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
Hematology
Salome Le Goff, Ismael Boussaid, Celia Floquet, Anna Raimbault, Isabelle Hatin, Charlotte Andrieu-Soler, Mohammad Salma, Marjorie Leduc, Emilie-Fleur Gautier, Boris Guyot, Diane d'Allard, Nathalie Montel-Lehry, Sarah Ducamp, Amandine Houvert, Francois Guillonneau, Stephane Giraudier, Elisabeth Cramer-Borde, Francois Morle, Jean-Jacques Diaz, Olivier Hermine, Naomi Taylor, Sandrina Kinet, Frederique Verdier, Rose-Ann Padua, Mohandas Narla, Pierre-Emmanuel Gleizes, Eric Soler, Patrick Mayeux, Michaela Fontenay
Summary: Ribosome biogenesis plays a crucial role in erythroid development, with premature termination impacting erythroid expansion by activating p53 and preventing normal proliferation of erythroid progenitors.
Article
Multidisciplinary Sciences
Amit K. Singh, Qingrong Chen, Cu Nguyen, Daoud Meerzaman, Dinah S. Singer
Summary: Cohesin plays a role in regulating alternative splicing by interacting with splicing factors and influencing splicing patterns. Mutations in cohesin are associated with distinct splicing patterns in acute myeloid leukemia, and cohesin interacts with another splicing regulator, BRD4, to generate unique splicing patterns. These findings provide insights into the role of cohesin in both normal and leukemic cells and its contribution to human disease.
Article
Oncology
Kai Qin, Danni Jian, Yaqiang Xue, Yi Cheng, Peng Zhang, Yaxun Wei, Jing Zhang, Huihua Xiong, Yi Zhang, Xianglin Yuan
Summary: Research has revealed the crucial role of DDX41 in regulating the cancer cell transcriptome, providing insight into its biological functions in inhibiting tumor cell growth and modulating cancer immunity.
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
Biochemistry & Molecular Biology
Guoxiang Jiang, Dandan Zhang, Zhiwei Li, Hanzhi Liang, Rufang Deng, Xinguo Su, Yueming Jiang, Xuewu Duan
Summary: Alternative splicing of MaMYB16L generates two isoforms, with the downregulation of MaMYB16L and upregulation of MaMYB16S promoting fruit ripening by activating ripening-related genes. The competitive interaction between MaMYB16L and MaMYB16S forms a self-regulatory loop to regulate banana fruit ripening.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Peter Tatrai, Fanni Gergely
Summary: This study shows the critical role of CDK5RAP2 and centrosomes in spindle formation during blood production. Lack of CDK5RAP2 leads to defective erythroid differentiation and the emergence of macrocytic anemia. The study suggests that disruption of centrosome and spindle function could contribute to the development of macrocytic anemias.
Article
Multidisciplinary Sciences
Liu Teng, Yu Chen Feng, Su Tang Guo, Pei Lin Wang, Teng Fei Qi, Yi Meng Yue, Shi Xing Wang, Sheng Nan Zhang, Cai Xia Tang, Ting La, Yuan Yuan Zhang, Xiao Hong Zhao, Jin Nan Gao, Li Yuan Wei, Didi Zhang, Jenny Y. Wang, Yujie Shi, Xiao Ying Liu, Jin Ming Li, Huixia Cao, Tao Liu, Rick F. Thorne, Lei Jin, Feng-Min Shao, Xu Dong Zhang
Summary: The study identified the lncRNA PLANE as a non-protein product of chromosome 3q amplification that promotes tumorigenesis by disrupting the splicing of transcriptional corepressor NCOR2 pre-mRNA.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Marelize Snyman, Sen Xu
Summary: Understanding the relationship between mutations and their effects on gene expression and alternative splicing is important in evolutionary biology. This study investigates the impact of mutations on gene expression and alternative splicing using whole-genome sequencing and RNA sequencing data from Daphnia mutant lines. The results show that trans-effects play a major role in the differences in gene expression and alternative splicing between wild-type and mutant lines, while cis mutations only affect a limited number of genes. Exonic mutations are found to be an important driver of altered gene expression.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Endocrinology & Metabolism
Yuanli Zhao, Kuangxin Chen, Fei Liu, Mouyan Jiang, Zonggui Chen, Huijie Chen, Yanlong Song, Binbin Tao, Xuefan Cui, Yongming Li, Zuoyan Zhu, Ji Chen, Wei Hu, Daji Luo
