Review
Plant Sciences
Yu Ding, Jiannan Zhu, Dongsheng Zhao, Qiaoquan Liu, Qingqing Yang, Tao Zhang
Summary: Rice grain quality is a complex trait influenced by various factors, making it a major target for breeding. Genome editing technologies offer new possibilities for improving rice quality by modifying CREs to fine-tune gene expression levels. While CREs hold promise for enhancing grain quality, challenges and experimental considerations must be taken into account.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Carly Weiss, Lana Harshman, Fumitaka Inoue, Hunter B. Fraser, Dmitri A. Petrov, Nadav Ahituv, David Gokhman
Summary: The study utilized massively parallel reporter assays to investigate the regulatory effects of modern human-specific variants, revealing that a portion of these variants drove differential gene expression between human populations, particularly in genes related to vocal tract and brain anatomy and function.
Article
Plant Sciences
Naoto Sano, Imen Lounifi, Gwendal Cueff, Boris Collet, Gilles Clement, Sandrine Balzergue, Stephanie Huguet, Benoit Valot, Marc Galland, Loic Rajjou
Summary: This study examines the genetic pathways and metabolic changes in the embryo and endosperm of rice seeds during germination using a multi-omics approach. The results show that the early phase of germination is a crucial turning point, and the endosperm and embryo exhibit distinct changes at the protein and metabolite levels. The study also highlights the importance of hormonal metabolism and energy supply-related proteins in rice seed germination.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Hiroki Nagata, Akemi Ono, Kaoru Tonosaki, Taiji Kawakatsu, Yutaka Sato, Kentaro Yano, Yuji Kishima, Tetsu Kinoshita
Summary: DNA methylation is necessary for maintaining genome integrity, but under certain circumstances, transposable elements (TEs) can escape from this repression and reactivate transcription. This study investigated the expression patterns of TE transcripts during rice endosperm development and found dynamic regulation of TE activity, particularly for miniature inverted-repeat TEs (MITEs).
Article
Plant Sciences
Zhenjun Li, Jianjie Gao, Bo Wang, Jing Xu, Xiaoyan Fu, Hongjuan Han, Lijuan Wang, Wenhui Zhang, Yongdong Deng, Yu Wang, Zehao Gong, Yongsheng Tian, Rihe Peng, Quanhong Yao
Summary: By overexpressing the rice GLK1 gene and other carotenogenic genes, a mini carotenoid biosynthetic pathway was established in rice endosperm, leading to increased carotenoid production and grain yield, but decreased grain quality.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Long Zhang, Yanzhou Qi, Mingming Wu, Lei Zhao, Zhichao Zhao, Cailin Lei, Yuanyuan Hao, Xiaowen Yu, Yinglun Sun, Xin Zhang, Xiuping Guo, Yulong Ren, Jianmin Wan
Summary: This study identified the P-type PPR protein PPR5 in rice as crucial for mitochondrial function and endosperm development, by controlling the cis-splicing of mitochondrial nad4 intron 3. Loss of PPR5 function resulted in decreased ATP production, upregulation of alternative oxidases expression, and abnormal mitochondrial morphology, impacting starch and protein content in the endosperm.
