Article
Biochemistry & Molecular Biology
Dongna Ma, Jingping Fang, Qiansu Ding, Liufeng Wei, Yiying Li, Liwen Zhang, Xingtan Zhang
Summary: In this study, we sequenced the transcriptome of tea leaves using PacBio sequencing technology and found that the post-transcriptional regulatory mechanism affecting the synthesis of catechins in tea is still not well understood. We identified a large number of alternative splicing and alternative polyadenylation events, which play a crucial role in regulating the catechins content.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Genetics & Heredity
Ali Ali, Gary H. H. Thorgaard, Mohamed Salem
Summary: The study achieved a full-length transcriptome assembly of rainbow trout using Iso-Seq, identifying numerous previously unannotated transcripts and isoforms not mapped to the reference genome. Most genes had multiple isoforms, with intron retention and exon skipping being major alternative splicing events. The improved annotation allowed for the identification of characteristic alternative splicing events associated with various phenotypic traits in rainbow trout.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Max Coulter, Juan Carlos Entizne, Wenbin Guo, Micha Bayer, Ronja Wonneberger, Linda Milne, Miriam Schreiber, Allison Haaning, Gary J. Muehlbauer, Nicola McCallum, John Fuller, Craig Simpson, Nils Stein, John W. S. Brown, Robbie Waugh, Runxuan Zhang
Summary: In this study, a comprehensive and highly resolved barley reference transcript dataset BaRTv2.18 was constructed using novel computational methods and multiple sequencing technologies. The accuracy of transcript level quantification, SJs, and transcript start and end sites in BaRTv2.18 was validated extensively. BaRTv2.18 represents the most comprehensive and resolved reference transcriptome in barley to date, providing a valuable resource for transcriptomic research.
Article
Plant Sciences
Zhongxin Jin, Xinning Lv, Yushuai Sun, Zongbao Fan, Guangqing Xiang, Yuxin Yao
Summary: The study identified a total of 8,453 AS events in grapevine roots, with retained intron (RI) being the most dominant type, and showed a global decrease in inclusion isoforms proportion under salt stress. Only a small overlap was found between salt-responsive AS events and differentially expressed genes, while differentially spliced genes were mainly related to RNA processing, nucleic acid binding, and ion channel activity. Additionally, the study identified salt-induced spliceosomal protein genes LSM2 and SRSF1 in grapevine roots and proposed a method to explore interactions between AS and alternative polyadenylation (APA) using Iso-Seq data.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Genetics & Heredity
Qi Zeng, Beijuan Hu, Andres Hortas Blanco, Wanchang Zhang, Daxian Zhao, Paulino Martinez, Yijiang Hong
Summary: This study combined Illumina RNA-seq and PacBio Isoform Sequencing to analyze the gonads of H. schlegelii and identified genes related to sex determination and gonadal development.
FRONTIERS IN GENETICS
(2022)
Article
Neurosciences
Andrew E. Weller, Thomas N. Ferraro, Glenn A. Doyle, Benjamin C. Reiner, Richard C. Crist, Wade H. Berrettini
Summary: The hippocampal transcriptomic and polyadenylation site usage alterations caused by genetic mutations in 5XFAD and T2KO mice were investigated. Differentially expressed genes (DEGs) and differential transcript usage (DTU) were identified in neuronal and glial cell subtypes, and the Ingenuity Pathway Analysis (IPA) revealed the involvement of energy imbalance and inflammatory processes in specific hippocampal cell types in Alzheimer's disease (AD)-related pathology.
JOURNAL OF ALZHEIMERS DISEASE
(2022)
Article
Biotechnology & Applied Microbiology
Michael A. Schon, Stefan Lutzmayer, Falko Hofmann, Michael D. Nodine
Summary: We developed a software package called Bookend, which integrates data from different RNA-seq techniques, focusing on identifying and utilizing RNA 5' and 3' ends. Correct identification of transcript start and end sites is crucial for accurate full-length transcript assembly. By using end-labeled reads in single-cell RNA-seq datasets, the precision of transcript assembly in single cells is significantly improved. Additionally, combining different types of RNA-seq datasets can produce high-quality end-to-end transcript annotations.
