Article
Plant Sciences
Hanhan Xie, Wenya Yin, Yedan Zheng, Yanshan Zhang, Hongming Qin, Zhiqiang Huang, Minglei Zhao, Jianguo Li
Summary: This study reveals that CHH methylation increases significantly throughout litchi seed development, and identifies 46 DNA methylation-regulated candidate genes, such as LcSR45, that play essential roles in litchi seed development. Hypermethylation of LcSR45 suppresses seed abortion during seed development.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Kun Li, Ziqiang Wang
Summary: SRSF2, a splicing factor, is regulated by HSV-1 infection and can in turn modulate the levels of immune checkpoint molecules in exhausted T cells, thus playing a crucial role in disease progression.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xuelei Lai, Romain Blanc-Mathieu, Loic GrandVuillemin, Ying Huang, Arnaud Stigliani, Jeremy Lucas, Emmanuel Thevenon, Jeanne Loue-Manifel, Laura Turchi, Hussein Daher, Eugenia Brun-Hernandez, Gilles Vachon, David Latrasse, Moussa Benhamed, Renaud Dumas, Chloe Zubieta, Francois Parcy
Summary: As a pioneer transcription factor, LFY has the ability to bind both methylated and non-methylated DNA, modify chromatin state to initiate gene expression, and induce chromatin accessibility in target genes APETALA1 and AGAMOUS in plant seedling tissues. This study suggests that LFY possesses key pioneer TF features contributing to launching the floral gene expression program.
Review
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Lori Pile, Athar Ansari
Summary: Introns play a crucial role in eukaryotic organisms by impacting various aspects of gene expression, including transcription. Studies in yeast have shown that introns contribute to the formation of multi-looped gene architecture, enhancing transcription through interactions like promoter-5 ' splice site, terminator-3 ' splice site, and promoter-terminator interactions. This splicing-facilitated changes in gene architecture may provide insight into transcriptional regulation in yeast and higher eukaryotes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xinyu Li, Mengxia Chen, Biru Liu, Peifen Lu, Xiang Lv, Xiang Zhao, Shuaiying Cui, Peipei Xu, Yukio Nakamura, Ryo Kurita, Bing Chen, David C. S. Huang, De-Pei Liu, Ming Liu, Quan Zhao
Summary: The study demonstrates that NonO interacts with SOX6 to repress gamma-globin gene expression in human erythroid cells, and depletion of NonO results in significant activation of gamma-globin expression. In vivo experiments using mice also confirm the role of NonO in reactivating globin gene expression, suggesting a conserved function of NonO during mammalian evolution.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Panagiotis Boumpas, Samir Merabet, Julie Carnesecchi
Summary: Transcription factors play a crucial role in orchestrating gene expression and splicing, promoting tissue-specific functions and cell fate. Despite the lack of clear understanding of the mechanisms, recent studies have shed light on the importance of transcription factors in these processes and proposed several possible models.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Multidisciplinary Sciences
Lila Allou, Sara Balzano, Andreas Magg, Mathieu Quinodoz, Beryl Royer-Bertrand, Robert Schopflin, Wing-Lee Chan, Carlos E. Speck-Martins, Daniel Rocha Carvalho, Luciano Farage, Charles Marques Lourenco, Regina Albuquerque, Srilakshmi Rajagopal, Sheela Nampoothiri, Belinda Campos-Xavier, Carole Chiesa, Florence Niel-Buetschi, Lars Wittler, Bernd Timmermann, Malte Spielmann, Michael I. Robson, Alessa Ringel, Verena Heinrich, Giulia Cova, Guillaume Andrey, Cesar A. Prada-Medina, Rosanna Pescini-Gobert, Sheila Unger, Luisa Bonafe, Phillip Grote, Carlo Rivolta, Stefan Mundlos, Andrea Superti-Furga
Summary: This study demonstrates that genetic ablation of a lncRNA locus on human chromosome 2 can result in a severe congenital limb malformation. The findings highlight the importance of the lncRNA locus in regulating En1 gene expression and controlling dorso-ventral polarity in the developing limb bud, leading to a specific subset of the En1-associated phenotype in human Mendelian disease.
