Biology subjects

Li, Q.

Publications and source records attributed to Li, Q..

At least 721 records · Page 40Linked to original sources

bioRxiv2019

Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

Adenosine-to-Inosine RNA editing is catalyzed by ADAR enzymes that deaminate adenosine to inosine. While many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass-spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a global negative regulator of editing. This work demonstrates the broad roles RNA binding proteins play in regulating editing levels and establishes DZF-domain containing proteins as a group of highly influential RNA editing regulators.

genetics↗

bioRxiv2019

Zinc finger RNA binding protein Zn72D regulates ADAR-mediated RNA editing in neurons

Adenosine-to-inosine RNA editing, catalyzed by ADAR enzymes, alters RNA sequences from those encoded by DNA. These editing events are dynamically regulated, but few trans regulators of ADARs are known in vivo. Here, we screen RNA binding proteins for roles in editing regulation using in vivo knockdown experiments in the Drosophila brain. We identify Zinc-Finger Protein at 72D (Zn72D) as a regulator of editing levels at a majority of editing sites in the brain. Zn72D both regulates ADAR protein levels and interacts with ADAR in an RNA-dependent fashion, and similar to ADAR, Zn72D is necessary to maintain proper neuromuscular junction architecture and motility in the fly. Furthermore, the mammalian homolog of Zn72D, Zfr, regulates editing in mouse primary neurons, demonstrating the conservation of this regulatory role. The broad and conserved regulation of ADAR editing by Zn72D in neurons represents a novel mechanism by which critically important editing events are sustained.

genetics↗

bioRxiv2019

TeraVR Empowers Precise Reconstruction of Complete 3-D Neuronal Morphology in the Whole Brain

Neuron morphology is recognized as a key determinant of cell type, yet the quantitative profiling of a mammalian neurons complete three-dimensional (3-D) morphology remains arduous when the neuron has complex arborization and long projection. Whole-brain reconstruction of neuron morphology is even more challenging as it involves processing tens of teravoxels of imaging data. Validating such reconstructions is extremely laborious. We developed TeraVR, an open-source virtual reality annotation system, to address these challenges. TeraVR integrates immersive and collaborative 3-D visualization, interaction, and hierarchical streaming of teravoxel-scale images. Using TeraVR, we produced precise 3-D full morphology of long-projecting neurons in whole mouse brains and developed a collaborative workflow for highly accurate neuronal reconstruction.

neuroscience↗

bioRxiv2019

Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis

Intronic transposable elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, which is directly associated with RNA Pol V to inhibit the entry of RNA Pol II and the occupancy of H3K4 methylation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that this is a common mechanism among intronic heterochromatin-containing genes. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.

plant biology↗

bioRxiv2019

Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing

Enhancer loci identified by ChIP-Seq or other experimental methods occupy hundreds of base pairs on the genome. It is the paradox comparing with the motif analysis, which usually contains only a few or tens nucleotides, achieved by bioinformatics analysis. To address this issue, we develop an experimental method, termed as massive active enhancer sequencing (MAE-Seq), to designate active enhancer sequences from arbitrary sources of 25bp random DNA libraries. These sequences are constructed in a mini-promoter vector with fluorescent reporter. After transfection, positive cells are sorted out and for sequencing. With the results, we successfully identify hundreds known accurate active enhancer sequences as expected. Besides that, large amounts of unmarked regulatory elements (UREs) without epigenetic features are also been spotted. In conclusion, MAE-Seq would be useful to refine enhancer sequences and precisely annotate the genome in eukaryotes.

genomics↗

bioRxiv2019

iRhom2 serves as a facilitator in obesity by enhancing adipose inflammation and insulin resistance