Article
Immunology
Chase E. Hawes, Sonny R. Elizaldi, Danielle Beckman, Giovanne B. Diniz, Yashavanth Shaan Lakshmanappa, Sean Ott, Blythe P. Durbin-Johnson, Ashok R. Dinasarapu, Andrea Gompers, John H. Morrison, Smita S. Iyer
Summary: Research highlights the immune surveillance of the rhesus CNS by innate and adaptive immune cells during homeostasis. Following SHIV infection, vulnerabilities of key cognitive and motor function brain regions to HIV-1 during the acute phase were demonstrated by viral entry and integration within multiple brain regions.
JOURNAL OF NEUROINFLAMMATION
(2022)
Article
Plant Sciences
Xiaojiao Chen, Yue Yao Tang, Haodong Yin, Xue Sun, Xiaoqian Zhang, Nianjun Xu
Summary: Our study sequenced the full-length transcriptome of Gracilariopsis lemaneiformis using third-generation sequencing (Pacific Biosciences single-molecule real-time long-read sequencing, SMRT-Seq) to identify alternatively spliced transcripts and alternative polyadenylation (APA) sites. We generated 346,544 nonchimeric reads, from which 13,630 unique full-length transcripts were obtained. Over 3000 new alternative splicing (AS) events were identified compared to known gene models. We also identified genes with poly (A) sites, microRNAs, long noncoding RNAs, and novel genes in G. lemaneiformis. Validation experiments showed that abiotic stresses and phytohormones induced specific AS events and alterations to transcript ratios, and differential APA resulted in novel 3' ends. Cu stress inhibited the growth of G. lemaneiformis, but this inhibition was alleviated by ACC treatment. RNA-Seq analysis revealed differential alternative splicing (DAS) events and upregulation of transcripts involved in carbon fixation and oxidative phosphorylation with ACC treatment.
Article
Genetics & Heredity
Sophie Elena Sage, Pamela Nicholson, Tosso Leeb, Vinzenz Gerber, Vidhya Jagannathan
Summary: The study utilized long-read sequencing technology to generate full-length transcript sequences in equine BALF cells, resulting in 14,234 full-length transcript isoforms. Among these transcripts, 3428 were newly discovered, along with 10,806 known transcripts, including fusion transcripts.
Article
Multidisciplinary Sciences
Zehu Yuan, Ling Ge, Jingyi Sun, Weibo Zhang, Shanhe Wang, Xiukai Cao, Wei Sun
Summary: This study utilized Iso-Seq technology to conduct transcriptomic analysis of sheep tail fat tissue, revealing transcriptomic complexity, identifying numerous potential gene loci and transcripts, and recognizing hundreds of differentially expressed transcripts between thin-tailed and fat-tailed sheep.
Article
Agronomy
Yunsong Gu, Shichen Han, Lin Chen, Junyi Mu, Luning Duan, Yaxuan Li, Yueming Yan, Xiaohui Li
Summary: This study identified key proteins and genes involved in wheat reserve starch biosynthesis through RNA-Seq libraries and expression analyses. The transcription factor TaMYB44 was found to potentially regulate the pathway. These findings provide insights for increasing starch content in wheat endosperm.
Editorial Material
Biochemistry & Molecular Biology
Pooja Singh, Ehsan Pashay Ahi
Summary: Alternative splicing is a widely present co-transcriptional gene regulatory mechanism in plants, animals and fungi, contributing to transcriptomic and proteomic diversity. Recent research suggests that alternative splicing plays a crucial role in ecological adaptations, highlighting its importance in adaptive evolution and speciation.
Article
Biochemical Research Methods
Oguzhan Begik, Gregor Diensthuber, Huanle Liu, Anna Delgado-Tejedor, Cassandra Kontur, Adnan Muhammad Niazi, Eivind Valen, Antonio J. Giraldez, Jean-Denis Beaudoin, John S. Mattick, Eva Maria Novoa
Summary: RNA polyadenylation plays a central role in RNA maturation, fate, and stability. Nanopore 3' end-capture sequencing (Nano3P-seq) is a method that uses nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. This method can accurately estimate transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.
Article
Entomology
Zhipeng Jia, Surong Hasi, Deng Zhan, Bin Hou, Claus Vogl, Pamela A. Burger
Summary: In this study, two sex-determination genes in Wohlfahrtia magnifica were isolated and characterized, providing a foundation for genetic control strategies against this species. Additionally, transcriptome analysis revealed five candidate genes that may be involved in Cas9-based gene drive systems, potentially contributing to the control of myiasis infestation caused by W. magnifica.
