Article
Multidisciplinary Sciences
Hongbin Li, Vishaal Rajani, Lu Han, Danielle Chung, James E. Cooke, Ameet S. Sengar, Michael W. Salter
Summary: NMDA receptors (NMDARs) are a principal subtype of excitatory neurotransmitter receptor, composed of two GluN1 and two GluN2 subunits. Alternative splicing of GluN1 can affect the signaling of glycine, which is crucial for the nonionotropic signaling by NMDARs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Zukai Liu, Nathaniel Jillette, Paul Robson, Albert Wu Cheng
Summary: We developed a novel platform called CREST that can simultaneously execute multiple RNA modulation functions on different RNA targets. By appending RNA scaffolds to Cas13 gRNA and fusing cognate RNA binding proteins with enzymatic domains, we achieved manipulation of RNA. Additionally, we reconstituted the enzyme activity of ADAR2 at target sites by fusing split fragments of its deaminase domain to dCas13 and/or PUFc, reducing off-target events significantly.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Engineering, Chemical
Valerie J. Y. Chng, Andrew C. A. Wan
Summary: The paper extends the concept of tissue engineering scaffold to alternative protein scaffolds. The use of scaffold can address the textural characteristics of alternative proteins, enhancing their nutritional properties. The scaffold processes for tissue engineering and alternative proteins can be classified as top-down or bottom-up approaches.
JOURNAL OF FOOD ENGINEERING
(2023)
Review
Pharmacology & Pharmacy
Dianyang Li, Wenying Yu, Maode Lai
Summary: Serine-and arginine-rich splicing factors play important roles in regulating splicing by binding to cis-acting elements in precursor mRNAs and facilitating spliceosome assembly. SR proteins also have diverse functions in RNA metabolism as they shuttle between the nucleus and cytoplasm. Overexpression and/or hyperactivation of SR proteins have been associated with tumorigenesis, suggesting their potential as therapeutic targets. This review highlights the physiological and pathological roles of SR proteins and discusses small molecules and oligonucleotides that can modulate SR protein function for future studies.
DRUG DISCOVERY TODAY
(2023)
Article
Plant Sciences
Tongtong Wang, Xiaofeng Wang, Haiyan Wang, Chao Yu, Chengyun Xiao, Yiwu Zhao, Huanan Han, Shuangshuang Zhao, Qun Shao, Jianhua Zhu, Yanxiu Zhao, Pingping Wang, Changle Ma
Summary: Alternative splicing of pre-mRNAs is crucial for plant growth and development. Serine/arginine-rich (SR) proteins are a conserved family of RNA-binding proteins that play a critical role in both constitutive and alternative splicing. However, the regulation of SR proteins' phosphorylation and its effect on gene transcription and alternative splicing during plant development remain poorly understood. In this study, we found that SRPKIIs in Arabidopsis specifically control the phosphorylation status of a subset of SR proteins, including SR45 and SC35, and regulate their subcellular localization.
Review
Genetics & Heredity
Jeru Manoj Manuel, Noe Guilloy, Ines Khatir, Xavier Roucou, Benoit Laurent
Summary: Alternative splicing (AS) is a mechanism that generates multiple mature transcripts from protein-coding genes and long non-coding RNA (lncRNA) genes, increasing transcriptome complexity and producing different protein isoforms. Despite the identification of numerous alternatively spliced transcripts, the low detection rate of protein isoforms has raised questions about the contribution of AS to proteomic diversity and the functional relevance of AS events.
FRONTIERS IN GENETICS
(2023)
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
Biochemistry & Molecular Biology
Sarah M. Smith, Gabrielle Larocque, Katherine M. Wood, Kyle L. Morris, Alan M. Roseman, Richard B. Sessions, Stephen J. Royle, Corinne J. Smith
Summary: The interaction between Clathrin and the AP2 complex plays a crucial role in coated-pit assembly, with a beta 2 appendage able to bind in at least two positions in the clathrin cage. This multi-modal binding is shown to be a fundamental property of clathrin-AP2 interactions.
