Analysis Of Gene Expression Of Transcription Factor And LincRNA In C.elegans

Transcription factors play a central role in differential regulation of gene expression.Alteration in transcription factor function and regulation are linked to phenotypic variation and diseases.Other regulatory factors,such as long noncoding RNAs are also involved in gene expression regulation.Thorough research of transcription factors and lncRNAs will lay the foundation for exploring the molecular mechanism of diseases and orgnismal complexity.And high-resolution expression profile of transcription factors and lncRNAs will help us to gain insight into their function.A simple anatomy,invariant cell lineage and transparent body make C.elegans a highly suitable model to study gene expression.Although gene expression study of transcription factor is very extensive,quantitative cellular gene expression data is still lacking.Knowledge about lncRNA gene expression is almost blank.Techniques to generate single-cell-resolution gene expression profile had been well developed,which will greatly promote analyzing gene expression at large scale.In this study,we generated gene expression profiles of 72%(673/934)transcription factors and 40%(68/170)lincRNAs in 558 cells of newly hached L1 larvae.Observed expression patterns revealed that the expression of lincRNAs are more specific,heterogeneous and at lower level than transcription factors.However,some transcription factor families displayed similar expression characteristics with lincRNAs,such as Homeodomain family,bHLH family and Hormone Receptor family.Genes of C2H2 Zinc Finger family and other transcription factors that contain Zinc Finger domain had no significant differences from other transcription factors.We also examined the spatiotemporal expression patterns of lincRNAs.Similar to miRNA promoters,lincRNA promoters are less active at embryo stage,but become comparable with that of transcription factors from larval stage;the expression of lincRNA has no significant tissue bias.We also established an image database for the storage and retrieval of lincRNA expression patterns and other relevant information,which will provide a valuable guide and resource for future functional exploration of lincRNAs.Based on the single-cell-resolution gene expression profile,we found a wide range of gene silencing in HSNs.Strains that carry a histone::reporter gene fused to C terminus of these silenced genes,generated by CRISPR/Cas9,futher verified this expression pattern.Moreover,the positions of HSNs were affected when increasing the gene transcriptional level in them.We also found a differential expression pattern between V5 cells and other V cells.37.5% of differentially expressed genes were responsible for V5s' development.Thus,the single-cell-resolution gene expression profile will provide a valuable resource for studing gene function,identifying co-associations and establishing precise regulatory circuits.What is more,it will provides a foundation for functional studies of transcription factor homologies in higher eukaryotes,including humans.