Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 757 records · Page 42Linked to original sources

bioRxiv2019

Nonobese subjects of Bacteroides and Prevotella enterotypes responded differentially to calorie restriction intervention

Calorie restriction (CR), which has the potential effect to weight loss and blood amino acids, has been demonstrated to associate with gut microbiota in human, especially in obese individuals. However, studies for simultaneously evaluating enterotype-dependent impacts of CR on the gut microbiota and blood amino acids in nonobese individuals are still limited.\n\nHere, 41 nonobese individuals received a 3-week CR diet with approximately 50% fewer calories than normal diet. We measured their BMI and blood amino acid concentration, along with the gut microbiota before and after the intervention. In this trial, 28 Enterotype Bacteroides (ETB) subjects and 13 Enterotype Prevotella (ETP) subjects were identified before the intervention. Short-term CR dietary intervention decreased the body mass index (BMI) in most subjects but varied in subjects with different enterotypes. ETP subjects exhibited significantly higher BMI loss ratio than the ETB subjects. CR additionally induced substantial enterotype-independent changes in blood amino acids, but only minor changes in gut microbial composition.\n\nWe further built a prediction model based on baseline relative abundances of 7 gut microbial species showing high performance in predicting CR-associated BMI loss ratio. Among them, the relative abundance of ETB-enriched Clostridium bolteae and C. ramosum were negatively correlated with BMI loss ratio while the relative abundance of Dorea longicatena which was slightly enriched in ETP subjects, was positively correlated with BMI loss ratio.\n\nTogether, our work points out that the individual variation of BMI loss after CR could be partially correlated with different microbial composition and highlights the potential application for microbiome stratification in personalized nutrition intervention.

microbiology↗

bioRxiv2019

Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Disease heterogeneity of immune gene expression patterns of luminal breast cancer (BC) has not been well studied. We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 Asian luminal BC patients and identified three distinct immune subtypes. Tumors in one subtype exhibited signs of T-cell activation, lower ESR1/ESR2 expression ratio and higher expression of immune checkpoint genes, nonsynonymous mutation burden, APOBEC-signature mutations, and increasing body mass index compared to other luminal tumors. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in cases drawn from The Cancer Genome Atlas and a Korean breast cancer study. Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification.

genomics↗

bioRxiv2019

Multilocus sequence analysis, a rapid and accurate identification tool for taxonomic classification, evolutionary relationship and population biology of the genus Shewanella.

The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA and topA) was established as a rapid and accurate identification tool in fifty-nine type Shewanella strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical G+C contents and high genetic similarities. Eighty-six tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species were Shewanella algae, Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis and Shewanella carassii. The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Combined with the genetic, genomic and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica.\n\nIMPORTANCEThe MLSA scheme based on six HKGs (gyrA, gyrB, infB, recN, rpoA and topA) is well established as a reliable tool for taxonomic, evolutionary and epidemiological analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella. The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further studies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships and ecological status of the genus Shewanella.

microbiology↗

bioRxiv2018

Nationwide population genetic screening improves outcomes of newborn screening for hearing loss in China

PurposeConcurrent newborn hearing and genetic screening has been reported, but its benefits have not been statistically proven due to limited sample sizes and outcome data. To fill this gap, we analyzed outcomes of a large number of newborns with genetic screening results.\n\nMethodsNewborns in China were screened for 20 hearing-loss-related genetic variants from 2012-2017. Genetic results were categorized as positive, at-risk, inconclusive, or negative. Hearing screening results, risk factors, and up-to-date hearing status were followed-up via phone interviews.\n\nResultsWe completed genetic screening on one million newborns and followed up 12,778. We found that a positive genetic result significantly indicated a higher positive predictive value of the initial hearing screening (60% vs. 5.0%, P<0.001) and a lower rate of loss-to-follow-up (5% vs. 22%, P<0.001) than an inconclusive one. Importantly, 42% of subjects in the positive group with reported or presymptomatic hearing loss were \"missed\" by conventional hearing screening. Furthermore, genetic screening identified 0.23% of subjects predisposed to preventable ototoxicity.\n\nConclusionOur results demonstrate that limited genetic screening identified additional cases, reduced loss-to-follow-up, and informed families of ototoxicity risks, providing convincing evidence to support integrating genetic screening into universal newborn hearing screening programs.