Chronic inflammation of adipose tissues contributes to obesity-triggered insulin resistance. Unfortunately, the potential molecular mechanisms regarding obesity associated systemic inflammation and metabolic disorder remain complicated. Here we display that inactive rhomboid-like protein 2 (iRhom2) is increased in mice fat with adipose inflammation. After 16 weeks on a high fat diet (HFD), obesity, chronic inflammation in adipose tissues and insulin resistance are markedly mitigated in iRhom2-knockout (iRhom2 KO) mice, but exaggerated in iRhom2-overactivated mice. The adverse impressions of iRhom2 on adipose inflammation and associated pathologies are determined in db/db mice. Also, we further exhibit that in response to HFD, iRhom2 KO mice and mice with deletion only in myeloid cells showed less severe adipose inflammation and insulin resistance than the control groups. Conversely, transplantation of bone marrow cells from normal mice to iRhom2 KO mice unleashed the severity of systemic inflammation and metabolic dysfunction after HFD ingestion. In conclusion, we identify iRhom2 as a key regulator that promotes obesity-associated metabolic disorder. Loss of iRhom2 from macrophages in adipose tissues inhibited the inflammation and insulin resistance. iRhom2 might be a therapeutic target for obesity-induced metabolic dysfunction.\n\nSignificanceIncreased inactive rhomboid-like protein 2 signaling has recently been shown to trigger inflammation-associated activation of innate immune responses. Herein we investigate that this signal also plays a crucial role in obesity-triggered adipose tissue inflammation infiltration and metabolic disorder, beyond the well-known assignment in innate immune supervision. Also, we have reported the iRhom2 as a key promoter in regulating metabolic function, which enhances obesity-stimulated inflammation and systemic insulin resistance by up regulation of macrophages pro-inflammatory activation. Our current study indicates that targeting the iRhom2 signaling in adipose tissues could possibly be an efficient strategy to mitigating obesity-associated systemic inflammation and metabolic dysfunction.

pathology↗

bioRxiv2019

Enhancer-promoter association determines Sox2 transcription regulation in mouse pluripotent cells

Distal enhancer-promoter associations are essential for transcription control and emerging as a common epigenetic way to determine gene expression in eukaryotes. However, it remains as an uncultivated land on how their diversity influences gene transcription during development. In this study, we select three defined Sox2 associated enhancers (E1, E2 and E3), representing different distal interaction categories, to further explore their biological effects. We construct three enhancer-knockout cells via CRISPR/Cas9 system in mouse embryonic stem cells. Results show that these associations carry out various biological features. Embryonic stem cell specific association (E1) speeds up cell cycle and involves in cardiac development, which has been validated in vivo. In contrast, the indirect one (E2) restrains nerve differentiation and has potential effect on lipid metabolism. The common one (E3) promotes nerve differentiation and inhibits oxidation-reduction process. Together, these different associations determine Sox2 transcription and function specificity in mouse embryonic stem cells. Our study will enable a way for exploring miscellaneous spatiotemporal gene transcription control and advancing quantitative knowledge by utilizing three-dimensional genomic information.\n\nSummary statementSox2 transcription is complicated in mouse embryonic stem cells. It involves in heavily enhancer-promoter associations, which might make it a suitable model for phase-separation study. To decompose this cooperative regulation, diverse interactions are investigated. The biological effects have been explored in multiple perspectives. This may represent a quantitative way to explore and a potential new strategy to transcription control study.

molecular biology↗

bioRxiv2019

Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize x teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 up-regulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation and sRNAs are similar between sickly plants and normal controls, although a few up-regulated transcripts and transposable elements are associated with altered sRNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon \"hybrid decay\" and present ideas on the mechanism that may underlie it.

genetics↗

bioRxiv2019

The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ

The female upper reproductive tract, including the uterus, fallopian tubes and ovaries, is believed to be a sterile environment. With the improvement of bacterial detection, the theory of the sterile female upper reproductive tract has been frequently challenged in recent years. However, thus far, no researchers have used ovaries as study targets. Six women who were diagnosed with ovarian cancer were included in the cancer group, and ten women who were diagnosed with a noncancerous ovarian condition (including three patients with uterine myoma and seven patients with uterine adenomyosis) were included in the control group. Immunohistochemistry staining using an antibacterial lipopolysaccharide (LPS) antibody was used to confirm the presence of bacteria in the ovarian tissues. In addition, 16S rRNA sequencing was used to compare the differences in the bacteria between ovarian cancer tissues and noncancerous ovarian tissues. BugBase and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to predict the functional composition of the bacteria. Bacterial LPS was present in ovarian cancer tissue and noncancerous ovarian tissue, which implied the presence of bacteria in ovarian tissue. When compared to the noncancerous ovarian bacteria at the phylum level, the cancerous ovarian bacteria were composed of increased Aquificae and Planctomycetes and decreased Crenarchaeota. When predicting metagenomes, gene functions associated with the potentially pathogenic and the oxidative stress-tolerant phenotype were enriched in the ovaries of the cancer group. Forty-six significantly different KEGG pathways existed in the ovarian bacteria of the cancer group compared to that of the control group. Different bacteria compositions were present in cancerous and noncancerous ovarian tissues. Author summaryAbdominal solid viscera have always been believed to be absolutely sterile. With the improvement of bacterial detection, this concept is being challenged. Researchers found some bacteria existed in endometrial diseases, the question of whether the ovaries are sterile is still unclear. Therefore, we assume that the bacteria in ovarian tissue are associated with ovarian cancer. When compared to the noncancerous ovarian bacteria at the phylum level, the cancerous ovarian bacteria were composed of increased Aquificae and Planctomycetes and decreased Crenarchaeota. When predicting metagenomes, gene functions associated with the potentially pathogenic and the oxidative stress-tolerant phenotype were enriched in the ovaries of the cancer group. Forty-six significantly different KEGG pathways existed in the ovarian bacteria of the cancer group compared to that of the control group. Different bacteria compositions were present in cancerous and noncancerous ovarian tissues.