Summary: The common carp is a significant species in freshwater aquaculture, and studying its gonadal differentiation is important. Females grow faster than males, making related research valuable. This study reveals the gene expression, regulation, and molecular mechanisms during testicular development in cyprinid species.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Cell Biology
Jiaying Qiu, Liucheng Wu, Yan Chang, Hualin Sun, Junjie Sun
Summary: The study found that alternative splicing is a novel mechanism involved in skeletal muscle atrophy, independent of changes at the transcript level, affecting the appearance of the atrophic phenotype, and exacerbating myotube atrophy by the inclusion of highly conserved exons.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Cell Biology
Marco Del Giudice, John G. Foster, Serena Peirone, Alberto Rissone, Livia Caizzi, Federica Gaudino, Caterina Parlato, Francesca Anselmi, Rebecca Arkell, Simonetta Guarrera, Salvatore Oliviero, Giuseppe Basso, Prabhakar Rajan, Matteo Cereda
Summary: FOXA1 plays a key role in dysregulation of alternative splicing in prostate cancer by controlling transcription factor expression and binding to splicing-related genes, leading to the production of dominant isoforms and influencing patient survival.
Article
Plant Sciences
Peng Tian, Zeteng Lin, Dongbo Lin, Shuangyu Dong, Jianzi Huang, Tengbo Huang
Summary: In response to phosphate starvation, tomato seedlings showed a slight increase in overall DNA methylation levels, with millions of differentially methylated cytosines and hundreds of differentially methylated regions. Thousands of genes displayed differential expression and alternative splicing under phosphate-deficient conditions, with differentially methylated cytosines more abundant in non-expressed genes. Additionally, DNA methylation changes weakly correlated with transcription changes, but not with alternative splicing events.
Article
Plant Sciences
Zhibin Zhang, Hongwei Xun, Ruili Lv, Xiaowan Gou, Xintong Ma, Juzuo Li, Jing Zhao, Ning Li, Lei Gong, Bao Liu
Summary: Homoeologous exchange (HE) is a mechanism that generates genetic variation and affects gene expression and transcript diversity in allopolyploids. This study shows that HE impacts gene expression primarily through cis-acting dosage effects in HE regions, leading to changes in expression levels of homoeologous gene pairs. Additionally, HE influences gene expression in non-HE regions through trans-regulation, resulting in convergent expression of homoeologs. Furthermore, HE induces individual-specific changes in alternative splicing events. Overall, HE has multifaceted immediate effects on gene expression and transcript diversity in nascent allopolyploidy.
Review
Biochemistry & Molecular Biology
Immanuel D. Green, Renjing Liu, Justin J. L. Wong
Summary: Vascular smooth muscle cells (VSMCs) exhibit remarkable phenotypic plasticity, allowing them to differentiate or dedifferentiate based on environmental cues. Alternative splicing plays a crucial role in VSMC gene expression regulation, contributing to protein diversity and alterations in gene expression levels. Recent advancements in splicing-modulating therapies hold promise for treating VSMC-related pathologies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Biochemistry & Molecular Biology
Sandra Catania, Phillip A. Dumesic, Harold Pimentel, Ammar Nasif, Caitlin I. Stoddard, Jordan E. Burke, Jolene K. Diedrich, Sophie Cooke, Terrance Shea, Elizabeth Gienger, Robert Lintner, John R. Yates, Petra Hajkova, Geeta J. Narlikar, Christina A. Cuomo, Jonathan K. Pritchard, Hiten D. Madhani
Article
Biochemical Research Methods
Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter
Article
Multidisciplinary Sciences
Shunfu Mao, Lior Pachter, David Tse, Sreeram Kannan
Article
Biotechnology & Applied Microbiology
Pall Melsted, A. Sina Booeshaghi, Lauren Liu, Fan Gao, Lambda Lu, Kyung Hoi (Joseph) Min, Eduardo da Veiga Beltrame, Kristjan Eldjarn Hjorleifsson, Jase Gehring, Lior Pachter
Summary: The preprocessing workflow for single-cell RNA-seq data achieves near-optimal speed and high efficiency, demonstrating flexibility and scalability for large datasets.
