Article
Biotechnology & Applied Microbiology
Tianning Chen, Kailun Huo, Dece Kong, Shan Su, Tieyi Yang, Weiwei Zhang, Jin Shao
Summary: By studying peripheral blood samples from early postmenopausal women, we identified key lncRNAs that are associated with the progression of postmenopausal osteoporosis. One of the candidates, MIR22HG, was found to potentially serve as a miRNA precursor and regulate the FoxO signaling pathway in bone metabolism. These findings are of great significance for predicting and diagnosing early postmenopausal osteoporosis (PMOP).
Article
Medicine, Research & Experimental
Yanan Jiang, Xiuyun Shen, Chaorun Dong, Fengnan Zhi, Yang Gao, Chunpeng Shi, Yuqiu Chao, Jincheng Xu, Desi Shang, Juan Xu, Baofeng Yang, Xia Li, Yunlong Bai
Summary: This study investigates the cardiotoxicity induced by arsenic trioxide (ATO) through whole transcriptome analysis. The results show that ATO alters the coding and noncoding RNA profiles in mouse myocardium and constructs an ATO-related lncRNA-circRNA co-regulation network. Genes in this network may play important roles in ATO-induced cardiotoxicity.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
Chih-Chieh Chen, Yung-Che Chou, Chia-Yi Hsu, Eing-Mei Tsai, Tze-Kiong Er
Summary: In this study, RNA sequencing analysis was used to identify a potential pathogenic gene of endometriosis. The differentially expressed genes were found to be enriched in several signaling pathways, providing new insights into the underlying mechanisms of endometriosis.
Article
Microbiology
Lorena Azevedo de Lima, Kristina Reinmets, Lars Keld Nielsen, Esteban Marcellin, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: RNA sequencing (RNA-seq) is a widely used technique for transcriptome analysis, but the choice of library preparation kits can significantly impact the results. Different commercial products show significant differences in rRNA removal, strand specificity, and transcript abundance distribution. Selecting appropriate sample processing workflows and products is crucial for RNA-seq studies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Cindy Karouta, Robert Kucharski, Kristine Hardy, Kate Thomson, Ryszard Maleszka, Ian Morgan, Regan Ashby
Summary: Research on inhibiting myopia in animals has shown significant overlap in retinal molecular changes, with transcription factors playing a key role in growth regulation. These findings suggest that a defined set of transcriptome changes in the retina is crucial for regulating eye growth.
Article
Biotechnology & Applied Microbiology
Chenxi Zhang, Ying Zhou, Bin Zhang, Zhihong Sheng, Nan Sun, Baiyin Yuan, Xiaoyuan Wu
Summary: In this study, the expression profiles of lncRNAs, miRNAs, and mRNAs in SCLC tumors and adjacent non-cancerous tissues were comprehensively analyzed. A ceRNA network consisting of 9 lncRNAs, 11 miRNAs, and 392 mRNAs was constructed through bioinformatics analysis. The study also identified the potential role of lncRNA TCONS_00020615 in regulating SCLC tumorigenesis through the TCONS_00020615-hsa-miR-26b-5p-TPD52 pathway.
Article
Multidisciplinary Sciences
Balazs Gocz, Eva Rumpler, Miklos Sarvari, Katalin Skrapits, Szabolcs Takacs, Imre Farkas, Veronika Csillag, Sarolta H. Trinh, Zsuzsanna Bardoczi, Yvette Ruska, Norbert Solymosi, Szilard Poliska, Zsuzsanna Szoke, Lucia Bartoloni, Yassine Zouaghi, Andrea Messina, Nelly Pitteloud, Ross C. Anderson, Robert P. Millar, Richard Quinton, Stephen M. Manchishi, William H. Colledge, Erik Hrabovszky
Summary: This study provides a comprehensive characterization of the estrogen-dependent kisspeptin neuron transcriptome and sheds light on the molecular mechanisms of ovary-brain communication, which is important for genetic research on human fertility disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Luciana W. Zuccherato, Christina M. T. Machado, Wagner C. S. Magalhaes, Patricia R. Martins, Larissa S. Campos, Leticia C. Braga, Andrea Teixeira-Carvalho, Olindo A. Martins-Filho, Telma M. R. F. Franco, Salua O. C. Paula, Israel Tojal da Silva, Rodrigo Drummond, Kenneth J. Gollob, Paulo Guilherme O. Salles
Summary: This study identified differential gene expression signatures in cervical cancer stem-like cells as potential biomarkers for intrinsic chemoradioresistance in cervical cancer. Analysis of 31 patients with locally advanced cervical cancer revealed 1050 differentially expressed genes, with implications for cancer recurrence and treatment outcome. Genes overlapping between the highest AUC and pAUC loci revealed potential biomarkers with strong capacity for identifying non-responders versus responders to chemoradiotherapy.
