Biology subjects

Sun, B.

Publications and source records attributed to Sun, B..

11 recordsLinked to original sources

bioRxiv2018

Acetic acid activates distinct taste pathways in Drosophila to elicit opposing, state-dependent feeding responses

Taste circuits are genetically determined to elicit an innate appetitive or aversive response, ensuring that animals consume nutritious foods and avoid the ingestion of toxins. We have examined the response of the fruit fly Drosophila melanogaster to acetic acid, a tastant that can be a metabolic resource but can also be toxic to the fly. Our data reveal that flies accommodate these conflicting attributes of acetic acid by virtue of a hunger-dependent switch in their behavioral response to this stimulus. Fed flies show taste aversion to acetic acid, likely a response to its potential toxicity, whereas starved flies show a robust appetitive response that may reflect their overriding need for calories. These opposing responses are mediated by two different classes of taste neurons. Acetic acid activates both the sugar and bitter pathways, which have opposing effects on feeding behavior. Hunger shifts the response from aversion to attraction by enhancing the appetitive sugar pathway as well as suppressing the aversive bitter pathway. Thus a single tastant can drive opposing behaviors by activating distinct taste pathways modulated by internal state.

neuroscience↗

bioRxiv2018

Transcriptional trajectories of human kidney disease progression

Our molecular understanding of clinical conditions progressing from acute organ injury to irreversible dysfunction is limited. We used renal transplantation as a model to characterize the transcriptional response along the transition from acute kidney injury to allograft fibrosis in humans. The integrated analysis of 163 transcriptomes with machine learning techniques identified shared and divergent transcriptional trajectories determining distinct clinical outcomes in a heterogeneous population. The molecular map of renal responses to injury was validated in a mouse ischemia-reperfusion injury model and highlighted early markers of disease progression. This generally applicable approach opens the way for an unbiased analysis of progressive diseases.

pathology↗

bioRxiv2018

Late B lymphocyte action in dysfunctional tissue repair following kidney injury and transplantation

The mechanisms initiating the late immune response to allografts are poorly understood. Through transcriptome analysis of serial protocol biopsies in kidney transplant recipients, we found a tight correlation between the initial response to kidney injury and a late B lymphocyte signature associated with renal dysfunction and fibrosis, suggesting a link between dysfunctional repair and immunoreactivity. To specifically investigate the immunological consequences of dysfunctional repair, we followed the mouse kidney up to 18 months after ischemia/reperfusion. Even in the absence of foreign antigens we identified a sustained immune response in conjunction with the transition to chronic kidney damage. This tissue-driven immunological process involved both the innate and the adaptive immune system and eventually induced an antigen-driven proliferation, selection and maturation of B lymphocytes into broadly-reacting antibody secreting cells. These findings reveal an unappreciated role of dysfunctional tissue repair on local immunoregulation with a particular relevance for late transplantation immunobiology.

immunology↗

bioRxiv2018

Helicase Promotes Replication Re-initiation from an RNA Transcript

To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind the DNA, resulting in a gap in the newly replicated DNA. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. As the helicase advances the fork, the DNAP also moves forward processively, via its association with the helicase. The presence of the DNAP, in turn, increases both helicases processivity and unwinding rate. We show that such a DNAP, together with its helicase, is indeed able to actively disrupt a stalled transcription elongation complex, and then initiates replication using the RNA transcript as a primer. These observations exhibit T7 helicases novel role in replication re-initiation, independent of replication restart proteins or primase.

biophysics↗

bioRxiv2018

Dual roles of electrostatic-steering and conformational dynamics in the binding of calcineurin’s intrinsically-disordered recognition domain to calmodulin