NATURE BIOTECHNOLOGY
(2021)
Article
Biophysics
Gennady Gorin, Lior Pachter
Summary: In this study, the impact of splicing cascades on expression dynamics is investigated. The authors examine a class of processes and associated distributions that arise from bursty promoters coupled to directed acyclic graphs of splicing. They provide time-dependent joint distributions for various species, offering insights into how splicing can regulate expression dynamics. The findings are validated through the analysis of long-read sequencing data.
BIOPHYSICAL JOURNAL
(2022)
Review
Biochemical Research Methods
Lambda Moses, Lior Pachter
Summary: This article reviews spatial transcriptomics research since 1987 and provides a detailed analysis of trends and applications of related technologies and methods. The study offers historical context and guidance for current research.
Correction
Biochemical Research Methods
Lambda Moses, Lior Pachter
Article
Biochemical Research Methods
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
Summary: We perform a thorough analysis of RNA velocity methods and propose an improved framework.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Gennady Gorin, John J. Vastola, Meichen Fang, Lior Pachter
Summary: This study investigates how cell-to-cell differences in transcription rate affect RNA count distributions. The authors introduce quantitative models to compare and contrast two biologically plausible hypotheses about transcription rate variation. They propose a framework for analyzing these models and use Bayesian model selection to identify candidate genes in single-cell transcriptomic data.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
A. Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Tara Chari, Lior Pachter
Summary: Dimensionality reduction is a common method for filtering noise and identifying relevant features in large-scale data analysis. However, reducing high-dimensional datasets to just 2 or 3 dimensions can lead to significant distortion. This study shows that low-dimensional embedding of single-cell data can be counter-productive for exploratory biological analysis due to extensive distortions and inconsistent practices. Alternative approaches for targeted embedding and feature exploration are discussed to enable hypothesis-driven biological discovery.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gennady Gorin, John J. Vastola, Lior Pachter
Summary: Recent experimental developments in genome-wide RNA quantification show great potential for systems biology. However, a unified mathematical framework is needed to comprehensively study the biology of living cells, taking into account technical variations in genomics assays and the stochasticity of single-molecule biology. In this paper, we review different models for RNA transcription processes and present a framework that integrates these phenomena through the manipulation of generating functions. Finally, we provide simulated scenarios and biological data to demonstrate the implications and applications of this approach.
Article
Biophysics
Gennady Gorin, Lior Pachter
Summary: Single-cell RNA sequencing data can be modeled using Markov chains to gain genome-wide insights into transcriptional physics. However, accurate analysis of the data requires careful consideration of noise sources. A length-based model of capture bias is proposed to explain the over-representation of long pre-mRNA transcripts in sequencing data, which may lead to false-positive observations. This model provides concordant parameter trends and helps identify systematic, mechanistically interpretable technical and biological differences in paired data sets.
BIOPHYSICAL REPORTS
(2023)
Article
Engineering, Electrical & Electronic
A. Sina Booeshaghi, Yeokyoung (Anne) Kil, Kyung Hoi (Joseph) Min, Jase Gehring, Lior Pachter
Summary: Colosseum is a low-cost, modular, and automated fluid sampling device that uses a single motor, can be built for less than $100, and assembled in less than an hour. Instructions and source files are available online.
Article
Biotechnology & Applied Microbiology
Johan Gustafsson, Jonathan Robinson, Jens Nielsen, Lior Pachter
Summary: This study introduces UMIs in single-cell RNA-seq assays to identify duplicated molecules, presenting an improved quantification method called BUTTERFLY based on unseen species modeling. This method effectively addresses the bias caused by the naive removal of duplicates by demonstrating its efficacy across cell types and genes, sometimes even inverting the relative abundance of genes.