microbiology↗

bioRxiv2019

Comparison of three different eye-tracking tasks for distinguishing autistic from typically developing children and autistic symptom severity

Altered patterns of visual social attention preference detected using eye-tracking and a variety of different paradigms are increasingly proposed as sensitive biomarkers for autism spectrum disorder. However, few eye tracking studies have compared the relative efficacy of different paradigms to discriminate between autistic compared with typically developing children and their sensitivity to specific symptoms. To target this issue, the current study used three common eye tracking protocols contrasting social versus non-social stimuli in young (2-7 years old) Chinese autistic (n = 35) and typically developing (n = 34) children matched for age and gender. Protocols included dancing people vs. dynamic geometrical images, biological motion (dynamic light point walking human or cat) vs. non-biological motion (scrambled controls) and child playing with toy vs. toy alone. Although all three paradigms differentiated autistic and typically developing children, the dancing people versus dynamic geometry pattern paradigm was the most effective, with autistic children showing marked reductions in visual preference for dancing people and correspondingly increased one for geometric patterns. Furthermore, this altered visual preference in autistic children was correlated with the ADOS social affect score and had the highest discrimination accuracy. Our results therefore indicate that decreased visual preference for dynamic social stimuli may be the most effective visual attention-based paradigm for use as a biomarker for autism in Chinese children. Clinical trial ID: NCT03286621 (clinicaltrials.gov); Clinical trial name: Development of Eye-tracking Based Markers for Autism in Young Children. Lay summaryEye-tracking measures may be useful in aiding diagnosis and treatment of autism, although it is unclear which specific tasks are optimal. Here we compare the ability of three different social eye-gaze tasks to discriminate between autistic and typically developing young Chinese children and their sensitivity to specific autistic symptoms. Our results show that a dynamic task comparing visual preference for social (individuals dancing) versus geometric patterns is the most effective both for diagnosing autism and sensitivity to its social affect symptoms.

clinical trials↗

bioRxiv2019

A Novel Neoantigen Discovery Approach based on Chromatin High Order Conformation: Mapping the Neoantigen to 3D Genome

The high-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that stimulate immune response of the T cells. However, when the somatic mutations are abundant, it is computationally challenging to efficiently prioritize the identified neoantigen candidates according to their ability of activating the T cell immuno-response. Numerous prioritization or prediction approaches have been proposed to address this issue but none of them considers the original DNA loci of the neoantigens from the perspective of 3D genome. Here we retrospect the DNA origins of the immune-positive and non-negative neoantigens in the context of 3D genome and discovered that 1) DNA loci of the immuno-positive neoantigens tend to cluster genome-wise. 2) DNA loci of the immuno-positive neoantigens tend to belong to active chromosomal compartment (compartment A) in some chromosomes. 3). DNA loci of the immuno-positive neoantigens tend to locate at specific regions in the 3D genome. We believe that the 3D genome information will help more precise neoantigen prioritization and discovery and eventually benefit precision and personalized medicine in cancer immunotherapy.

bioinformatics↗

bioRxiv2019

Earliest-known intentionally deformed human cranial fossil from Asia and the initiation of hereditary hierarchy in the early Holocene