Article
Agriculture, Multidisciplinary
Yanrui Zhang, Penghui Li, Guangbiao She, Yujie Xu, Anqi Peng, Xiaochun Wan, Jian Zhao
Summary: The study reveals significant physiological and metabolic differences between shoot tips and roots of tea plants at the transcriptome level, with important implications for improving genome annotation. Additionally, the regulation of characteristic secondary metabolites such as catechins, theanine, and caffeine is closely related to a large number of alternative splicing (AS) and long noncoding RNA (lncRNA) transcripts. This research lays the groundwork for further investigation into metabolic genomics and regulation in tea plants.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Yan Yun, Yun Zhang, Chen Zhang, Liyan Huang, Shichuan Tan, Pin Wang, Carles Vilarino-Guell, Weihong Song, Xiulian Sun
Summary: The study reveals that RCAN1 is a novel RNA-binding protein, and its RNA aptamer can block RCAN1-induced inhibition of NFAT and NF-kappa B signaling pathways, reducing neuronal apoptosis and playing a neuroprotective role.
MOLECULAR PSYCHIATRY
(2021)
Article
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Alisa Gega, Athar Ansari
Summary: Introns play a conserved role in enhancing gene expression, with proximity to both the promoter and the terminator regions affecting their regulatory potential. While a promoter-proximal intron is most efficient in enhancing gene expression, a terminator-proximal intron can also positively influence transcription by affecting both the assembly of preinitiation complex and promoter directionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Steven Heshusius, Laura Grech, Nynke Gillemans, Rutger W. W. Brouwer, Xander T. den Dekker, Wilfred F. J. van IJcken, Benjamin Nota, Alex E. Felice, Thamar B. van Dijk, Marieke von Lindern, Joseph Borg, Emile van den Akker, Sjaak Philipsen
Summary: Haploinsufficiency of KLF1 gene is associated with hereditary persistence of fetal hemoglobin. Decreasing the activity of KLF1 has been proposed as a potential therapeutic strategy for beta-hemoglobinopathies. However, individuals with the same KLF1 variant in the same family show a wide range of HbF levels, which cannot be explained by co-inheritance of known HbF-modulating variants. Studying erythroid progenitors, researchers find that variation in expression of the wildtype KLF1 allele may explain a significant part of the variability in HbF levels observed in KLF1 haploinsufficiency. These findings have implications for the understanding of haploinsufficiency phenotypes and the pathogenicity of variants in other transcriptional regulators.
SCIENTIFIC REPORTS
(2022)
Article
Forestry
Xianliang Zhu, Jiayue He, Changpin Zhou, Qijie Weng, Shengkan Chen, David Bush, Fagen Li
Summary: This study investigates the effects of gene transcription and alternative splicing on wood formation in Eucalyptus urophylla x tereticornis, an economically important tree species in southern China. The results suggest that gene transcription and alternative splicing play important regulatory roles in wood properties and are controlled by independent regulatory systems. Additionally, the study identifies potential molecular mechanisms involved in the regulation of wood properties, which may contribute to the genetic improvement of Eucalyptus.
Article
Agriculture, Multidisciplinary
Jian Zhang, Linlin Li, Yan Yang, Chaofan Zhao, Jiuju Hu, Xianli Xue, Qiang Gao, Depei Wang, Zhenhong Zhuang, Ying Zhang
Summary: This study characterized the role of AnOTAbZIP in morphological development, OTA biosynthesis, and pathogenicity in A. niger. It was found that AnOTAbZIP positively regulates OTA biosynthesis, affects pathogenicity on grape berries, and enhances oxidative stress tolerance.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Plant Sciences
Yilong Hu, Limeng Zhou, Yuhua Yang, Wenbin Zhang, Zhonghui Chen, Xiaoming Li, Qian Qian, Fanjiang Kong, Yuge Li, Xu Liu, Xingliang Hou
Summary: The research demonstrates that in Arabidopsis, gibberellin signaling is involved in the regulation of seed storage protein accumulation through the negative regulator RGL3. RGL3 interacts with the critical transcription factor ABI3 to activate the transcription of seed storage protein genes, advancing the understanding of mechanisms in GA-mediated seed storage reserve accumulation.