FRONTIERS IN ONCOLOGY
(2021)
Article
Genetics & Heredity
Yuanyuan Jiang, Yicun Liu, Yongshun Gao, Jiangrong Peng, Wenbing Su, Yuan Yuan, Xianghui Yang, Chongbin Zhao, Man Wang, Shunquan Lin, Ze Peng, Fangfang Xie
Summary: Flowering is essential for plant survival and crop production. Exogenous GA(3) application on loquat plants resulted in vigorous vegetative growth rather than floral bud formation. RNA-seq analysis identified several candidate genes involved in the regulation of loquat flowering.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Weixian Zhou, Libin Zhang, Jianjie He, Wang Chen, Feifan Zhao, Chunhua Fu, Maoteng Li
Summary: Interspecific crosses between Brassica rapa and B. napus result in transcriptome shock in the developing seeds, leading to overall changes in gene expression patterns. The hybrids show expression bias towards B. rapa and significant changes in key transcription factors, which may be responsible for phenotype change.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Yangbo Xi, Dongping Chen, Zhihui Dong, Hingcheung Lam, Jiading He, Keyi Du, Can Chen, Jun Guo, Jianmin Xiao
Summary: This study profiled the expression signature of specific lncRNAs and mRNAs in DCM and constructed a regulatory network involving lncRNAs. The study also identified potential prognostic biomarkers, providing new insights into the pathogenesis of DCM.
FRONTIERS IN GENETICS
(2022)
Article
Environmental Sciences
Qingping Liu, Wentao Hu, Yaling Zhang, Jie Ning, Yaxian Pang, Huaifang Hu, Meiyu Chen, Mengqi Wu, Mengruo Wang, Peihao Yang, Lei Bao, Yujie Niu, Rong Zhang
Summary: This study investigated the role of lncRNA in depressive-like responses induced by exposure to 25 nm polystyrene nanoplastics. Mice exposed to chronic PS NPs developed dose-dependent depressive-like responses. RNA sequencing revealed significant differences in 987 mRNAs, 29 miRNAs, and 116 lncRNAs between the exposed and control groups. A ceRNA network was constructed, suggesting that PS NPs may contribute to depression-like responses through activation of axon guidance, neurotrophin signaling pathways, and dopaminergic synapses.
Article
Multidisciplinary Sciences
Thira Faruangsaeng, Sermporn Thaweesapphitak, Chompak Khamwachirapitak, Thantrira Porntaveetus, Vorasuk Shotelersuk
Summary: The molecular control of tooth development differs between the maxilla and mandible, with PITX1 gene expression significantly higher in mandibular posterior teeth compared to maxillary posterior teeth. These differences should be considered in molecular studies of dental pulp stem cells and may contribute to more precise treatments in regenerative dentistry.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Qiushuo Song, Madhumita Joshi, Shichen Wang, Charles D. Johnson, Vijay Joshi
Summary: This study investigated transcriptional changes in the roots of drought-tolerant and drought-sensitive sesame genotypes under osmotic stress induced by Polyethylene glycol (PEG), revealing contrasting reactions between the two genotypes. Gene ontology and transcription-factor enrichment analysis showed significant differences in genes related to catalytic activity and transferase activity among different genotypes.
JOURNAL OF PLANT GROWTH REGULATION
(2021)
Article
Medicine, Research & Experimental
Jizhang Bao, Xinhua Zhao, Jiahui Lu, Zhaoyang Hu, Minghui Hu, Xiaoxia Hu, Libing Wang, Qi Hu, Weiling Sun, Jie Wang, Hailin Chen, Hao Lu, Changgui Li, Jing Xu, Yongming Zhou, Wenwei Zhu
Summary: AML is the most common acute leukemia in adults, with a median age of 68 in clinical diagnosis. This study analyzed transcriptome profiles in platelets of AML patients of different ages, finding differential gene expression between elderly and young patients. Genes related to protein processing in the endoplasmic reticulum and immunity were down-regulated in elderly patients, suggesting potential biomarker ATF4 for individualized chemotherapy strategies.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
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.