Article
Biochemistry & Molecular Biology
Anna A. Lobas, Elizaveta M. Solovyeva, Lev I. Levitsky, Anton O. Goncharov, Elena Y. Lyssuk, Sergey S. Larin, Sergei A. Moshkovskii, Mikhail V. Gorshkov
Summary: This study developed new algorithms for the identification and validation of protein splice isoforms in proteomic data without the need for RNA sequencing. The bioinformatic approaches were tested on proteome analysis of human melanoma cell lines. The identified splicing events were further validated at the mRNA level by quantitative PCR.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Zi-Chang Jia, Xue Yang, Xuan-Xuan Hou, Yong-Xin Nie, Jian Wu
Summary: This review summarizes the importance of alternative splicing in regulating gene expression, particularly in plant responses to abiotic stresses and growth and development processes. It also presents the application of genome-wide association analysis in studying alternatively spliced variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Bao-Xing Huang, Zi-Chang Jia, Xue Yang, Chao-Lin Cheng, Xiao-Rong Liu, Jianhua Zhang, Mo-Xian Chen, Jing-Fang Yang, Yun-Sheng Chen
Summary: This study systematically analyzed the gene structure and expression profiles of SYF2 in different animal species, revealing its conservation and functionality. The study also suggested that changes in SYF2 expression may be associated with disease development in certain cells, tissues, or organs.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Nathaniel Kwok, Zita Aretz, Sumiko Takao, Zheng Ser, Paolo Cifani, Alex Kentsis
Summary: Recent advances in nucleic acid sequencing and mass spectrometry proteomics have enabled genome-scale analysis of genetic variation and transcription as well as whole proteome-scale studies of protein expression. However, most proteomic studies are limited to canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), which integrates genome and transcriptome sequencing to incorporate protein variants and other non-canonical features caused by genomic and transcriptomic variation. PG2 has been benchmarked using synthetic data and analysis of human leukemia cells and can be used with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms. It is open-source and available at https://github.com/kentsisresearchgroup/ProteomeGenerator2.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Cell Biology
Zhe Liu, Wei Wang, Xinru Li, Xiujuan Zhao, Hongyu Zhao, Wuritu Yang, Yongchun Zuo, Lu Cai, Yongqiang Xing
Summary: Alternative splicing plays an important role in zebrafish embryo development, especially during the maternal-to-zygotic transition process where it is highly abundant and dynamic. Splicing factors are expressed with developmental stage specificity, with a higher expression during the maternal-to-zygotic transition. The inclusion level of alternative splicing events performs well in cluster analysis and can be used as a novel parameter.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Esdras Matheus Gomes da Silva, Leticia Graziela Costa Santos, Flavia Santiago de Oliveira, Flavia Cristina de Paula Freitas, Vinicius da Silva Coutinho Parreira, Hellen Geremias dos Santos, Raphael Tavares, Paulo Costa Carvalho, Ana Gisele da Costa Neves-Ferreira, Andrea Siqueira Haibara, Patricia Savio de Araujo-Souza, Adriana Abalen Martins Dias, Fabio Passetti
Summary: Using a proteogenomics strategy, this study identified orthologous AS proteoforms between humans and mice. Identical proteotypic peptides of six orthologous AS proteoforms were found in both species and validated at the transcript level. Additionally, higher abundances of certain proteoforms were detected in an AD mouse model, suggesting a potential role in amyloid-like aggregate formation. This study provides valuable insights for future neurodegenerative disease research using mouse models.
