been deleted because this particular map has not yet been published. This change does not affect the conclusion. An additional supplemental table (S5) has been added to show Spo11-oligo datasets used in this study. Figures and preprint have been reformatted. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/089367v2_fig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@871eaforg.highwire.dtl.DTLVardef@ef7995org.highwire.dtl.DTLVardef@176441org.highwire.dtl.DTLVardef@1b6e772_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Higher DSB levels on homolog-engagement defective chromosomes. (A) Cartoons of wild-type, homeologous, monosomic and trisomic chromosome configurations. Grey lines are S. cerevisiae chromosomes and orange lines are S. pastorianus. The homeologous chrV pair rarely synapses or recombines. The trisomic chromosomes can adopt different synaptic configurations ("II+I", partner switch, and triple synapsis). (B) Representative PFGE Southern blots probed for chrIII and chrV. P, signal from parental-length DNA; W, signal in wells. Asterisk indicates an ectopic recombination product between leu2::hisG (on chrIII) and ho::hisG (on chrIV) in the monosomic strain. The other strains do not form this product because they do not have a hisG insert at ho. (C) Poisson-corrected DSB quantification of PFGE Southern blots. (D) Quantification of time-averaged DSBs on chrV relative to chrIII for wild-type, homeologous and monosomic strains. * p<0.05, unpaired t test. Error bars in C, D are mean {+/-} SD except for the monosomic strain (mean {+/-} range). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/089367v2_fig6.gif" ALT="Figure 6"> View larger version (36K): org.highwire.dtl.DTLVardef@1152edforg.highwire.dtl.DTLVardef@1b853daorg.highwire.dtl.DTLVardef@89392dorg.highwire.dtl.DTLVardef@108d65a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO gmc2{Delta} and ecm11{Delta} mutants share similar homolog-engagement signatures as zip3{Delta}. (A, B) Representative labeling of Spo11-oligo complexes in gmc2{Delta} (A) and ecm11{Delta} (B) mutants and quantification relative to wild-type cultures processed in parallel. Error bars indicate mean {+/-} SD for 3 cultures. Radiolabeled Spo11-oligo complexes are detected by autoradiography (left panel, top) and total Spo11 is detected by anti-Flag western blot (WB; left panel, bottom). The two main labeled species differ in the sizes of oligos (Neale et al. 2005). Most Spo11 protein does not end up making DSBs, so nearly all of the visible western blot signal is from free Spo11 that does not have an oligo attached (Neale et al. 2005). (C) Principal component analysis of 21 wild-type and mutant Spo11-oligo maps. (D) Loss of anticorrelation between chromosome length and DSB density in homolog-engagement-defective mutants. Each point is one chromosome. Correlation coefficients (Pearsons r) are shown. (E) Fold change of Spo11-oligo counts in different chromosomal domains. Tel, within 20 kb of telomeres; Cen, within 10 kb of centromeres; rDNA, from 60 kb leftward to 30 kb rightward of rDNA; Interstitial, all others. Horizontal dashed lines mark values assumed as no change (black) and average change (1.8-fold for zip3{Delta}, cyan; 1.7-fold for ecm11{Delta}, purple). Boxes indicate median and interquartile range; whiskers indicate the most extreme data points that are [≤] 1.5 times the interquartile range from the box; individual points are outliers C_FIG O_FIG O_LINKSMALLFIG WIDTH=174 HEIGHT=200 SRC="FIGDIR/small/089367v2_figS5.gif" ALT="Figure 5"> View larger version (35K): org.highwire.dtl.DTLVardef@130cbf6org.highwire.dtl.DTLVardef@9ebe8forg.highwire.dtl.DTLVardef@1f0a2b4org.highwire.dtl.DTLVardef@14a0fcf_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplemental Figure S5.C_FLOATNO DSB patterns in gmc2{Delta} and ecm11{Delta} mutants. (A) Meiotic progression showing percentage of cells completing the first divisions (total bi- and tetra-nucleate cells, mean {+/-} SD, 3 cultures each). At least 100 cells were counted at each time point for each culture. (B) Hierarchical clustering analysis using the "Ward D2" method for 21 wild-type and mutant maps. The y-axis represents height of the cluster dendrogram. In the label for each data set, the letters A, B, C and D stand for maps generated by Xiaojing Mu, Neeman Mohibullah, Megan van Overbeek, and Xuan Zhu, respectively, and the numerals distinguish biological replicate maps. (C) Regional variation in response to zip3{Delta} and ecm11{Delta} mutations for chromosome XII. Lines, local regression (loess) based on Spo11-oligo density changes in 5 kb-bins; green circle, centromere; rDNA location is labeled. (D, E) Fold change of Spo11-oligo densities for zip3{Delta} and ecm11{Delta} compared to wild type in pericentric (D) and telomere-proximal (E) regions. Lines, local regression (loess) for data in 5 kb-bins averaged across 32 chromosome arms; dashed line, no change in black and genome average change in cyan (1.8-fold, zip3{Delta}) and purple (1.7-fold, ecm11{Delta}); yellow shading, zones suppressed for DSB formation as previously defined (Pan etal. 2011). C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@15408baorg.highwire.dtl.DTLVardef@9171aorg.highwire.dtl.DTLVardef@cbabfaorg.highwire.dtl.DTLVardef@187d594org.highwire.dtl.DTLVardef@d6eb68_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOSupplemental Table S5.C_FLOATNO O_TABLECAPTIONSpo11-oligo datasets used in this study C_TABLECAPTION C_TBL