Article
Multidisciplinary Sciences
Ida Lauritsen, Pernille Ott Frendorf, Silvia Capucci, Sophia A. H. Heyde, Sarah D. Blomquist, Sofie Wendel, Emil C. Fischer, Agnieszka Sekowska, Antoine Danchin, Morten H. H. Norholm
Summary: Microbial evolution often involves transient and complex changes, including sequential adaptive mutations in hotspot genes. This study shows that alterations in pyrimidine nucleoside levels and mutations in metabolic or regulatory genes can drive the evolution of non-growing E. coli cells. The findings highlight the regulatory role of pyrimidine nucleosides in carbon catabolism and the interaction between transcription factors in sensing carbon availability and metabolic flux.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Niha Beig, Salendra Singh, Kaustav Bera, Prateek Prasanna, Gagandeep Singh, Jonathan Chen, Anas Saeed Bamashmos, Addison Barnett, Kyle Hunter, Volodymyr Statsevych, Virginia B. Hill, Vinay Varadan, Anant Madabhushi, Manmeet S. Ahluwalia, Pallavi Tiwari
Summary: This study identified sexually dimorphic radiogenomic models that could be used to help with personalized treatment decisions for GBM patients by revealing biological changes and prognostic differences between different genders.
Article
Genetics & Heredity
Feixiong Cheng, Junfei Zhao, Yang Wang, Weiqiang Lu, Zehui Liu, Yadi Zhou, William R. Martin, Ruisheng Wang, Jin Huang, Tong Hao, Hong Yue, Jing Ma, Yuan Hou, Jessica A. Castrillon, Jiansong Fang, Justin D. Lathia, Ruth A. Keri, Felice C. Lightstone, Elliott Marshall Antman, Raul Rabadan, David E. Hill, Charis Eng, Marc Vidal, Joseph Loscalzo
Summary: Recent advancements in genomics and interactomics have allowed researchers to identify how disease mutations disrupt protein-protein interaction networks within human cells. Disease-associated germline variants and somatic missense mutations are significantly enriched in protein-protein interaction interfaces, and oncoPPIs identified in cancer analysis are correlated with patient survival and drug resistance/sensitivity. Experimental validation of oncoPPIs and their effects on tumor cell growth demonstrate the potential of using this interactome network framework for prioritizing therapeutic targets.
Article
Biochemistry & Molecular Biology
Bryan M. Webb, Benjamin L. Bryson, Eduardo Williams-Medina, Jessica R. Bobbitt, Darcie D. Seachrist, Lindsey J. Anstine, Ruth A. Keri
Summary: This study reveals that inhibiting the TGF-beta/Activin-ABCG2 pathway is a potential avenue for preventing or overcoming resistance to CDK7 inhibitors.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Rokana Taftaf, Xia Liu, Salendra Singh, Yuzhi Jia, Nurmaa K. Dashzeveg, Andrew D. Hoffmann, Lamiaa El-Shennawy, Erika K. Ramos, Valery Adorno-Cruz, Emma J. Schuster, David Scholten, Dhwani Patel, Youbin Zhang, Andrew A. Davis, Carolina Reduzzi, Yue Cao, Paolo D'Amico, Yang Shen, Massimo Cristofanilli, William A. Muller, Vinay Varadan, Huiping Liu
Summary: CTC clusters are more efficient in mediating metastasis and ICAM1 may be a novel therapeutic target for the initiation of TNBC metastasis.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Ramachandra Katabathula, Peronne Joseph, Salendra Singh, Songzhu Zhao, Bhavna Kumar, Patricia Gaule, Quintin Pan, Matthew Old, David P. Tuck, Vinay Varadan
Summary: This study investigated the expression and clinical significance of VSIR in tumors. It found that VSIR overexpression in oral cavity and ovarian cancers was associated with poorer overall survival and decreased CD4 helper T-cell activity. VSIR overexpressing tumors also exhibited higher STAT3 signaling activity. The findings suggest that the STAT3-VSIR axis may play a significant role in the immune response of these types of cancer.
CLINICAL CANCER RESEARCH
(2022)
Review
Endocrinology & Metabolism
Katrina M. Piemonte, Lindsey J. Anstine, Ruth A. Keri
Summary: Chromosomal instability (CIN) plays a crucial role in cancer, with centrosome defects being a key factor contributing to CIN. Breast cancer patients often exhibit centrosome defects, which can drive genomic changes in cancer cells, leading to aggressive disease and poor outcomes.
Review
Oncology
Darcie D. Seachrist, Lindsey J. Anstine, Ruth A. Keri
Summary: The review discusses the role of FOXA1 in regulating gene activity, cell biology, and the response of breast cancers to hormone therapies. It also highlights the potential for future studies to explore the roles of FOXA1 independent of its regulation of nuclear receptors.