genetics↗

bioRxiv2018

Phylogenetic reconstruction and divergence time estimation of Blumea DC. (Asteraceae: Inuleae) in China based on nrDNA ITS and cpDNA trnL-F sequences

The genus Blumea DC. is one of the economically most important genera of Inuleae (Asteraceae) in China. It is particularly diverse in south China, where 30 species occur, more than half of which are used as herbal medicine or in the chemical industry. However, little is known about the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea DC. in China. Results indicated the genus of Blumea DC. was monophyletic and could be divided into two clades, the two clades were resolved that differ with respect to habitat, morphology, chromosome type and chemical composition, of their members. Furthermore, based on the two root time of Asteraceae, the divergence time of Blumea DC. were compare estimated. Results indicated the most recent common ancestor of Asteraceae maybe originated from 76-66 Ma, and Blumea DC. maybe originated from 72.71-52.42 Ma, and had an explosive expansion during Oligocene and Miocene (30.09-11.44 Ma), two major clades were differentiated during the Palaeocene and Oligocene (66.29-46.72 Ma), also the evidence from paleogeography and paleoclimate also supported Blumea DC. had an differentiation and explosive expansion during Oligocene and Miocene.

systems biology↗

bioRxiv2018

Reference genes for RT-qPCR normalisation in different tissues, developmental stages and stress conditions of Hypericum perforatum

AbstactHypericum perforatum is a widely known medicinal herb used mostly as a remedy for depression because of its abundant secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is very necessary for the interpretation of qRT-PCR data. In this study, we investigated the expression of fourteen candidate genes, including nine housekeeping genes and five potential candidate genes. Additionally, the HpHYP1 gene, belonging to the PR-10 family associated with stress control, was used for validation of the candidate reference genes. Three programs were applied to evaluate the gene expression stability across four different plant tissues, three developmental stages and a set of abiotic stress and hormonal treatments. The candidate genes showed a wide range of Ct values in all samples, indicating that they are differentially expressed. Integrating all of the algorithms and evaluations, ACT2 and TUB-{beta} were the most stable combination overall and for different developmental stages samples. Moreover, ACT2 and EF1- were considered to be the two most applicable reference genes for different tissues and for stress samples. Majority of the conventional housekeeping genes exhibited better than the potential reference genes. The obtained results will contribute to improving credibility of standardization and quantification of transcription levels in future expression research of H. perforatum.

plant biology↗

bioRxiv2018

Beyond a ribosomal RNA methyltransferase, the wider role of MraW in DNA methylation, motility and colonization in Escherichia coli O157:H7

MraW (RsmH) is an AdoMet-dependent 16S rRNA methyltransferase conserved in bacteria and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus in host animals. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that deletion of mraW led to decreased motility and flagellar production. Whole-genome bisulfite sequencing showed genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant. The methylation level of 4 flagellar gene sequences were further confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated the transcription of these genes was also affected. MraW was observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common motif in differentially methylated regions of promoters and coding regions of the 4 flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase (DNMT) activity assay in vitro. The mraW mutant colonized poorer than wild type in mice. we further found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and has a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.\n\nIMPORTANCEMraW is a well-studied 16S rRNA methyltransferase and was recently found have an impact on bacterial virulence. Here we demonstrated its new function as a DNA methylase and effect on motility, colonization in mice, DNA methylation in genome wide and contribution to virulence. Its direct binding of differentially methylated flagellar-encoding DNA sequences was observed, indicating a correlation between DNA methylation and regulation of flagellar genes. In addition, the expression of mraZ which function as an antagonist of mraW was increased in the mraW mutant. mraW plays an important role in gene regulation likely through DNA methylation. Clearly it plays a role in virulence in E. coli O157:H7. It also opens a new research field for virulence study in bacteria.

