Lu Zhang

All Publications

• Hi-Tag: a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers. Science China. Life sciences Qi, X., Zhang, L., Zhao, Q., Zhou, P., Zhang, S., Li, J., Zheng, Z., Xiang, Y., Dai, X., Jin, Z., Jian, Y., Li, X., Fu, L., Zhao, S. 2024; 67 (5): 1027-1034

  Abstract

  Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin immunoprecipitation. However, these techniques require complex experimental procedures and millions of cells per experiment, which limits their widespread application in life science research. Here, we develop a novel method, Hi-Tag, that identifies high-resolution, long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation (with a phosphorothioate-modified linker). Hi-Tag can be implemented using as few as 100,000 cells, involving simple experimental procedures that can be completed within 1.5 days. Meanwhile, Hi-Tag is capable of using its own data to identify the binding sites of specific proteins, based on which, it can acquire accurate interaction information. Our results suggest that Hi-Tag has great potential for advancing chromatin interaction studies, particularly in the context of limited cell availability.

  View details for DOI 10.1007/s11427-023-2441-0

  View details for PubMedID 38280143

  View details for PubMedCentralID 6748947

• Genome-Scale CRISPR Knockout Screening Identifies BACH1 as a Key Regulator of Aflatoxin B1-Induced Oxidative Damage. Antioxidants (Basel, Switzerland) Zhang, J., Hu, S., Zhao, C., Zhou, Y., Zhang, L., Liu, H., Zhou, P., Li, S., Fu, L., Zheng, Z., Xiang, Y., Xu, X., Ruan, J., Li, X., Sun, L., Cao, G., Zhao, S., Wang, X., Xie, S. 2022; 11 (9)

  Abstract

  Aflatoxin B1 (AFB1) is amongst the mycotoxins commonly affecting human and animal health, raising global food safety and control concerns. The mechanisms underlying AFB1 toxicity are poorly understood. Moreover, antidotes against AFB1 are lacking. Genome-wide CRISPR/Cas9 knockout screening in porcine kidney cells identified the transcription factor BTB and CNC homolog 1 (BACH1) as a gene required for AFB1 toxicity. The inhibition of BACH1 expression in porcine kidney cells and human hepatoma cells resulted in increased resistance to AFB1. BACH1 depletion attenuates AFB1-induced oxidative damage via the upregulation of antioxidant genes. Subsequently, virtual structural screening identified the small molecule 1-Piperazineethanol, α-[(1,3-benzodioxol-5-yloxy)methyl] -4-(2-methoxyphenyl) (M2) as an inhibitor of BACH1. M2 and its analogues inhibited AFB1-induced porcine and human cell death in vitro, while M2 administration significantly improved AFB1-induced symptoms of weight loss and liver injury in vivo. These findings demonstrate that BACH1 plays a central role in AFB1-induced oxidative damage by regulating antioxidant gene expression. We also present a potent candidate small-molecule inhibitor in developing novel treatments for AFB1 toxicity.

  View details for DOI 10.3390/antiox11091787

  View details for PubMedID 36139865

  View details for PubMedCentralID PMC9495794

• Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome. BMC biology Li, J., Xiang, Y., Zhang, L., Qi, X., Zheng, Z., Zhou, P., Tang, Z., Jin, Y., Zhao, Q., Fu, Y., Zhao, Y., Li, X., Fu, L., Zhao, S. 2022; 20 (1): 136

  Abstract

  Gene expression programs are intimately linked to the interplay of active cis regulatory elements mediated by chromatin contacts and associated RNAs. Genome-wide association studies (GWAS) have identified many variants in these regulatory elements that can contribute to phenotypic diversity. However, the functional interpretation of these variants remains nontrivial due to the lack of chromatin contact information or limited contact resolution. Furthermore, the distribution and role of chromatin-associated RNAs in gene expression and chromatin conformation remain poorly understood. To address this, we first present a comprehensive interaction map of nuclear dynamics of 3D chromatin-chromatin interactions (H3K27ac BL-HiChIP) and RNA-chromatin interactions (GRID-seq) to reveal genomic variants that contribute to complex skeletal muscle traits.In a genome-wide scan, we provide systematic fine mapping and gene prioritization from GWAS leading signals that underlie phenotypic variability of growth rate, meat quality, and carcass performance. A set of candidate functional variants and 54 target genes previously not detected were identified, with 71% of these candidate functional variants choosing to skip over their nearest gene to regulate the target gene in a long-range manner. The effects of three functional variants regulating KLF6 (related to days to 100 kg), MXRA8 (related to lean meat percentage), and TAF11 (related to loin muscle depth) were observed in two pig populations. Moreover, we find that this multi-omics interaction map consists of functional communities that are enriched in specific biological functions, and GWAS target genes can serve as core genes for exploring peripheral trait-relevant genes.Our results provide a valuable resource of candidate functional variants for complex skeletal muscle-related traits and establish an integrated approach to complement existing 3D genomics by exploiting RNA-chromatin and chromatin-chromatin interactions for future association studies.