genetics↗

bioRxiv2020

Role of short-chain fatty acids in the gut-brain axis in schizophrenia: contribution to immune activation and pathophysiology in humans and mice

ObjectiveGut microbiota dysbiosis and aberrant gut-brain functional modules including short-chain fatty acid (SCFA) production and long-lasting immune activation (IA) are presented in schizophrenia. Given the key roles of gut microbiota and SCFA in shaping immunity, we propose that dysbiosis-induced SCFA upregulation could contribute to IA and behavioral symptoms in schizophrenia. DesignGut microbiota, SCFA, and IA biomarkers were compared between schizophrenic patients and healthy controls. The roles of SCFA in schizophrenia-related IA were analyzed in cultured peripheral blood mononuclear cells (PBMCs) and a mouse model of schizophrenia. The effects of SCFAs on schizophrenia-related phenotypes were analyzed in both human and mouse. ResultsBoth microbial-derived SCFA and SCFA-producing bacteria were elevated in the guts of schizophrenic patients, and this increased SCFA production in gut was associated with IA in schizophrenia. The microbiome signature underpinning schizophrenia-related IA includes increased diversity and increased SCFA-producing bacteria and inflammation-associated bacteria. The impact of SCFAs on immune responses of cultured PBMC depend on the diagnosis and IA status of donors. Small-molecule serum filtrates from immune-activated schizophrenic patients increased the inflammatory response of PBMCs from healthy volunteers, which can be enhanced and attenuated by SCFAs supplementation and inhibition of SCFA signaling, respectively. Chronically elevated SCFAs in adolescence induced neuroinflammation and schizophrenia-like behaviors in adult mice. Moreover, chronically elevated SCFAs in adult mice prenatally exposed to IA potentiated their expression of schizophrenia-like behaviors. Conclusionmicrobiota-derived SCFAs are important mediators of dysregulated gut-brain axis and participant in pathogenesis via enhance IA in schizophrenia. SummaryO_ST_ABSSignificance of this studyC_ST_ABSO_LIWhat is already known about this subject? [tpltrtarr]Schizophrenia pathogenesis goes beyond the brain since increasing peripheral abnormalities are revealed including gut microbiota dysbiosis, GI dysfunction, and systemic immune activation (IA). [tpltrtarr]Systemic IA/inflammation contributes to the neuroinflammation and brain impairment underlying schizophrenia, and adjunctive immunotherapy can improve psychotic symptoms. [tpltrtarr]Short-chain fatty acids (SCFA) mediate the microbiota-gut-brain communication and modulate several pathways involved in schizophrenia, including pathways of immunity and neurotransmitters. C_LIO_LIWhat are the new findings? [tpltrtarr]Patients with schizophrenia displayed increased rates of IA and increased SCFA production compared with healthy controls, and increased SCFA is associated with IA in patients. [tpltrtarr]A unique microbiota signature including enriched SCFA-producing bacterial species can distinguish patients with IA from other patients and controls. [tpltrtarr]Small molecules in the serum of immune-activated patients with schizophrenia enhance LPS-induced immune response of cultured peripheral blood mononuclear cell (PBMCs), which is partially mediated by SCFA signaling. [tpltrtarr]SCFA intake upregulates both peripheral and brain inflammation and potentiates the expression of schizophrenia-like behaviors in mice prenatally exposed to IA. C_LIO_LIHow might it impact on clinical practice in the foreseeable future? [tpltrtarr]Interference of SCFA signaling or targeted destruction of SCFA-producing bacteria may provide a new approach for the prevention and treatment of schizophrenia. [tpltrtarr]Immune activation status of patients should be an important condition considered when selecting immunotherapy for future precision psychiatric therapy. C_LI