microbiology↗

bioRxiv2018

DAZL is a master translational regulator of murine spermatogenesis

Expression of DAZ-like (DAZL) is a hallmark of vertebrate germ cells and essential for embryonic germ cell development and differentiation, yet gametogenic function of DAZL has not been fully characterized with most of its in vivo direct targets unknown. We showed that postnatal stage-specific deletion of Dazl in mouse germ cells did not affect female fertility, but caused complete male sterility with gradual loss of spermatogonial stem cells (SSCs), meiotic arrest and spermatid arrest respectively. Using the genome-wide HITS-CLIP and mass spectrometry approach, we found that DAZL bound to a large number of testicular mRNA transcripts (at least 3008) at 3' UnTranslated Region (3' UTR) and interacted with translation proteins including PABP. In the absence of DAZL, polysome-associated target transcripts, but not their total transcripts were significantly decreased, resulting in drastic reduction of an array of spermatogenic proteins and thus developmental arrest. Thus, DAZL is a master translational regulator essential for spermatogenesis.

developmental biology↗

bioRxiv2018

ManiNetCluster: A Manifold Learning Approach to Reveal the Functional Linkages Across Multiple Gene Networks

The coordination of genome encoded function is a critical and complex process in biological systems, especially across phenotypes or states (e.g., time, disease, organism). Understanding how the complexity of genome-encoded function relates to these states remains a challenge. To address this, we have developed a novel computational method based on manifold learning and comparative analysis, ManiNetCluster, which simultaneously aligns and clusters multiple molecular networks to systematically reveal function links across multiple datasets. Specifically, ManiNetCluster employs manifold learning to match local and non-linear structures among the networks of different states, to identify cross-network linkages. By applying ManiNetCluster to the developmental gene expression datasets across model organisms (e.g., worm, fruit fly), we found that our tool significantly better aligns the orthologous genes than existing state-of-the-art methods, indicating the non-linear interactions between evolutionary functions in development. Moreover, we applied ManiNetCluster to a series of transcriptomes measured in the green alga Chlamy-domonas reinhardtii, to determine the function links between various metabolic processes between the light and dark periods of a diurnally cycling culture. For example, we identify a number of genes putatively regulating processes across each lighting regime, and how comparative analyses between ManiNetCluster and other clustering tools can provide additional insights. ManiNetCluster is available as an R package together with a tutorial at https://github.com/namtk/ManiNetCluster.

bioinformatics↗

bioRxiv2018

Subthalamic nucleus and sensorimotor cortex activity during speech production

The sensorimotor cortex is somatotopically organized to represent the vocal tract articulators, such as lips, tongue, larynx, and jaw. How speech and articulatory features are encoded at the subcortical level, however, remains largely unknown. We analyzed local field potential (LFP) recordings from the subthalamic nucleus (STN) and simultaneous electrocorticography recordings from the sensorimotor cortex of 11 patients (1 female) with Parkinsons disease during implantation of deep brain stimulation (DBS) electrodes, while patients read aloud three-phoneme words. The initial phonemes involved either articulation primarily with the tongue (coronal consonants) or the lips (labial consonants). We observed significant increases in high gamma (60-150 Hz) power in both the STN and the sensorimotor cortex that began before speech onset and persisted for the duration of speech articulation. As expected from previous reports, in the sensorimotor cortex, the primary articulator involved in the production of the initial consonant was topographically represented by high gamma activity. We found that STN high gamma activity also demonstrated specificity for the primary articulator, although no clear topography was observed. In general, subthalamic high gamma activity varied along the ventral-dorsal trajectory of the electrodes, with greater high gamma power recorded in the more dorsal locations of the STN. These results demonstrate that articulator-specific speech information is contained within high gamma activity of the STN, with similar temporal but less specific topographical organization, compared to similar information encoded in the sensorimotor cortex.\n\nSIGNIFICANCE STATEMENTClinical and electrophysiological evidence suggests that the subthalamic nucleus is involved in speech, however, this important basal ganglia node is ignored in current models of speech production. We previously showed that subthalamic nucleus neurons differentially encode early and late aspects of speech production, but no previous studies have examined subthalamic functional organization for speech articulators. Using simultaneous local field potential recordings from the sensorimotor cortex and the subthalamic nucleus in patients with Parkinsons disease undergoing deep brain stimulation surgery, we discovered that subthalamic nucleus high gamma activity tracks speech production at the level of vocal tract articulators, with high gamma power beginning to increase prior to the onset of vocalization, similar to cortical articulatory encoding.