Article
Cardiac & Cardiovascular Systems
Pablo Montanes-Agudo, Simona Aufiero, Eva N. Schepers, Ingeborg van der Made, Lucia Cocera-Ortega, Auriane C. Ernault, Stephane Richard, Diederik W. D. Kuster, Vincent M. Christoffels, Yigal M. Pinto, Esther E. Creemers
Summary: This study aims to investigate the function and relevance of QKI in the adult mouse heart. The results show that QKI regulates the alternative splicing of multiple genes and affects the functional properties of cardiomyocytes. Loss of QKI leads to severe disruption of sarcomeres and rapid development of heart failure.
CARDIOVASCULAR RESEARCH
(2023)
Article
Cell Biology
Riho Komuro, Yuka Honda, Motoaki Yanaizu, Masami Nagahama, Yoshihiro Kino
Summary: Genetic variations of CD33, specifically the rs12459419 polymorphism on exon 2, affect its alternative splicing and have been associated with the risk of Alzheimer's disease. The minor allele promotes skipping of exon 2, resulting in a shorter CD33 isoform lacking the ligand-binding domain and reduced suppressive signaling on microglial activity. HNRNPA1 was found to promote exon 2 skipping, but simultaneous knockdown of HNRNPA1, HNRNPA2B1, and HNRNPA3 increased exon 2 inclusion, suggesting functional redundancy among these proteins.
Article
Oncology
Nazila Navvabi, Pavla Kolikova, Petr Hosek, Frantisek Zitricky, Azita Navvabi, Ondrej Vycital, Jan Bruha, Richard Palek, Jachym Rosendorf, Vaclav Liska, Pavel Pitule
Summary: The study identified deregulation of MBNL genes in colorectal cancer for the first time, with down-regulation of their transcripts in tumor tissue compared to non-tumor mucosa. Additionally, lower expression of FOXP1 and EPB41L3 variants was observed, while higher expression was detected for total CD44 and its cancer-related variants 3 and 6 in tumor tissue. Multiple significant associations were found in the target gene panel, including higher transcript levels of FOXP1 and CD44v3 in patients with distant metastases and connections between recurrence-free survival and altered levels of FOXP1 and CD44v3.
CANCER GENOMICS & PROTEOMICS
(2021)
Article
Plant Sciences
Xiaohui Cheng, Chuanji Zhao, Lixia Gao, Lingyi Zeng, Yu Xu, Fan Liu, Junyan Huang, Lijiang Liu, Shengyi Liu, Xiong Zhang
Summary: This study systematically explored the genome-scale alternative splicing (AS) events of Sclerotinia sclerotiorum during infection and identified genes associated with successful infection and putative effectors. These findings are important for understanding the pathogenic mechanisms of S. sclerotiorum.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Lu Zhang, Yuanming Liu, Qiaohui Wang, Chao Wang, Shikai Lv, Yanzhen Wang, Jianfeng Wang, Yajuan Wang, Jing Yuan, Hong Zhang, Zhensheng Kang, Wanquan Ji
Summary: This study reveals the mechanism of alternative splicing and protein interaction of the wheat R gene TaYRG1, which enhances resistance to Puccinia striiformis f. sp. tritici and triggers cell death. It also identifies the interaction between TaYRG1 and a dynamin-related protein, suggesting a potential role in membrane trafficking and endocytosis pathway.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Microbiology
Om Basukala, Oscar Trejo-Cerro, Michael P. Myers, David Pim, Paola Massimi, Miranda Thomas, Corrado Guarnaccia, David Owen, Lawrence Banks
Summary: HPV-E7 plays a crucial role in HPV-induced malignancy by targeting AP2 complex and modulating clathrin-mediated endocytosis, which may contribute to cellular transformation.