Hereditary hierarchy is one of the major features of complex societies. Without a written record, prehistoric evidence for hereditary hierarchy is rare. Intentional cranial deformation (ICD) is a cross-generational cultural practice that embodies social identity and culture beliefs in adults through the behavior of altering infant head shape. Therefore, ICD is usually regarded as an archeological clue for the occurrence of hereditary hierarchy. With a calibrated radiocarbon age of 11245-11200 years BP, a fossil skull of an adult male displaying ICD discovered in Northeastern China is among the oldest-known ICD practices in the world. Along with the other earliest global occurrences of ICD, this discovery points to the early initiation of complex societies among the non-agricultural local societies in Northeastern Asia in the early Holocene. A population increase among previously more isolated terminal Pleistocene/early Holocene hunter-gatherer groups likely increased their interactions, possibly fueling the formation of the first complex societies.View Full Text

paleontology↗

bioRxiv2018

Immunomodulatory activity of Ganoderma lucidum immunomodulatory protein via PI3K/Akt and MAPK signaling pathways in macrophage RAW264.7 cells

Ganoderma lucidum, a traditional edible and medicinal fungus, holds an important status in health care systems in China and other Asian countries. Fungal immunomodulatory protein (FIP), one of the active ingredients isolated from G. lucidum, is a class of naturally occurring proteins and possesses potential biological functions. This study was conducted to explore the molecular mechanism of its immunomodulatory potency in immune responses of macrophages. In vitro assays of biological activity indicated that rFIP-glu significantly activated macrophage RAW264.7 cells, and possessed the ability of pro-and anti-inflammation the cells. RNA sequencing analysis showed that macrophage activation involved Toll-like receptors and mitogen-activated protein kinases pathways. Furthermore, qRT-PCR indicated that phosphoinositide 3 kinase inhibitor LY294002 blocked the mRNA levels of MCP-1, MEK1/2 inhibitor U0126 reduced the mRNA levels of TNF- and MCP-1, and JNK inhibitor SP600125 prevented the up-regulation of iNOS mRNA in the rFIP-glu-induced cells. FIP-glu mediated these inflammatory effects not through a general pathway, instead through a different pathway for different inflammatory mediator. These data indicate the possibility that rFIP-glu has an important immune-regulation function and thus has potential therapeutic uses.

immunology↗

bioRxiv2018

Dynamic landscape and genetic regulation of RNA editing in schizophrenia

RNA editing is vital for neurodevelopment and the maintenance of normal neuronal function. We surveyed the global landscape and genetic regulation of RNA editing across several hundred schizophrenia and control postmortem brain samples from the CommonMind Consortium covering two regions, the dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex. In schizophrenia, RNA editing sites encoding AMPA glutamate receptors and post-synaptic density genes were less edited, while more editing was detected in sites implicated in translational initiation. These sites replicate between brain regions, map to 3UTRs, enrich for common sequence motifs and coincide for RNA binding proteins crucial for neurodevelopment. Importantly, these findings cross-validate in hundreds of non-overlapping DLPFC samples. Furthermore, ~30% of RNA editing sites associate with cis-regulatory variants (edQTLs). Fine-mapping edQTLs with schizophrenia GWAS loci revealed colocalization of 11 edQTLs with 6 GWAS loci. This supports a causal role of RNA editing in risk for schizophrenia. Our findings illustrate widespread altered RNA editing in schizophrenia and its genetic regulation, and shed light onto RNA editing-mediated mechanisms in schizophrenia neuropathology.

neuroscience↗

bioRxiv2018

Genetic interactions among Ghd7, Ghd7.1, Ghd8 and Hd1 contribute to large variation in heading date in rice

Several major heading date genes are sensitive to photoperiod and jointly regulate heading date in rice. However, it is not clear how these genes coordinate rice heading. In this study, a near-isogenic F2 population with Ghd7, Ghd7.1, Ghd8 and Hd1 segregating in the Zhenshan 97 (ZS97) background was used to evaluate the genetic interactions among these four genes under natural long-day (NLD) and natural short-day (NSD) conditions, and a series of Ghd7.1-segregating populations in different backgrounds were developed to estimate the genetic effects of Ghd7.1 on heading date under both conditions. Tetragenic, trigenic and digenic interactions among these four genes were observed under both conditions. In the functional Hd1 backgrounds, the strongest digenic interaction was Ghd7 by Ghd8 under NLD conditions but was Ghd7 by Ghd7.1 under NSD conditions. Interestingly, Ghd7.1 acted as a flowering suppressor under NLD conditions, while it functioned alternatively as an activator or a suppressor under NSD conditions depending on the status of the other three genes. Based on the performances of 16 homozygous four-gene combinations, a positive correlation between heading date and yield was found under NSD conditions, but changed to a negative correlation when heading date was over 90 days under NLD conditions. These results demonstrate the importance of genetic interactions in the rice flowering regulatory network and will help breeders to select favorable combinations to maximize rice yield potential for different ecological areas.