neuroscience↗

bioRxiv2018

Cytologic, Genetic, and Proteomic Analysis of a Yellow Leaf Mutant of Sesame (Sesamum indicum L.), Siyl-1

Leaf color mutation in sesame always affects the growth and development of plantlets, and their yield. To clarify the mechanisms underlying leaf color regulation in sesame, we analyzed a yellow-green leaf mutant. Genetic analysis of the mutant selfing revealed 3 phenotypes--YY, light-yellow (lethal); Yy, yellow-green; and yy, normal green--controlled by an incompletely dominant nuclear gene, Siyl-1. In YY and Yy, the number and morphological structure of the chloroplast changed evidently, with disordered inner matter, and significantly decreased chlorophyll content. To explore the regulation mechanism of leaf color mutation, the proteins expressed among YY, Yy, and yy were analyzed. All 98 differentially expressed proteins (DEPs) were classified into 5 functional groups, in which photosynthesis and energy metabolism (82.7%) occupied a dominant position. Our findings provide the basis for further molecular mechanism and biochemical effect analysis of yellow leaf mutants in plants.

genetics↗

bioRxiv2018

Genome structure and evolution of Antirrhnum majus L.

Snapdragon (Antirrhinum majus L.), a member of Plantaginaceae, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a high-quality genome assembly of A. majus cultivated JI7 (A. majus cv.JI7) of a 510 Mb with 37,714 annotated protein-coding genes. The scaffolds covering 97.12% of the assembled genome were anchored on 8 chromosomes. Comparative and evolutionary analyses revealed that Plantaginaceae and Solanaceae diverged from their most recent ancestor around 62 million years ago (MYA). We also revealed the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility including a unique TCP duplication around 46-49 MYA and a near complete{psi} S-locus of ca.2 Mb. The genome sequence obtained in this study not only provides the first genome sequenced from Plantaginaceae but also bring the popular plant model system of Antirrhinum into a genomic age.

genomics↗

bioRxiv2018

Dissecting the pharmacological landscape of cancer cells to reveal novel target populations

Personalised medicine has predominantly focused on genetically-altered cancer genes that stratify drug responses, but there is a need to objectively evaluate differential pharmacology patterns at a subpopulation level. Here, we introduce an approach based on unsupervised machine learning to compare the pharmacological response relationships between 327 pairs of cancer therapies. This approach integrated multiple measures of response to identify subpopulations that react differently to inhibitors of the same or different targets to understand mechanisms of resistance and pathway cross-talk. MEK, BRAF, and PI3K inhibitors were shown to be effective as combination therapies for particular BRAF mutant subpopulations. A systematic analysis of preclinical data for a failed phase III trial of selumetinib combined with docetaxel in lung cancer suggests potential indications in urogenital and colorectal cancers with KRAS mutation. This data-informed study exemplifies a method for stratified medicine to identify novel cancer subpopulations, their genetic biomarkers, and effective drug combinations.

bioinformatics↗

bioRxiv2018

Localization of balanced chromosome translocation breakpoints by long-read sequencing on the Oxford Nanopore platform