neuroscience↗

bioRxiv2020

Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins

During development, retinal progenitor cells (RPCs) take on different trajectories for distinct cell fates. Previous studies have identified key regulators involved in two key steps of retinal ganglion cell (RGC) genesis; Atoh7 functions in a subpopulation of RPCs to render them competent for the RGC fate, whereas Pou4f2 and Isl1 function to specify the RGC fate and promote RGC differentiation. Extensive research has been performed on the roles of these transcription factors in RGC development, but properties of these two phases they represent and the cellular context in which these two factors function have not been thoroughly investigated, largely due to the cellular heterogeneity of developing retina. In this paper, we describe two novel knock-in mouse alleles, Atoh7zsGreenCreERT2 and Pou4f2FlagtdTomato, which enabled us to label retinal cells in the two phases of RGC development by fluorescent proteins. In addition, the Atoh7zsGreenCreERT2 allele also allowed for indirect labeling of RGCs and other cell types upon tamoxifen induction in a dose-dependent manner. Further, these alleles could be used to purify retinal cells of these different phases by fluorescence assisted cell sorting (FACS). Thus, these two alleles can serve as very useful tools for studying the molecular and genetic mechanisms underlying RGC formation.

developmental biology↗

bioRxiv2020

RNA-seq and scRNA-seq reveal trajectory progression of the retinal ganglion cell lineage in wild-type and Atoh7-null retinas

Past studies concluded that Atoh7 is critical for the emergence of the retinal ganglion cell (RGC) lineage in the developing retina, whereas Pou4f2 and Isl1 function in RGC differentiation. Atoh7 is expressed in a subset of retinal progenitor cells (RPCs) and is considered a competence factor for the RGC fate, but the molecular properties of these RPCs have not been well characterized. In this study, we first used conventional RNA-seq to investigate transcriptomic changes in Atoh7-, Pou4f2-, and Isl1-null retinas at embryonic (E) day 14.5 and identified the differentially expressed genes (DEGs), which expanded our understanding of the scope of downstream events. We then performed single cell RNA-seq (scRNA-seq) on E13.5 and E17.5 wild-type and Atoh7-null retinal cells. Clustering analysis not only correctly identified known cell types at these developmental stages but also revealed a transitional cell state which was marked by Atoh7 and genes for other lineages in a highly overlapping fashion and shared by all early developmental trajectories. Further, analysis of the Atoh7-null retina revealed that, unlike previously believed, the RGC lineage still progressed considerably and a substantial amount of RGC-specific gene expression still occurred. Thus, Atoh7 likely collaborates with other factors to shepherd the transitional RPCs to the RGC lineage by competing with other lineage factors and activating RGC-specific genes. This study thus provides significant insights into the nature of RPC competence for different retinal cell fates and revises our current view on the emergence of the RGC lineage.