Article
Cell Biology
Dong Huang, Bolin Xu, Lu Liu, Lingzhi Wu, Yuangang Zhu, Alireza Ghanbarpour, Yawei Wang, Feng-Jung Chen, Jia Lyu, Yating Hu, Yunlu Kang, Wenjing Zhou, Xiao Wang, Wanqiu Ding, Xin Li, Zhaodi Jiang, Jizheng Chen, Xu Zhang, Hongwen Zhou, John Zhong Li, Chunguang Guo, Wen Zheng, Xiuqin Zhang, Peng Li, Thomas Melia, Karin Reinisch, Xiao-Wei Chen
Summary: This study revealed the role of TMEM41B in phospholipid shuttling process, highlighting its critical importance in maintaining ER function and lipid homeostasis.
Article
Genetics & Heredity
Lei Li, Kai-Lieh Huang, Yipeng Gao, Ya Cui, Gao Wang, Nathan D. Elrod, Yumei Li, Yiling Elaine Chen, Ping Ji, Fanglue Peng, William K. Russell, Eric J. Wagner, Wei Li
Summary: The study presents a multi-tissue atlas of alternative polyadenylation (APA) quantitative trait loci (3 ' aQTLs) identifying approximately 0.4 million common genetic variants associated with the APA of target genes. About 16% of trait-associated variants colocalize with 3 ' aQTLs, indicating their substantial contribution to the molecular mechanisms behind human complex traits and diseases.
Article
Biochemistry & Molecular Biology
Deepanwita Sengupta, Liyong Zeng, Yumei Li, Simone Hausmann, Debopam Ghosh, Gang Yuan, Thuyen N. Nguyen, Ruitu Lyu, Marcello Caporicci, Ana Morales Benitez, Garry L. Coles, Vladlena Kharchenko, Iwona Czaban, Dulat Azhibek, Wolfgang Fischle, Mariusz Jaremko, Ignacio I. Wistuba, Julien Sage, Lukasz Jaremko, Wei Li, Pawel K. Mazur, Or Gozani
Summary: The etiological role of NSD2 enzymatic activity in solid tumors is unclear. NSD2, through H3K36me2 catalysis, cooperates with oncogenic KRAS signaling to drive LUAD pathogenesis. Depletion of NSD2 along with MEK1/2 inhibition can cause significant regression of LUAD tumors.
Article
Gastroenterology & Hepatology
Yunfei Bai, Zhenghao Yang, Xiaochan Xu, Wanqiu Ding, Juntian Qi, Feng Liu, Xiaoxiao Wang, Bin Zhou, Wenpeng Zhang, Xiaomei Zhuang, Guanglu Li, Yang Zhao
Summary: Cell fate can be directly reprogrammed into functional cell types using small molecule stimuli. This study demonstrates the successful direct chemical reprogramming of mouse fibroblasts into functional hepatocyte-like cells. The chemically induced hepatocytes exhibit comparable activity and function to primary hepatocytes and have high-quality physiological properties. The findings suggest the potential of chemical reprogramming in organ/tissue repair and regeneration therapies.
Article
Cardiac & Cardiovascular Systems
Shuangjin Ding, Jiankun Liu, XiaoRui Han, Wanqiu Ding, Zhirui Liu, Ying Zhu, Wenxing Zhan, Yiqi Wan, Shujie Gai, Junjie Hou, Xiaoxia Wang, Yixia Wu, Andong Wu, Chuan-Yun Li, Zhe Zheng, Xiao-Li Tian, Huiqing Cao
Summary: This study identified the key role of long noncoding RNA (lncRNA) ICR in early atherosclerosis. ICR promotes the formation of atherosclerotic plaques through regulation of the nuclear factor kappa B (NF-kappa B) signaling pathway. Inhibiting ICR could be a promising early intervention strategy for atherosclerosis.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2022)
Article
Ecology
Ni A. A. An, Jie Zhang, Fan Mo, Xuke Luan, Lu Tian, Qing Sunny Shen, Xiangshang Li, Chunqiong Li, Fanqi Zhou, Boya Zhang, Mingjun Ji, Jianhuan Qi, Wei-Zhen Zhou, Wanqiu Ding, Jia-Yu Chen, Jia Yu, Li Zhang, Shaokun Shu, Baoyang Hu, Chuan-Yun Li
Summary: Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant. The distinctive U1 elements and RNA splice-related sequences drive the origin of de novo genes from lncRNA loci and distinguish them from lncRNAs. The functional new genes acquire functions along with the achievement of their coding potential.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Morgan Dragan, Zeyu Chen, Yumei Li, Johnny Le, Peng Sun, Daniel Haensel, Suhas Sureshchandra, Anh Pham, Eddie Lu, Katherine Thanh Pham, Amandine Verlande, Remy Vu, Guadalupe Gutierrez, Wei Li, Cholsoon Jang, Selma Masri, Xing Dai
Summary: The skin epidermis acts as a barrier to protect the body from external assaults. However, the mechanisms that maintain barrier integrity in adult skin and the impact of epidermal dysregulation on immune microenvironment and metabolism are not well understood. This study demonstrates that the loss of transcription factors Ovol1 and Ovol2 in adult epidermis leads to barrier dysregulation, epithelial-mesenchymal plasticity, and inflammatory gene expression. This results in abnormal skin immune activation, elevated levels of inflammatory factors, and impaired whole-body metabolism, which can be partially restored by immunosuppressant treatment.
