Publications

The binding of SARS-CoV-2 nucleocapsid (N) protein to both the 5′- and 3′-ends of genomic RNA has different implications arising from its binding to the central region during virion assembly. However, the mechanism underlying selective binding remains unknown. Herein, we performed the high-throughput RNA-SELEX (HTR-SELEX) to determine the RNA-binding specificity of the N proteins of various SARS-CoV-2 variants as well as other β-coronaviruses and showed that N proteins could bind two unrelated sequences, both of which were highly conserved across all variants and species. Interestingly, both sequences are virtually absent from the human transcriptome; however, they exhibit a highly enriched, mutually complementary distribution in the coronavirus genome, highlighting their varied functions in genome packaging. Our results provide mechanistic insights into viral genome packaging, thereby increasing the feasibility of developing drugs with broad-spectrum anti-coronavirus activity by targeting RNA binding by N proteins.

Fan, Shaorong;Sun, Wenju;Fan, Ligang;Wu, Nan;Sun, Wei;Ma, Haiqian;Chen, Siyuan;Li, Zitong;Li, Yu;Zhang, Jilin;Yan, Jian

Computational and Structural Biotechnology Journal, (2022)

Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures, we produced a nearly complete chromosomal assembly of a female Pekin duck. Analyses based on thi high quality genome have revealed that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals.

Jing Li, Jilin Zhang , Jing Liu, Yang Zhou, Cheng Cai, Luohao Xu, Xuelei Dai, Shaohong Feng, Chunxue Guo, Jinpeng Rao, Kai Wei, Erich D Jarvis, Yu Jiang, Zhengkui Zhou, Guojie Zhang, Qi Zhou

GigaScience 10:1, (2021)

We assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-throughput RNA-SELEX (HTR-SELEX). Approximately 30% preferred structured motifs folding into stem–loops. We also found that many RBPs can bind to multiple distinctly different motifs. Structural analysis revealed that unconventional RBDs containing active sites or molecule-binding pockets could interact with short, structured RNA molecules.

Arttu Jolma, Jilin Zhang, Estefania Mondragón, Ekaterina Morgunova, Teemu Kivioja, Kaitlin U. Laverty, Yimeng Yin, Fangjie Zhu, Gleb Bourenkov, Quaid Morris, Timothy R. Hughes, Louis James Maher III and Jussi Taipale

Genome Res. (2020)

We have developed CRISPR-assisted RNA–protein interaction detection method (CARPID), which leverages CRISPR–CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method’s wide applicability in identifying RNA-binding proteins.

Wenkai Yi, Jingyu Li, Xiaoxuan Zhu, Xi Wang, Ligang Fan, Wenju Sun, Linbu Liao, Jilin Zhang, Xiaoyu Li, Jing Ye, Fulin Chen, Jussi Taipale, Kui Ming Chan, Liang Zhang & Jian Yan

Nature Methods volume 17, pages685–688 (2020)

Loss-of-function screening by CRISPR/Cas9 gene knockout with pooled, lentiviral guide libraries is a widely applicable method for systematic identification of genes contributing to diverse cellular phenotypes. Here, Random Sequence Labels (RSLs) are incorporated into the guide library, which act as unique molecular identifiers (UMIs) to allow massively parallel lineage tracing and lineage dropout screening. RSLs greatly improve the reproducibility of results by increasing both the precision and the accuracy of screens. They reduce the number of cells needed to reach a set statistical power, or allow a more robust screen using the same number of cells.

Bernhard Schmierer, Sandeep K Botla, Jilin Zhang , Mikko Turunen, Teemu Kivioja, Jussi Taipale

Molecular Systems Biology, 13:945 (2017)

We analyze newly available genomes of 17 bird species representing the avian phylogenetic range, and find that more than half of them do not have as fully degenerated W chromosomes as that of chicken. We show that avian sex chromosomes harbor tremendous diversity among species in their composition of pseudoautosomal regions and degree of Z/W differentiation. Punctuated events of shared or lineage-specific recombination suppression have produced a gradient of “evolutionary strata” along the Z chromosome, which initiates from the putative avian sex-determining gene DMRT1 and ends at the pseudoautosomal region.

Qi Zhou, Jilin Zhang, Doris Bachtrog, Na An, Quanfei Huang, Erich D Jarvis, M Thomas P Gilbert, Guojie Zhang

Science, 346(6215) (2014)