Article
Cell Biology
Chungen Lan, Huikun Zhang, Kezhen Wang, Xiaoli Liu, Yawen Zhao, Zhifang Guo, Ning Zhang, Yongxia Zhou, Manzhi Gao, Feng Gu, Yongjie Ma
Summary: The study demonstrates that PTBP1 modulates the alternative splicing of ITSN1, promoting glioma proliferation and motility by up-regulating the ratio of ITSN1-S/ITSN1-L, suggesting that PTBP1 may be a promising therapeutic target for gliomas.
CELL DEATH & DISEASE
(2022)
Article
Biochemistry & Molecular Biology
Oleksandr Dergai, Mykola Dergai, Alla Rynditch
Article
Genetics & Heredity
Tetyana Gryaznova, Olga Gubar, Mariia Burdyniuk, Sergii Kropyvko, Alla Rynditch
Article
Biochemistry & Molecular Biology
Erik I. Hallin, Maria S. Eriksen, Sergei Baryshnikov, Oleksii Nikolaienko, Sverre Grodem, Tomohisa Hosokawa, Yasunori Hayashi, Clive R. Bramham, Petri Kursula
JOURNAL OF NEUROCHEMISTRY
(2018)
Review
Cell Biology
Oleksii Nikolaienko, Sudarshan Patil, Maria Steene Eriksen, Clive R. Bramham
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2018)
Article
Oncology
Hanna Svitina, Inessa Skrypkina, Pavlo Areshkov, Vitaliy Kyryk, Tetiana Bukreieva, Pavlo Klymenko, Liudmyla Garmanchuk, Galyna Lobintseva, Volodymyr Shablii
Article
Food Science & Technology
Oksana Naumenko, Inessa Skrypkina, Yaroslava Zhukova, Mykola Vakulenko, Natalia Kigel
INTERNATIONAL JOURNAL OF DAIRY TECHNOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
V. Shablii, M. Kuchma, H. Svitina, I. Skrypkina, P. Areshkov, V. Kyryk, T. Bukreieva, V. Nikulina, Iu. Shablii, G. Lobyntseva
BIOMED RESEARCH INTERNATIONAL
(2019)
Article
Biochemistry & Molecular Biology
Maria S. Eriksen, Oleksii Nikolaienko, Erik I. Hallin, Sverre Grodem, Helene J. Bustad, Marte I. Flydal, Ian Merski, Tomohisa Hosokawa, Daniela Lascu, Shreeram Akerkar, Jorge Cuellar, James J. Chambers, Rory O'Connell, Gopinath Muruganandam, Remy Loris, Christine Touma, Tambudzai Kanhema, Yasunori Hayashi, Margaret M. Stratton, Jose M. Valpuesta, Petri Kursula, Aurora Martinez, Clive R. Bramham
Summary: The study identified a 28-amino-acid stretch in the mammalian Arc N-terminal domain that is crucial for self-association and a 7-residue oligomerization motif critical for virus-like capsid formation. The atomic-resolution crystal structure of the oligomerization region peptide revealed an antiparallel coiled-coil interface supporting NT-NT domain interactions in Arc oligomerization. The study also showed that Arc mRNA enhances higher-order oligomerization dependent on the oligomerization motif, leading to the formation of virus-like capsids.
Article
Biochemical Research Methods
Oleksii Nikolaienko, Per Eystein Lonning, Stian Knappskog
Summary: With recent advances in the field of epigenetics, there is a growing focus on rare transmitted constitutional epimutations. The research team developed a method called ramr to identify aberrantly methylated DNA regions and confirmed its applicability for cancer risk analysis.