Article
Biochemistry & Molecular Biology
Xiangshang Li, Chunfu Xiao, Juntian Qi, Weizhen Xue, Xinwei Xu, Zelin Mu, Jie Zhang, Chuan-Yun Li, Wanqiu Ding
Summary: STellaris is an online server that assigns spatial information to scRNA-seq data based on their transcriptomic similarity with public spatial transcriptomics (ST) data. It is built on 101 manually curated ST datasets comprising 823 sections from different organs, developmental stages, and pathological states of humans and mice. STellaris takes raw count matrix and cell type annotation of scRNA-seq data as input, and maps single cells to spatial locations in properly matched ST sections.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell & Tissue Engineering
Chenglu Xiao, Junjie Hou, Fang Wang, Yabing Song, Jiyuan Zheng, Lingfei Luo, Jianbin Wang, Wanqiu Ding, Xiaojun Zhu, Jing-Wei Xiong
Summary: This study reveals that Brg1-Kdm7aa-Notch axis in cardiac endothelial cells is crucial for myocardial proliferation and regeneration in zebrafish. The induction of brg1 mRNA and protein after ventricular resection suggests the importance of Brg1 in heart regeneration. The endothelium-specific overexpression of dn-xbrg1 leads to abnormal activation of Notch family genes and inhibits myocardial proliferation and regeneration.
NPJ REGENERATIVE MEDICINE
(2023)
Article
Cell Biology
Hao Wu, Wenshuo Zhang, Fengli Xu, Kun Peng, Xiaoyu Liu, Wanqiu Ding, Qi Ma, Heping Cheng, Xianhua Wang
Summary: Wu et al. have identified C17orf80 as a bona fide mitochondrial nucleoid protein that promotes mtDNA replication. This discovery sheds light on the regulation of mtDNA maintenance and offers a potential target for treating diseases associated with defective mtDNA metabolism.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Cell Biology
Chengchuan Ma, Tingling Xue, Qi Peng, Jie Zhang, Jialiang Guan, Wanqiu Ding, Yi Li, Peixue Xia, Liankui Zhou, Tianyu Zhao, Sheng Wang, Li Quan, Chuan-Yun Li, Ying Liu
Summary: N-6-Methyldeoxyadenine (6mA) is a DNA modification found in metazoans that has potential biological function. Researchers have discovered that the levels of genomic 6mA change in response to pathogenic infection in Caenorhabditis elegans. The methyltransferase METL-9 has been identified as the enzyme responsible for catalyzing DNA 6mA modifications during pathogen infection. Deficiency of METL-9 impairs the induction of innate immune response genes and increases susceptibility to pathogen infection. These findings demonstrate that 6mA is a functional DNA modification involved in immunomodulation in C. elegans.
Article
Biotechnology & Applied Microbiology
Heather J. Zhou, Lei Li, Yumei Li, Wei Li, Jingyi Jessica Li
Summary: This study benchmarks popular hidden variable inference methods and finds that principal component analysis (PCA) not only underlies the statistical methodology behind these methods, but is also faster, better-performing, and easier to interpret and use. To help researchers use PCA in their QTL analysis, the authors provide an R package and a detailed guide, believing that using PCA will substantially improve and simplify hidden variable inference in QTL mapping, as well as increase the transparency and reproducibility of QTL research.