Biology subjects

Liang, C.

Publications and source records attributed to Liang, C..

135 records · Page 8Linked to original sources

bioRxiv2018

CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity

The CRISPR-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 system varies among different gRNA sequences. We reanalyzed the published CRISPR-Cpf1 gRNAs data and found many sequence and structural features related to their target efficiency. Using machine learning technology, a SVM model was created to predict target efficiency for any given gRNAs. We have developed the first web service application, CRISPR-DT (CRISPR DNA Targeting), to help users design optimal gRNAs for the CRISPR-Cpf1 system by considering both target efficiency and specificity. CRISPR-DT is available at http://bioinfolab.miamioh.edu/CRISPR-DT.

bioinformatics↗

bioRxiv2018

The mammalian decidual cell evolved from a cellular stress response

Among animal species, cell types vary greatly in terms of number and kind. The broad range of number of cell types among species suggests that cell type origination is a significant source of evolutionary novelty. The molecular mechanisms giving rise to novel cell types, however, are poorly understood. Here we show that a novel cell type of eutherian mammals, the decidual stromal cell (DSC), evolved by rewiring an ancestral cellular stress response. We isolated the precursor cell type of DSCs, endometrial stromal fibroblasts (ESFs), from the opossum Monodelphis domestica. We show that, in opossum ESF, the majority of decidual core regulatory genes respond to decidualizing signals, but do not regulate decidual effector genes. Rather, in opossum ESF, decidual transcription factors function in apoptotic and oxidative stress response. We propose that the rewiring of cellular stress responses could be a general mechanism for the evolution of novel cell types.

evolutionary biology↗

bioRxiv2017

Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings

In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits develop with distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digit identities are conserved across amniotes. Transcriptomics of developing limbs shows diversity in the patterns of genetic differentiation of digits, although the anterior-most digit of the pentadactyl limb has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude that only the identity of the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.

evolutionary biology↗

bioRxiv2017

IFITM proteins inhibit HIV-1 protein synthesis

Interferon induced transmembrane proteins (IFITMs) inhibit the cellular entry of a broad range of viruses, but it has been suspected that for HIV-1 IFITMs may also inhibit a post-integration replicative step. We show that IFITM expression reduces HIV-1 viral protein synthesis by preferentially excluding viral mRNA transcripts from translation and thereby restricts viral production. Codon-optimization of proviral DNA rescues viral translation, implying that IFITM-mediated restriction requires recognition of viral RNA elements. In addition, we find that expression of the viral accessory protein Nef can help overcome the IFITM-mediated inhibition of virus production. Our studies identify a novel role for IFITMs in inhibiting HIV replication at the level of translation, but show that the effects can be overcome by the lentiviral protein Nef.

microbiology↗

bioRxiv2017

PrimerServer: a high-throughput primer design and specificity-checking platform

SummaryDesigning specific primers for multiple sites across the whole genome is still challenging, especially in species with complex genomes. Here we present PrimerServer, a high-throughput primer design and specificity-checking platform with both web and command-line interfaces. This platform efficiently integrates site selection, primer design, specificity checking and data presentation. In our case study, PrimerServer achieved high accuracy and a fast running speed for a large number of sites, suggesting its potential for molecular biology applications such as molecular breeding or medical testing.\n\nAvailability and ImplementationSource code for PrimerServer is available at https://github.com/billzt/PrimerServer. A demo server is freely accessible at https://primerserver.org, with all major browsers supported.\n\nContactzhangrui@caas.cn or guosandui@caas.cn

bioinformatics↗

bioRxiv2017

GFF3sort: An efficient tool to sort GFF3 files for tabix indexing

BackgroundThe traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse.\n\nResultsWe developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, GFF3sort can properly deal with the order of features that have the same chromosome and start position, either by remembering their original orders or by conducting parent-child topology sorting. Based on our test datasets from seven species, GFF3sort produced accurate sorting results with acceptable efficiency compared with currently available tools.\n\nConclusionsGFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization.

bioinformatics↗

bioRxiv2017

Systematic Analysis Of RNA-Seq-Based Gene Co-Expression Across Multiple Plants

The complex cellular network was formed by the interacting gene modules. Building the high-quality RNA-seq-based Gene Co-expression Network (GCN) is critical for uncovering these modules and understanding the phenotypes of an organism. Here, we established and analyzed the RNA-seq-based GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed modules. Taking rice as an example, we associated these modules with biological functions and agronomic traits by enrichment analysis, and discovered a large number of conditin-specific or tissue-specific modules. In addition, we also explored the regulatory mechanism of the modules by enrichment of the known cis-elements, transcription factors and miRNA targets. Their coherent enrichment with the inferred functions of the modules revealed their synergistic effect on the gene expression regulation. Moreover, the comparative analysis of gene co-expression was performed to identify conserved and species-specific functional modules across 4 plant species. We discovered that the modules shared across 4 plants participate in the basic biological processes, whereas the species-specific modules were involved in the spatiotemporal-specific processes linking the genotypes to phenotypes. Our research provides the massive modules relating to the cellular activities and agronomic traits in several model and crop plant species.

bioinformatics↗

bioRxiv2017

High-Quality Rice RNA-Seq-Based Co-Expression Network For Predicting Gene Function And Regulation

Inferring the genome-scale gene co-expression network is important for understanding genetic architecture underlying the complex and various biological phenotypes. The recent availability of large-scale RNA-seq sequencing-data provides great potential for co-expression network inference. In this study, for the first time, we presented a novel heterogeneous ensemble pipeline integrating three frequently used inference methods, to build a high-quality RNA-seq-based Gene Co-expression Network (GCN) in rice, an important monocot species. The quality of the network obtained by our proposed method was first evaluated and verified with the curated positive and negative gene functional link datasets, which obviously outperformed each single method. Secondly, the powerful capability of this network for associating unknown genes with biological functions and agronomic traits was showed by enrichment analysis and case studies. Particularly, we demonstrated the potential applications of our proposed method to predict the biological roles of long non-coding RNA (lncRNA) and circular RNA (circRNA) genes. Our results provided a valuable data source for selecting candidate genes to further experimental validation during rice genetics research and breeding. To enhance identification of novel genes regulating important biological processes and agronomic traits in rice and other crop species, we released the source code of constructing high-quality RNA-seq-based GCN and rice RNA-seq-based GCN, which can be freely downloaded online at https://github.com/czllab/NetMiner.

bioinformatics↗

bioRxiv2017

CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity

CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model organisms and can be easily extended to cover other species. CRISPR-RT will empower researchers in RNA editing. It is available at http://bioinfolab.miamioh.edu/CRISPR-RT.

bioinformatics↗