Article
Gastroenterology & Hepatology
Yurii Stepanov, Iuliia Golovynska, Nataliia Dziubenko, Halyna M. Kuznietsova, Nataliia Petriv, Inessa Skrypkina, Sergii Golovynskyi, Liudmyla Stepanova, Yevhenii Stohnii, Liudmyla Garmanchuk, Liudmyla Ostapchenko, Tetyana Yevsa, Junle Qu, Tymish Y. Ohulchanskyy
Summary: We have demonstrated the expression of NMDAR during the early stages of cancer, specifically HCC, in the cell transformation process. The aim of our study was to define the disease stages from precancerous liver disease to liver cancer progression when NMDAR subunits were expressed/detected. A fibrosis/HCC rat model, immunohistochemistry combined with epifluorescence microscopy imaging, and Western blotting were employed. The dynamics of appearance of NMDAR subunits, their expression, and methylation status during the development of HCC were shown and discussed.
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2022)
Article
Oncology
Andreas Venizelos, Hege Elvebakken, Aurel Perren, Oleksii Nikolaienko, Wei Deng, Inger Marie B. Lothe, Anne Couvelard, Geir Olav Hjortland, Anna Sundlov, Johanna Svensson, Harrish Garresori, Christian Kersten, Eva Hofsli, Sonke Detlefsen, Merete Krogh, Halfdan Sorbye, Stian Knappskog
Summary: High-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN) are a rare and understudied type of tumors, with a very poor prognosis. Molecular analysis of 181 HG GEP-NEN patients revealed unique genetic alterations and copy number changes in different subgroups of tumors, indicating potential personalized treatment options. Limited similarities were found with small-cell lung cancer (SCLC), suggesting the need for subtype-specific therapeutic approaches.
ENDOCRINE-RELATED CANCER
(2022)
Article
Biochemistry & Molecular Biology
Indre Valiulyte, Aiste Pranckeviciene, Adomas Bunevicius, Arimantas Tamasauskas, Hanna Svitina, Inessa Skrypkina, Paulina Vaitkiene
Summary: This study examines the potential of miR-181a as a biomarker for the diagnosis and prognosis of glioma patients. Lower expression of miR-181a is associated with higher tumor grade, IDH1 wild-type gliomas, and worse overall survival. Additionally, miR-181a levels are correlated with functional status and quality of life in glioma patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Per E. Lonning, Oleksii Nikolaienko, Kathy Pan, Allison W. Kurian, Hans P. Eikesdal, Mary Pettinger, Garnet L. Anderson, Ross L. Prentice, Rowan T. Chlebowski, Stian Knappskog
Summary: This study found a significant association between constitutional normal tissue BRCA1 promoter methylation and the risk of developing triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSOC).
Article
Biochemistry & Molecular Biology
Tetiana Bukreieva, Hanna Svitina, Viktoriia Nikulina, Alyona Vega, Oleksii Chybisov, Iuliia Shablii, Alina Ustymenko, Petro Nemtinov, Galyna Lobyntseva, Inessa Skrypkina, Volodymyr Shablii
Summary: This study investigated the effects of mesenchymal stem cell (MSC) transplantation on severe COVID-19 patients. The results showed that triple MSC transplantation was safe and did not cause severe adverse reactions. CT imaging revealed that MSC transplantation resulted in significantly lower fibrotic changes in the lung compared to conventional anti-viral treatment. Additionally, MSC therapy improved lymphocyte recovery and reduced inflammation markers in the peripheral blood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Oleksii Nikolaienko, Hans P. Eikesdal, Elisabet Ognedal, Bjornar Gilje, Steinar Lundgren, Egil S. Blix, Helge Espelid, Jurgen Geisler, Stephanie Geisler, Emiel A. M. Janssen, Synnove Yndestad, Laura Minsaas, Beryl Leirvaag, Reidun Lillestol, Stian Knappskog, Per E. Lonning
Summary: This study found that approximately 20% of TNBC and low-ER expression breast cancers may be caused by prenatal BRCA1 epimutations. The constitutional mosaic BRCA1 methylation likely arises through gender-related mechanisms in utero, independent of Mendelian inheritance.
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