Article
Biochemical Research Methods
Sirvan Khalighi, Peronne Joseph, Deepak Babu, Salendra Singh, Thomas LaFramboise, Kishore Guda, Vinay Varadan
Summary: SYSMut is an extendable systems biology platform that can infer the biological consequences of gene mutations by integrating multiomics profiles. It has been used to identify driver genes across 29 cancers and discover new therapeutic targets in head and neck squamous cell cancer.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Gastroenterology & Hepatology
Srividya Venkitachalam, Deepak Babu, Durgadevi Ravillah, Ramachandra M. Katabathula, Peronne Joseph, Salendra Singh, Bhavatharini Udhayakumar, Yanling Miao, Omar Martinez-Uribe, Joyce A. Hogue, Adam M. Kresak, Dawn Dawson, Thomas LaFramboise, Joseph E. Willis, Amitabh Chak, Katherine S. Garman, Andrew E. Blum, Vinay Varadan, Kishore Guda
Summary: The study suggests that the EphB2 signaling pathway is frequently hyperactivated in the early development of Barrett's esophagus-associated esophageal adenocarcinoma (BE-EAC) and acts as an upstream regulator of the MYC gene. Inhibiting EphB2 can significantly impede the proliferation of BE and EAC cells. Targeting EphB2/MYC could be a promising strategy for treating this common refractory and aggressive cancer.
Letter
Gastroenterology & Hepatology
Andrew E. Blum, Durgadevi Ravillah, Ramachandra M. Katabathula, Sirvan Khalighi, Vinay Varadan, Kishore Guda
Article
Oncology
Leslie Cuellar-Vite, Kristen L. Weber-Bonk, Fadi W. Abdul-Karim, Christine N. Booth, Ruth A. Keri
Summary: This study discovered that blocking FAK can improve the therapeutic response to mTORC1 inhibitors in resistant breast cancer. It suggests a potential strategy of dual targeting FAK and mTORC1.
Article
Oncology
Lindsey J. Anstine, Parth R. Majmudar, Amy Aponte, Salendra Singh, Ran Zhao, Kristen L. Weber-Bonk, Fadi W. Abdul-Karim, Mitchell Valentine, Darcie D. Seachrist, Katelyn E. Grennel-Nickelson, Leslie Cuellar-Vite, Gina M. Sizemore, Steven T. Sizemore, Bryan M. Webb, Cheryl L. Thompson, Ruth A. Keri
Summary: Breast cancer subtypes and their phenotypes correspond to different stages of mammary epithelial cell development. The discovery of mechanisms that control lineage identity may offer new opportunities for reducing disease progression. This study reveals that the transcriptional corepressor TLE3 functions as a guardian of luminal cell fate in breast cancer, independent of the estrogen receptor. TLE3 represses the gene-expression signature associated with aggressive basal-like breast cancers, thereby reducing metastatic capacity and aggressive behaviors.
Review
Endocrinology & Metabolism
Jessica R. Bobbitt, Darcie D. Seachrist, Ruth A. Keri
Summary: The development of sequencing technologies has provided valuable information about the organization of the 3-dimensional genome and its influence on cancer progression. Chromatin folding and accessibility changes can lead to abnormal transcriptional programs and drive the development of various cancers, including different subtypes of breast cancer. Understanding the chromatin architecture in breast cancer subtypes can help define their phenotypic characteristics and identify potential targets for aggressive disease treatment.
Article
Medicine, Research & Experimental
Yihong Guan, Metis Hasipek, Dongxu Jiang, Anand D. Tiwari, Dale R. Grabowski, Simona Pagliuca, Sunisa Kongkiatkamon, Bhumika Patel, Salendra Singh, Yvonne Parker, Thomas LaFramboise, Daniel Lindner, Mikkael A. Sekeres, Omar Y. Mian, Yogen Saunthararajah, Jaroslaw P. Maciejewski, Babal K. Jha
Summary: Eltrombopag binds to the TET2 catalytic domain and inhibits its dioxygenase activity, leading to the expansion of normal hematopoietic stem cells and the prevention of neoplastic evolution in TET2 mutant malignant myeloid cells. This finding provides a scientific rationale for the treatment of myeloid malignancies associated with TET2 mutations or TET deficiency.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Biochemistry & Molecular Biology
Valery Adorno-Cruz, Andrew D. Hoffmann, Xia Liu, Nurmaa K. Dashzeveg, Rokana Taftaf, Brian Wray, Ruth A. Keri, Huiping Liu
Summary: The study revealed that miR-206 inhibits ITGA2 to reduce breast cancer stemness and metastasis. Knockdown of ITGA2 suppressed self-renewal, cell cycling, migration, invasion, and lung metastasis, related to CCND1 and ACLY.