developmental biology↗

bioRxiv2019

Mechanism of in vivo activation of the MutLγ-Exo1 complex for meiotic crossover formation

Crossovers generated during the repair of programmed double-strand breaks (DSBs) during homologous recombination are essential for fertility to allow accurate homolog segregation during the first meiotic division. Most crossovers arise through the cleavage of recombination intermediates by the Mlh1-Mlh3 (MutL{gamma}) endonuclease and an elusive non-catalytic function of Exo1, and require the Polo kinase Cdc5. Here we show in budding yeast that MutL{gamma} forms a constitutive complex with Exo1, and in meiotic cells transiently contacts the Msh4-Msh5 (MutS{gamma}) heterodimer, also required for crossover formation. We further show that MutL{gamma}-Exo1 associates with recombination intermediates once they are committed to the crossover repair pathway, and then Exo1 recruits Cdc5 through a direct interaction that is required for activating MutL{gamma} and crossover formation. Exo1 therefore serves as a non-catalytic matchmaker between Cdc5 and MutL{gamma}. We finally show that in vivo, MutL{gamma} associates with the vast majority of DSB hotspots, but at a lower frequency near centromeres, consistent with a strategy to reduce at-risk crossover events in these regions. Our data highlight the tight temporal and spatial control of the activity of a constitutive, potentially harmful, nuclease.

molecular biology↗

bioRxiv2019

Sex-specific phenotypic effects and evolutionary history of an ancient deletion polymorphism of the human growth hormone receptor

The deletion of the third exon of the growth hormone receptor (GHR) is one of the most common genomic structural variants in the human genome. This deletion (GHRd3) has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of puberty, adult height, and longevity. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. Here, we analyzed thousands of genomes and provide evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals. However, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago in East Asia that roughly corresponds with the emergence of archaeological evidence for multiple modern human behaviors, dramatic changes in climate, and a concurrent population expansion. Further, we provide evidence that GHRd3 is associated with protection from edematous severe acute malnutrition primarily in males. Using a mouse line engineered to contain the deletion, we found Ghrd3s effect on the liver transcriptome of male mice grown without any calorie restriction mimics response to calorie restriction through regulation of circadian pathways. In contrast, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers. As a likely consequence, the dramatic weight difference between male and female mice disappears among GHRd3 mice under calorie restriction. Our data provide evidence for sex- and environment-dependent effects of GHRd3 and are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.

evolutionary biology↗

bioRxiv2018

An origin of the immunogenicity of in vitro transcribed RNA

The emergence of RNA-based therapeutics demands robust and economical methods to produce RNA with few byproducts from aberrant activity. While in vitro transcription using the bacteriophage T7 RNA polymerase is one such popular method, its transcripts are known to display an immune-stimulatory activity that is often undesirable and uncontrollable. We here showed that the immune-stimulatory activity of T7 transcript is contributed by its aberrant activity to initiate transcription from a promoter-less DNA end. This activity results in the production of an antisense RNA that is fully complementary to the intended sense RNA product, and consequently a long double-stranded RNA (dsRNA) that can robustly stimulate a cytosolic pattern recognition receptor, MDA5. This promoter-independent transcriptional activity of the T7 RNA polymerase was observed for a wide range of DNA sequences and lengths, but can be suppressed by altering the transcription reaction with modified nucleotides or by reducing the Mg concentration. The current work thus not only offers a previously unappreciated mechanism by which T7 transcripts stimulate the innate immune system, but also shows that the immune-stimulatory activity can be readily regulated.

molecular biology↗