calcineurin (CaN) is a serine/threonine phosphatase that regulates a variety of physiological and pathophysiological processes in mammalian tissue. The CaN regulatory domain (RD) is responsible for regulating the enzymes phosphatase activity, and is believed to be highly-disordered when inhibiting CaN, but undergoes a disorderto-order transition upon diffusion-limited binding with the regulatory protein calmodulin (CaM). The prevalence of polar and charged amino acids in the regulatory domain (RD) suggests electrostatic interactions are involved in mediating CaM binding, yet the lack of atomistic-resolution data for the bound complex has stymied efforts to probe how the RD sequence controls its conformational ensemble and long-range attractions contribute to target protein binding. In the present study, we investigated via computational modeling the extent to which electrostatics and structural disorder cofacilitate or hinder CaM/CaN association kinetics. Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics versus conformational diversity in controlling diffusion-limited association rates, via microsecond-scale molecular dynamics (MD) and Brownian dynamic (BD) simulations. Our results indicate that the RD amino acid composition and sequence length influence both the dynamic availability of conformations amenable to CaM binding, as well as long-range electrostatic interactions to steer association. These findings provide intriguing insight into the interplay between conformational diversity and electrostatically-driven protein-protein association involving CaN, which are likely to extend to wide-ranging diffusion-limited processes regulated by intrinsically-disordered proteins.

biophysics↗

bioRxiv2018

Reversion of the photoperiod dependence of flowering in rice with synthetic Hd1-microProteins

Rice (Oryza sativa) is a facultative short-day plant that flowers very late when grown in non-inductive long day conditions. Photoperiod-dependent flowering in rice is regulated by heading date (Hd1) which acts as both an activator and repressor of flowering in a day length-dependent manner. In order to regulate flowering of rice in long days (LD), overexpression of a synthetic Hd1miP, which is capable of interacting with Hd1, was employed. Transgenic Hd1miP rice plants flowered significantly earlier when grown in LD compared to SD, showing that synthetic microProteins can be used to revert short-day plants to long-day plants. Yield analysis revealed that although the OX-Hd1miP grains are comparable to WT in terms of the size of the grains produced, OX-Hd1miP plants like hd1 knockout plants, are compromised in the number of grains produced and the grain maturity rate, suggesting an additional unrecognized role of Hd1 in grain maturity.

plant biology↗

bioRxiv2018

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

MicroProteins have emerged as potent regulators of transcription factor activity. Here we use a combination of forward genetics and proteomics to dissect the miP1a/b microProtein complex that acts to delay the floral transition in Arabidopsis. The microProteins miP1a and miP1b can bridge an interaction between the flowering promoting factor CONSTANS (CO) and the TOPLESS (TPL) co-repressor protein to represses flowering. We find that the JUMONJI14 (JMJ14) histone demethylase is part of this repressor complex that can initiate chromatin changes in FLOWERING LOCUS T (FT) gene, the direct target of CO. Plants with mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on the activity of CO, supporting a role for CO in this repressive complex. When mis-expressed at the shoot apex, CO can induce early flowering only in the jmj14 background. Our results indicate that the repressor acts in the shoot apical meristem to keep it in an undifferentiated state until the leaf-derived florigen signal induces the conversion into a floral meristem.

plant biology↗

bioRxiv2017

ProGeM: A framework for the prioritisation of candidate causal genes at molecular quantitative trait loci

Quantitative trait locus (QTL) mapping of molecular phenotypes such as metabolites, lipids, and proteins through genome-wide association studies (GWAS) represents a powerful means of highlighting molecular mechanisms relevant to human diseases. However, a major challenge of this approach is to identify the causal gene(s) at the observed QTLs. Here we present a framework for the \"Prioritisation of candidate causal Genes at Molecular QTLs\" (ProGeM), which incorporates biological domain-specific annotation data alongside genome annotation data from multiple repositories. We assessed the performance of ProGeM using a reference set of 227 previously reported and extensively curated metabolite QTLs. For 98% of these loci, the expert-curated gene was one of the candidate causal genes prioritised by ProGeM. Benchmarking analyses revealed that 69% of the causal candidates were nearest to the sentinel variant at the investigated molecular QTLs, indicating that genomic proximity is the most reliable indicator of \"true positive\" causal genes. In contrast, cis-gene expression QTL data led to three false positive candidate causal gene assignments for every one true positive assignment. We provide evidence that these conclusions also apply to other molecular phenotypes, suggesting that ProGeM is a powerful and versatile tool for annotating molecular QTLs. ProGeM is freely available via GitHub.

bioinformatics↗

bioRxiv2017

Resting-state connectivity predicts patient-specific effects of deep brain stimulation for Parkinson’s disease