  View details for DOI 10.1186/s12915-022-01322-2

  View details for PubMedID 35681201

  View details for PubMedCentralID PMC9185926

• The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Ecology and evolution Xiao, C., Li, J., Xie, T., Chen, J., Zhang, S., Elaksher, S. H., Jiang, F., Jiang, Y., Zhang, L., Zhang, W., Xiang, Y., Wu, Z., Zhao, S., Du, X. 2021; 11 (12): 7779-7795

  Abstract

  The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.

  View details for DOI 10.1002/ece3.7611

  View details for PubMedID 34188851

  View details for PubMedCentralID PMC8216945

• Three functional mutation sites affect the immune response of pigs through altering the expression pattern and IgV domain of the CD4 protein. BMC molecular and cell biology Zhang, W., Ni, J., Zhang, J., Zhang, L., Zhou, H., Zhao, C., Zhu, M., Wang, H., Han, J., Li, X., Zhao, S. 2020; 21 (1): 91

  Abstract

  The CD4 protein is an important surface marker of T lymphocytes, which can mediate the antigen presentation process by interacting with MHC II and TCR molecules in human and mouse.In this study, two haplotypes (A and B) of the CD4 gene were found within Chinese indigenous and Western commercial pig breeds. These two haplotypes were defined by 22 fully linked SNPs in the CDS region of the CD4 gene. The expression level and localization of the CD4 protein were significantly different between haplotypes A and B. Transcriptome analysis revealed that the immune response-related genes and signaling pathways were down-regulated in genotype AA. Finally, three linked functional SNPs were identified, which affected the expression level and membrane localization of the CD4 protein in pigs. These three SNPs led to the replacements of two amino acids in the IgV1 domain of the CD4 protein, and related to the function of the CD4 protein in the immune response.These three linked SNPs were the key functional mutation sites in the CD4 gene, which played important roles in the immune response, and could be utilized as new molecular markers in breeding for disease resistance in pigs.

  View details for DOI 10.1186/s12860-020-00333-7

  View details for PubMedID 33297958

  View details for PubMedCentralID PMC7724863

• Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. Genes Luan, Y., Zhang, L., Hu, M., Xu, Y., Hou, Y., Li, X., Zhao, S., Zhao, Y., Li, C. 2019; 10 (5)

  Abstract

  The liver plays a key role in metabolism and affects pig production. However, the functional annotation of noncoding regions of the pig liver remains poorly understood. We revealed the landscape of cis-regulatory elements and their functional characterization in pig liver. We identified 102,373 cis-regulatory elements in the pig liver, including enhancers, promoters, super-enhancers, and broad H3K4me3 domains, and highlighted 26 core transcription regulatory factors in the pig liver as well. We found similarity of cis-regulatory elements among those of pigs, humans, and cattle. Despite the low proportion of functionally conserved enhancers (~30%) between pig and human liver tissue, ~78% of the pig liver enhancer orthologues sequence could play an enhancer role in other human tissues. Additionally, we observed that the ratio of consistent super-enhancer-associated genes was significantly higher than the ratio of functionally conserved super-enhancers. Approximately 54% of the core regulation factors driven by super-enhancers were consistent across the liver from these three species. Our pig liver annotation and functional characterization studies provide a system and resource for noncoding annotation for future gene regulatory studies in pigs. Furthermore, our study also showed the high level functional conservation of cis-regulatory elements in mammals; it also improved our understanding of regulation function of mammal cis-regulatory elements.

  View details for DOI 10.3390/genes10050348

  View details for PubMedID 31067820

  View details for PubMedCentralID PMC6562536

• Synergistic effects of TGFβ2, WNT9a, and FGFR4 signals attenuate satellite cell differentiation during skeletal muscle development. Aging cell Zhang, W., Xu, Y., Zhang, L., Wang, S., Yin, B., Zhao, S., Li, X. 2018; 17 (4): e12788

  Abstract

  Satellite cells play a key role in the aging, generation, and damage repair of skeletal muscle. The molecular mechanism of satellite cells in these processes remains largely unknown. This study systematically investigated for the first time the characteristics of mouse satellite cells at ten different ages. Results indicated that the number and differentiation capacity of satellite cells decreased with age during skeletal muscle development. Transcriptome analysis revealed that 2,907 genes were differentially expressed at six time points at postnatal stage. WGCNA and GO analysis indicated that 1,739 of the 2,907 DEGs were mainly involved in skeletal muscle development processes. Moreover, the results of WGCNA and protein interaction analysis demonstrated that Tgfβ2, Wnt9a, and Fgfr4 were the key genes responsible for the differentiation of satellite cells. Functional analysis showed that TGFβ2 and WNT9a inhibited, whereas FGFR4 promoted the differentiation of satellite cells. Furthermore, each two of them had a regulatory relationship at the protein level. In vivo study also confirmed that TGFβ2 could regulate the regeneration of skeletal muscle, as well as the expression of WNT9a and FGFR4. Therefore, we concluded that the synergistic effects of TGFβ2, WNT9a, and FGFR4 were responsible for attenuating of the differentiation of aging satellite cells during skeletal muscle development. This study provided new insights into the molecular mechanism of satellite cell development. The target genes and signaling pathways investigated in this study would be useful for improving the muscle growth of livestock or treating muscle diseases in clinical settings.

  View details for DOI 10.1111/acel.12788

  View details for PubMedID 29869452

  View details for PubMedCentralID PMC6052404