genetics↗

bioRxiv2018

Generation of Cynomolgus Monkeys (Macaca fascicularis) Embryos with ICSI Based on the MII-Stage Oocytes Acquired by Personalized Superovulation Protocol

The use of cynomolgus monkeys (Macaca fascicularis) has facilitated the establishment of gene-modified animal models, and the appropriate number of high-quality mature oocytes (MII-stage oocytes) are crucial in assisted reproductive technologies (ART) of cynomolgus macaques. In this study we performed 3 different superovulation protocols on 24 female cynomolgus monkeys aimed to improve the proportion of MII-stage oocyte retrieval. The results suggested some differences in the proportion of MII-stage oocytes between the personalized superovulation protocol and the superovulation protocols I and II. Afterwards, we performed Intracytoplasmic sperm injection (ICSI) on 22 MII-stage oocytes derived from one animal with personalized superovulation protocol, obtained 15 embryos of 2-4-cells, 2 cases of successful pregnancy after transferring to 4 surrogate female, and obtained 3 aborted fetuses. These results suggested that personalized superovulation protocol incorporated the menstrual cycle length of each cynomolgus monkey, and the timing of oocytes retrieval based on the equation: menstrual cycle length/2 {+/-} 1, which increased the rate of MII-stage oocytes acquired and generation of cynomolgus monkeys embryos with ICSI based on these oocytes, and finally could successfully develop into fetus under conditions that effectively guarantee the synchronization of the surrogate mothers.\n\nSUMMARY STATEMENTThe personalized superovulation protocol based on the menstrual cycle length of each cynomolgus monkey can increase the rate of MII-stage oocytes acquired, and finally could successfully develop into fetus under conditions that minimize damage to the surrogate mothers and effectively guarantee the synchronization of the surrogate mothers.

developmental biology↗

bioRxiv2018

Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq

Spermatogenesis is an important physiological process associated with male infertility. But whether there are RNA editings (REs) and whats the role of REs during the process are still unclear. In this study, we integrated published RNA-Seq datasets and established a landscape of REs during the development of mouse spermatogenesis. 7530 editing sites among all types of male germ cells were found, which enrich on some regions of chromosome, including chromosome 17 and both ends of chromosome Y. Totally, REs occur in 2012 genes during spermatogenesis, more than half of which harbor at two different sites of the same gene at least. We also found REs mainly occur in introns, coding regions (CDSs) and intergenic regions. Moreover, about half of the REs in CDSs can cause amino acids changes. Finally, based on our adult male Kunming mice, we verified that there is a non-synonymous A-to-I RNA editing site in Cog3 during spermatogenesis, which is conserved not only between species but also across tissues. In short, based on the power of integrating RNA-Seq datasets, we provided the landscape of REs and found their dynamic changes during mouse spermatogenesis. This research strategy is general for other types of sequencing datasets and biological problems.

developmental biology↗

bioRxiv2018

Statistical properties of the optimal sensitivity matrix for compressed sensing with nonlinear sensors

There are numerous different odorant molecules in nature. Typical odors are sparse mixtures of a few types of odorant molecules each with a wide range of concentrations. However, there are only a relatively small number of olfactory receptor neurons (ORNs), which respond to odorant concentration nonlinearly (sigmoidal) with a finite sensitivity range. Thus, how to encode a large number of sparse odor mixtures with a relatively small number of nonlinear ORNs - the nonlinear compressed sensing problem - remains a puzzle. Here, by using an information theory approach, we study the optimal coding strategies that enable nonlinear ORNs to best represent olfactory information (both the odorants identities and their concentrations) in sparse odor mixtures. Our extensive numerical simulations and analytical analysis show that the optimal odor-receptor sensitivity matrix is sparse and the nonzero sensitivities follow roughly a log-normal distribution(matching the statistics of the odorants), both of which are consistent with existing experiments. For ORNs with a finite basal activity, our study shows that co-existence of both odor-evoked excitation and inhibition increases coding capacity, which provides a plausible explanation for such co-existence observed in the fly olfactory system. Furthermore, we show that coding the inputs with the optimal sensitivity matrix can enhance accuracy of the downstream decoding and learning tasks. These general statistical properties of the optimal sensitivity matrix for nonlinear compressed sensing may shed light on understanding the peripheral olfactory sensory system and improving performance of artificial neural networks.

neuroscience↗