Structural variants (SVs) in genomes, including translocations, inversions, insertions, deletions and duplications, remain difficult to be detected reliably by traditional genomic technologies. In particular, balanced translocations and inversions cannot be detected by microarrays since they do not alter chromosome copy numbers; they cannot be reliably detected by short-read sequencing either, since many breakpoints are located within repetitive regions of the genome that are unmappable by short reads. However, the detection and the precise localization of breakpoints at the nucleotide level are important to study the genetic causes in patients carrying balanced translocations or inversions. Long-read sequencing techniques, such as the Oxford Nanopore Technology (ONT), may detect these SVs in a more direct, efficient and accurate manner. In this study, we applied whole-genome long-read sequencing on the Oxford Nanopore GridION sequencer to detect the breakpoints from 6 carriers of balanced translocations and one carrier of inversion, where SVs had initially been detected by karyotyping at the chromosome level. The results showed that all the balanced translocations were detected with [~]10X coverage and were consistent with the karyotyping results. PCR and Sanger sequencing confirmed 8 of the 14 breakpoints to single base resolution, yet other breakpoints cannot be refined to single-base due to their localization at highly repetitive regions or pericentromeric regions, or due to the possible presence of local deletions/duplications. Our results indicate that low-coverage whole-genome sequencing is an ideal tool for the precise localization of most translocation breakpoints and may provide haplotype information on the breakpoint-linked SNPs, which may be widely applied in SV detection, therapeutic monitoring, assisted reproduction technology (ART) and preimplantation genetic diagnosis (PGD).

genetics↗

bioRxiv2018

Non-driver somatic alteration burden confers good prognosis in non-small cell lung cancer

BackgroundGenomic profiling of patient tumors has linked somatic driver mutations to survival outcomes of non-small cell lung cancer (NSCLC) patients, especially for those receiving targeted therapies. However, it remains unclear whether specific non-driver mutations have any prognostic utility.\n\nMethodsWhole exomes and transcriptomes were measured from NSCLC xenograft models of patients with diverse clinical outcomes. Penalised regression analysis was performed to identify a set of 865 genes associated with patient survival. The number of somatic copy number aberrations, point mutations and associated expression changes within the 865 genes were used to stratify independent NSCLC patient populations, filtered for chemotherapy naive and early-stage. In-depth genomic analysis and functional testing was conducted on the genomic alterations to understand their effect on improving survival.\n\nResultsHigh burden of somatic alterations are associated with longer disease-free survival (HR=0.153, P=1.48x10-4) in NSCLC patients. When somatic alterations burden was integrated with gene expression, we were able to predict prognosis in three independent patient datasets. Patients with high alteration burden could be further stratified based on the presence of immunogenic mutations, revealing another subgroup of patients with even better prognosis (85% with >5 years survival), and associated with cytotoxic T-cell expression. In addition, 95% of these 865 genes lack documented activity relevant to cancer, but are in pathways regulating cell proliferation, motility and immune response were implicated.\n\nConclusionOur results demonstrate that non-driver somatic alterations may influence the outcome of cancer patients by increasing beneficial immune response and inhibiting processes associated to tumorigenesis.

cancer biology↗

bioRxiv2018

Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses

MotivationThe virulence of influenza viruses is a complex multigenic trait. Previous studies about the virulence determinants of influenza viruses mainly focused on amino acid sites, ignoring the influence of nucleotide mutations.\n\nResultsWe collected more than 200 viral strains from 21 subtypes of influenza A viruses with virulence in mammals and obtained over 100 mammalian virulence-related nucleotide sites across the genome by computational analysis. Interestingly, 50 of these nucleotide sites only experienced synonymous mutations. Further experiments showed that synonymous mutations in the top two of these nucleotide sites, i.e., PB1-2031 and PB1-633, enhanced the pathogenicity of the viruses in mice. Finally, machine-learning models with accepted accuracy for predicting mammalian virulence of influenza A viruses were built. Overall, this study highlighted the importance of nucleotide mutations, especially synonymous mutations in viral virulence, and provided rapid methods for evaluating the virulence of influenza A viruses. It could be helpful for early warning of newly emerging influenza A viruses.