Neural circuit-based guidance for optimizing patient screening, target selection and parameter tuning for deep brain stimulation (DBS) remains limited. To this end, we propose a functional brain connectome-based modeling approach that simulates network-spreading effects of stimulating different brain regions and quantifies rectification of abnormal network topology in silico. We validate these analyses by predicting nuclei in basal-ganglia circuits as top-ranked targets for 43 local patients with Parkinsons disease and 90 patients from public database. However, individual connectome-based predictions demonstrate that globus pallidus and subthalamic nucleus (STN) constituted as the best choice for 21.1% and 19.5% of patients, respectively. Notably, the priority rank of STN significantly correlated with motor symptom severity in the local cohort. By introducing whole-brain network diffusion dynamics, these findings unfold a new dimension of brain connectomics and underscore the importance of neural network modeling for personalized DBS therapy, which warrants experimental investigation to validate its clinical utility.

neuroscience↗

bioRxiv2017

The GENIUS Approach to Robust Mendelian Randomization Inference

Mendelian randomization (MR) is a popular instrumental variable (IV) approach, in which one or several genetic markers serve as IVs that can be leveraged to recover under certain conditions, valid inferences about a given exposure-outcome causal association subject to unmeasured confounding. A key IV identification condition known as the exclusion restriction states that the IV has no direct effect on the outcome that is not mediated by the exposure in view. In MR studies, such an assumption requires an unrealistic level of knowledge and understanding of the mechanism by which the genetic markers causally affect the outcome, particularly when a large number of genetic variants are considered as IVs. As a result, possible violation of the exclusion restriction can seldom be ruled out in such MR studies, and if present, such violation can invalidate IVbased inferences even if unbeknownst to the analyst, confounding is either negligible or absent. To address this concern, we introduce a new class of IV estimators which are robust to violation of the exclusion restriction under a large collection of data generating mechanisms consistent with parametric models commonly assumed in the MR literature. Our approach which we have named \"MR G-Estimation under No Interaction with Unmeasured Selection\" (MR GENIUS) may in fact be viewed as a modification to Robins G-estimation approach that is robust to both additive unmeasured confounding and violation of the exclusion restriction assumption. We also establish that estimation with MR GENIUS may also be viewed as a robust generalization of the well-known Lewbel estimator for a triangular system of structural equations with endogeneity. Specifically, we show that unlike Lewbel estimation, MR GENIUS is under fairly weak conditions also robust to unmeasured confounding of the effects of the genetic IVs on both the exposure and the outcome, another possible violation of a key IV Identification condition. Furthermore, while Lewbel estimation involves specification of linear models both for the outcome and the exposure, MR GENIUS generally does not require specification of a structural model for the direct effect of invalid IVs on the outcome, therefore allowing the latter model to be unrestricted. Finally, unlike Lewbel estimation, MR GENIUS is shown to equally apply for binary, discrete or continuous exposure and outcome variables and can be used under prospective sampling, or retrospective sampling such as in a case-control study, as well as for right censored time-to-event outcomes under an additive hazards model.

epidemiology↗

bioRxiv2017

Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis

Many long non-coding RNAs (lncRNAs) are expressed during central nervous system (CNS) development, yet their in vivo roles and molecular mechanisms of action remain poorly understood. Paupar, a CNS expressed lncRNA, controls neuroblastoma cell growth by binding and modulating the activity of genome-wide transcriptional regulatory elements. We show here that Paupar transcript directly binds KAP1, an essential epigenetic regulatory protein, and thereby regulates the expression of shared target genes important for proliferation and neuronal differentiation. Paupar promotes KAP1 chromatin occupancy and H3K9me3 deposition at a subset of distal targets, through formation of a DNA binding ribonucleoprotein complex containing Paupar, KAP1 and the PAX6 transcription factor. Paupar-KAP1 genome-wide co-occupancy reveals a 4-fold enrichment of overlap between Paupar and KAP1 bound sequences. Furthermore, both Paupar and Kap1 loss of function in vivo accelerates lineage progression in the mouse postnatal subventricular zone (SVZ) stem cell niche and disrupts olfactory bulb neurogenesis. These observations provide important conceptual insights into the trans-acting modes of lncRNA-mediated epigenetic regulation, the mechanisms of KAP1 genomic recruitment and identify Paupar and Kap1 as regulators of SVZ neurogenesis.

neuroscience↗