Review
Cell Biology
Marina Reixachs-Sole, Eduardo Eyras
Summary: High-throughput sequencing of cellular RNAs has revealed the wide-ranging impact of alternative splicing on the transcriptome, and differential production of transcript isoforms is recognized as a critical mechanism in cell differentiation, organismal development, and disease. However, the extent of the effect of alternative splicing on protein production and cellular function is still a matter of debate. Recent advances in experimental and computational approaches have shed light on how molecular changes in the RNA processing pathway can affect protein production and function.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Biochemistry & Molecular Biology
Elise N. Engquist, Anna Greco, Leo A. B. Joosten, Baziel G. M. van Engelen, Peter S. Zammit, Christopher R. S. Banerji
Summary: In this study, RNA sequencing data from FSHD patients were analyzed to identify molecular subtypes and pathomechanisms of FSHD. The study found that mitochondrial biogenesis is suppressed in FSHD muscle, and fibroadipogenic progenitor (FAP) gene expression is up-regulated, especially in inflamed samples. Antigen presentation is also suppressed in PBMCs from FSHD patients. Further analysis showed that FAP expansion is a consistent feature of FSHD muscle, and clustering of muscle biopsies revealed clinically mild and severe subtypes of FSHD independent of known disease modifiers. Moreover, the first genome-wide analysis of alternative splicing in FSHD muscle revealed perturbation of autophagy, BMP2, and HMGB1 signaling pathways.
HUMAN MOLECULAR GENETICS
(2023)
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Fisheries
Lin Liu, Qiubai Zhou, Changgao Lin, Li He, Lili Wei
Summary: Copper contamination can have adverse effects on lipid metabolism in swamp eel livers, leading to significant changes in gene expression and alternative splicing, particularly with more pronounced impacts on lipid metabolism pathways under high copper concentrations.
Review
Biochemical Research Methods
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
Summary: Alternative splicing (AS), a key pathway for transcriptional regulation, has been shown to be associated with complex diseases. Computational approaches for detecting disease-associated AS events have been developed. This review discusses the metrics used for characterizing AS events quantitatively. It also reviews and discusses three types of methods for detecting disease-associated splicing events: differential splicing analysis, aberrant splicing detection, and splicing-related network analysis. Additionally, methods for detecting genetic variants that potentially regulate splicing are described. Experimental comparisons are conducted to illustrate the performance of each method. The limitations of these methods are discussed, as well as potential ways to address them. This review aims to provide a systematic understanding of computational approaches for analyzing disease-associated splicing.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Aliki Xanthopoulou, Theodoros Moysiadis, Christos Bazakos, Evangelos Karagiannis, Ioanna Karamichali, George Stamatakis, Martina Samiotaki, Maria Manioudaki, Michail Michailidis, Panagiotis Madesis, Ioannis Ganopoulos, Athanassios Molassiotis, Georgia Tanou
Summary: The study provides new insights into plant biology through the integration of genomics and proteomics, identifying a large number of genes and proteins in sweet cherries. Analysis reveals differences between gene and protein quantities, key regulators of fruit development, and novel cherry proteins. Additionally, a new protein-level annotation and database were developed for further research in Prunus species.
Article
Biochemical Research Methods
Tommaso De Marchi, Paul Theodor Pyl, Martin Sjostrom, Stina Klasson, Hanna Sartor, Lena Tran, Gyula Pekar, Johan Malmstrom, Lars Malmstrom, Emma Nimeus
Summary: Proteogenomic approaches enhance understanding of breast cancer with novel protein-level insights, showing splicing processes and complementarity between RNA and protein data. Differentially regulated protein networks in diverse tumor subgroups may alter cancer biology and biomarker/drug target abundance.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yu Jin, Maxim Ivanov, Anna Nelson Dittrich, Andrew D. L. Nelson, Sebastian Marquardt
Summary: This study identified a long noncoding RNA (FLAIL) in Arabidopsis that is associated with flowering. FLAIL directly interacts with target genes and affects their expression through RNA-DNA interactions and alternative splicing. The findings suggest that lncRNAs can regulate gene expression and organismal development as accessory components of the spliceosome.
Article
Cardiac & Cardiovascular Systems
Yu Han, Sara A. Wennersten, Julianna M. Wright, R. W. Ludwig, Edward Lau, Maggie P. Y. Lam
Summary: The risks of heart diseases are modulated by age and sex, and this study reveals that genes related to cardiac function show sex and age-dependent differences in expression. Additionally, there are changes in RNA splicing patterns that have the potential to influence cardiac protein structure and function.
AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Adan Codina, Paul A. Renauer, Guangchuan Wang, Ryan D. Chow, Jonathan J. Park, Hanghui Ye, Kerou Zhang, Matthew B. Dong, Brandon Gassaway, Lupeng Ye, Youssef Errami, Li Shen, Alan Chang, Dhanpat Jain, Roy S. Herbst, Marcus Bosenberg, Jesse Rinehart, Rong Fan, Sidi Chen
Article
Biotechnology & Applied Microbiology
Lupeng Ye, Jonathan J. Park, Matthew B. Dong, Quanjun Yang, Ryan D. Chow, Lei Peng, Yaying Du, Jianjian Guo, Xiaoyun Dai, Guangchuan Wang, Youssef Errami, Sidi Chen
NATURE BIOTECHNOLOGY
(2019)
Article
Immunology
Guangchuan Wang, Ryan D. Chow, Zhigang Bai, Lvyun Zhu, Youssef Errami, Xiaoyun Dai, Matthew B. Dong, Lupeng Ye, Xiaoya Zhang, Paul A. Renauer, Jonathan J. Park, Li Shen, Hanghui Ye, Charles S. Fuchs, Sidi Chen
Article
Genetics & Heredity
Jinghua Ruan, Meiyu Wu, Xiaogang Ye, Shuo Zhao, Jianshe Liang, Lupeng Ye, Zhengying You, Boxiong Zhong
Summary: The study identified two mutant strains of Bombyx mori with extremely low silk fibroin production, Naked pupa sericin and Naked pupa, and highlighted the need for further research on the molecular mechanisms of long non-coding RNAs in regulating fibroin synthesis. Differences in gene expression levels were observed between high silk fibroin-producing strains like Qiufeng and Baiyu, and the Nd strain with decreased expression of genes related to protein synthesis and secretion. GO and KEGG analyses revealed enriched pathways related to nucleotide excision repair, mRNA surveillance, and protein degradation in comparisons between different strains.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Shuo Zhao, Xiaogang Ye, Meiyu Wu, Jinghua Ruan, Xiaoxiao Wang, Xiaoli Tang, Boxiong Zhong
Summary: By utilizing transgenic technology, the structures of exogenous protein molecules that can enhance the mechanical properties of silkworm silk were successfully constructed and shown to improve the quality of silk. Further research indicated that silk with more polyalanine motifs had higher fracture strength and Young's modulus, demonstrating the potential for improving mechanical properties of silk through genetic modification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Meiyu Wu, Jinghua Ruan, Xiaogang Ye, Shuo Zhao, Xiaoli Tang, Xiaoxiao Wang, Huiping Li, Boxiong Zhong
Summary: The expression of human epidermal growth factor (hEGF) in a P25 gene knockout silkworm was reported, where the knockout of the P25 gene increased hEGF production while maintaining similar physical properties of cocoon silks compared to wild type silkworms. This suggests that P25 gene knockout silkworms could be an efficient bioreactor for producing exogenous proteins and protein-containing silk biomaterials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Biomedical
Meiyu Wu, Shenyu Huang, Xiaogang Ye, Jinghua Ruan, Shuo Zhao, Juan Ye, boxiong Zhong
Summary: This study successfully produced transgenic silkworms expressing the hEGF fusion protein using piggyBac transposon technology, and the extracted silk from the cocoons showed a significant increase in cell proliferation without cytotoxicity. The transgenic silk could potentially be a cost-effective and functional biomaterial for wound dressing applications.
JOURNAL OF BIOMATERIALS APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Xiaogang Ye, Shuo Zhao, Meiyu Wu, Jinghua Ruan, Xiaoli Tang, Xiaoxiao Wang, Boxiong Zhong
Summary: This study successfully disrupted the sericin 1 gene in domestic silkworms using CRISPR/Cas9-mediated gene editing, resulting in the generation of homozygous mutants. The research findings suggest that sericin 1 plays an important role in the cellular immune system and has a synergistic effect with certain protease inhibitors, shedding light on the function of sericin 1 and the mechanism of silk secretion.