microbiology↗

bioRxiv2018

Genome-wide identification and expression specificity analysis of the DNA methyltransferase gene family under adversity stresses in cotton

DNA methylation is an important epigenetic mode of genomic DNA modification that is an important part of maintaining epigenetic content and regulating gene expression. DNA methyltransferases (MTases) are the key enzymes in the process of DNA methylation. Thus far, there has been no systematic analysis the DNA MTases found in cotton. In this study, the whole genome of cotton C5-Mtase coding genes was identified and analyzed using a bioinformatics method based on information from the cotton genome. In this study, 51 DNA MTase genes were identified, of which 8 belonged to G. raimondii (group D), 9 belonged to G. arboretum L. (group A), 16 belonged to G. hirsutum L. (group AD1) and 18 belonged to G. barbadebse L. (group AD2). Systematic evolutionary analysis divided the 51 genes into four subfamilies, including 7 MET homologous proteins, 25 CMT homologous proteins, 14 DRM homologous proteins and 5 DNMT2 homologous proteins. Further studies showed that the DNA MTases in cotton were more phylogenetically conserved. The comparison of their protein domains showed that the C-terminal functional domain of the 51 proteins had six conserved motifs involved in methylation modification, indicating that the protein has a basic catalytic methylation function and the difference in the N-terminal regulatory domains of the 51 proteins divided the proteins into four classes, MET, CMT, DRM and DNMT2, in which DNMT2 lacks an N-terminal regulatory domain. Gene expression in cotton is not the same under different stress treatments. Different expression patterns of DNA MTases show the functional diversity of the cotton DNA methyltransferase gene family. VIGS silenced Gossypium hirsutum l. in the cotton seedling of DNMT2 family gene GhDMT6, after stress treatment the growth condition was better than the control. The distribution of DNA MTases varies among cotton species. Different DNA MTase family members have different genetic structures, and the expression level changes with different stresses, showing tissue specificity. Under salt and drought stress, G. hirsutum L. TM-1 increased the number of genes more than G. raimondii and G. arboreum L. Shixiya 1. The resistance of Gossypium hirsutum L.TM-1 to cold, drought and salt stress was increased after the plants were silenced with GhDMT6 gene.

genomics↗

bioRxiv2018

Intensive and Specific Feedback Self-control of MicroRNA Targeting Activity

The miRNA pathway consists of three segments - biogenesis, targeting and downstream regulatory effectors. How the cells control their activities remains incompletely understood. This study explored the intrinsically complex miRNA-mRNA targeting relationships, and suggested differential mechanistic control of the three segments. We first analyzed evolutionarily conserved sites for conserved miRNAs in the human transcriptome. Strikingly, AGO1, AGO2 and AGO3 are all among the top 14 mRNAs with highest numbers of unique conserved miRNA sites, and so is ANKRD52, the phosphatase regulatory subunit of the recently identified AGO phosphorylation cycle (AGOs, CSNK1A1, ANKRD52 and PPP6C). The mRNAs for TNRC6, which acts together with loaded AGO to channel miRNA-mediated regulation actions onto specific mRNAs, are also heavily miRNA-targeted. Moreover, mRNAs of the AGO phosphorylation cycle share much more than expected miRNA binding sites. In contrast, upstream miRNA biogenesis mRNAs do not display these characteristics, and neither do the downstream regulatory effector mRNAs. In a word, miRNAs heavily and directly feedback-regulate their targeting machinery mRNAs, but neither upstream biogenesis nor downstream regulatory effector mRNAs. The observation was then confirmed with experimentally determined miRNA-mRNA target relationships. In summary, our exploration of the miRNA-mRNA target relationship uncovers intensive, and specific, feedback auto-regulation of miRNA targeting activity directly by miRNAs themselves, i.e., segment-specific feedback auto-regulation of miRNA pathway. Our results also suggest that the complexity of miRNA-mRNA targeting relationship - a defining feature of miRNA biology - should be a rich source for further functional exploration.

cell biology↗