Article
Biochemistry & Molecular Biology
Xiaogang Ye, Xiaoli Tang, Shuo Zhao, Jinghua Ruan, Meiyu Wu, Xiaoxiao Wang, Huiping Li, Boxiong Zhong
Summary: In this study, the Fib-L gene of silkworm was edited using CRISPR/Cas9, resulting in premature degeneration of the PSGs. Comparative transcriptome and proteomic analyses of different genotypes revealed that apoptosis and autophagy pathways were prematurely activated in the PSGs of homozygous mutants.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Xiaoli Tang, Xiaogang Ye, Xiaoxiao Wang, Shuo Zhao, Meiyu Wu, Jinghua Ruan, Boxiong Zhong
Summary: In this study, specific expression of two putative spider silk genes was achieved in the posterior silk glands of silkworms using the piggyBac transposon technique. This led to the enhancement of mechanical properties of silk fiber by up to 91.5%, providing a basis for spidroin silk production.
SCIENTIFIC REPORTS
(2021)
Article
Medicine, Research & Experimental
Lingjuan Hong, Na Li, Victor Gasque, Sameet Mehta, Lupeng Ye, Yinyu Wu, Jinyu Li, Andreas Gewies, Juergen Ruland, Karen K. Hirschi, Anne Eichmann, Caroline Hendry, David van Dijk, Arya Mani
Summary: The study identified Prdm6 as an epigenetic modifier that regulates the fate of migrating cardiac NCCs (CNCCs) by controlling the expression of CNCC specification genes. Loss of Prdm6 resulted in impaired CNCC differentiation and migration, leading to congenital heart diseases.
Article
Multidisciplinary Sciences
Lei Peng, Yingxia Hu, Madeleine C. Mankowski, Ping Ren, Rita E. Chen, Jin Wei, Min Zhao, Tongqing Li, Therese Tripler, Lupeng Ye, Ryan D. Chow, Zhenhao Fang, Chunxiang Wu, Matthew B. Dong, Matthew Cook, Guilin Wang, Paul Clark, Bryce Nelson, Daryl Klein, Richard Sutton, Michael S. Diamond, Craig B. Wilen, Yong Xiong, Sidi Chen
Summary: This study reports the development of monoclonal antibodies (mAbs) that effectively neutralize SARS-CoV-2 variants of concern. By using high-throughput single cell sequencing, the researchers identified two highly potent mAb clones with strong neutralizing activity against SARS-CoV-2 and its emerging variants. Cryo-EM structures revealed the distinct epitopes, binding patterns, and conformations of these neutralizing antibodies. The lead clones also showed potent efficacy in vivo against authentic SARS-CoV-2 in both preventive and therapeutic settings. Furthermore, a humanized antibody was generated and showed strong potency against both the original virus and the B.1.617.2 Delta variant. These mAbs expand the repertoire of therapeutics against SARS-CoV-2 and emerging variants.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Xiaogang Ye, Xiangping Dai, Xinqiu Wang, Shihua Yu, Meiyu Wu, Shuo Zhao, Jinghua Ruan, Boxiong Zhong
Summary: This study generated a homozygous Fib-L gene mutant population of a nonpractical variety using the CRISPR/Cas9 system. The homozygous mutants displayed a thin cocoon layer, but their viability was not affected by the Fib-L mutation. Furthermore, a comparative proteomic analysis of homozygous mutant cocoons and wildtype cocoons was performed. The analysis of the abundance of silk proteins in the cocoons revealed that P25 could be secreted almost normally. The analysis of the abundance of cocoon proteins other than silk proteins showed that the homozygous mutants responded to greater environmental stress by increasing the secretion of defense-related proteins, such as protease inhibitors. These results will further help explain the silk secretion mechanism of silkworm.
JOURNAL OF PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Xiaogang Ye, Meiyu Wu, Xinqiu Wang, Xiangping Dai, Shihua Yu, Xiaoli Tang, Xiaoxiao Wang, Boxiong Zhong
Summary: In this study, a DsRed expression cassette was inserted into the silkworm W chromosome as a visible marker for sex separation. The transgenic silkworms showed female-specific body color, making it easier to separate males from females. This strategy can be applied to other light-colored insects as well.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Shuo Zhao, Xiaogang Ye, Xiangping Dai, Xinqiu Wang, Shihua Yu, Boxiong Zhong
Summary: This study used transgenic technology to insert Drosophila resilin gene into the silkworm genome, resulting in the enhancement of mechanical properties of silk. The recombinant silk showed higher beta-sheet content, fracture strength, and resilience compared to wild-type silk. This approach broadens the possibilities for biomimetic silk materials design and application.