Article
Plant Sciences
Han Zhou, Xing Wang Deng, Hang He
Summary: In this study, a transcriptomics atlas of rice caryopses at the early developmental stage was successfully constructed using single-nucleus RNA sequencing. Novel specific marker genes were identified for each nuclear cluster in the rice caryopsis, and the differentiation trajectory of endosperm subclusters was revealed. Transcriptional divergence was observed in different endosperm clusters among the three rice samples. This research provides valuable resources for understanding the molecular mechanism underlying caryopsis development in rice and other monocots.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Tsutomu Ishimaru, Sabiha Parween, Yuhi Saito, Takehiro Masumura, Motohiko Kondo, Nese Sreenivasulu
Summary: This study identified tissue- and stage-specific gene co-regulons in the developing rice endosperm, demonstrating their role in modulating programmed cell death and desiccation tolerance mechanisms. The spatial distribution of starch accumulation in the endosperm is regulated by specific transcription factors and hormone-regulated genes. These findings provide insights into the molecular physiological mechanisms of endosperm development.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiaojian Peng, Wei Yu, Yirong Chen, Yingli Jiang, Yaru Ji, Long Chen, Beijiu Cheng, Jiandong Wu
Summary: In this study, a novel starch regulatory gene, ZmCBM48-1, was identified, which was found to play a positive regulatory role in the starch synthesis pathway by up-regulating several starch synthesis-related genes. Furthermore, its overexpression in rice led to changes in the endosperm cell shape and starch structure of transgenic seeds.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Baixiao Niu, Zhenyu Zhang, Juan Zhang, Yong Zhou, Chen Chen
Summary: OsNF-YB9 and OsNF-YB7 in rice exhibit sub-functionalization in seed development, with OsNF-YB9 implicated in abnormal seed development and OsNF-YB7 defects causing lethality. OsNF-YB9 plays a critical role in rice seed development.
Article
Plant Sciences
Jiawen Chen, Alexander Watson-Lazowski, Nitin Uttam Kamble, Martin Vickers, David Seung
Summary: This study generated a high-quality transcriptomics dataset to study endosperm development in the Kronos variety. It revealed key processes such as starch metabolism and provided valuable insights into this important crop species.
Article
Biotechnology & Applied Microbiology
Aniko Meijer, Tim De Meyer, Klaas Vandepoele, Tina Kyndt
Summary: By investigating the expression of sRNAs in different stages of rice development, this study identified many potential regulators of rice yield and quality, highlighting their importance in optimizing rice production.
Article
Biochemistry & Molecular Biology
Me-Sun Kim, Kwon-Kyoo Kang, Yong-Gu Cho
Summary: This study identified the characteristics of 77 OsPUB genes in rice and conducted a systematic and comprehensive analysis including conserved domains, phylogenetic relationships, and gene structure. 16 OsPUB genes showed similar expression patterns in drought stress and blast infection, with numerous cis-acting elements in their promoter sequences suggesting involvement in complex regulatory networks. The results indicate that OsPUB genes have various functions in the responses of rice to abiotic and biotic stresses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Daoheng Hu, Yiming Yu, Chun Wang, Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong, Lei Gong, Kejian Wang, Jixian Zhai
Summary: This study utilized CRISPR-Cas9 technology to edit all nine DNA methyltransferases in rice, revealing the significant roles of certain methyltransferases in maintaining non-CG methylation in rice.
Article
Multidisciplinary Sciences
Ronak Lakhia, Harini Ramalingam, Chun-Mien Chang, Patricia Cobo-Stark, Laurence Biggers, Andrea Flaten, Jesus Alvarez, Tania Valencia, Darren P. Wallace, Edmund C. Lee, Vishal Patel
Summary: This study demonstrates that removing the miR-17 binding element can enhance the expression of PKD1 and PKD2 genes, thereby alleviating the symptoms of autosomal dominant polycystic kidney disease and improving cellular function and mitochondrial membrane potential.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xin Wang, Wei Zhou, Zhanhua Lu, Yidan Ouyang, Chol O. Su, Jialing Yao
Article
Biotechnology & Applied Microbiology
Wei Zhou, Xin Wang, Dan Zhou, Yidan Ouyang, Jialing Yao
PLANT BIOTECHNOLOGY JOURNAL
(2017)
Article
Plant Sciences
Xiaolong Huang, Zhanhua Lu, Xin Wang, Yidan Ouyang, Wei Chen, Koulong Xie, Dongying Wang, Min Luo, Jie Luo, Jialing Yao
Article
Biochemistry & Molecular Biology
Shuzhao Jia, Yufei Xiong, Peipei Xiao, Xin Wang, Jialing Yao
Article
Biochemistry & Molecular Biology
Xin Wang, Huan Zhang, Lu-Yuan Shao, Xin Yan, Hui Peng, Jie-Xiu Ouyang, Shao-Bo Li
Article
Biochemistry & Molecular Biology
Peng-Fei Liao, Jie-Xiu Ouyang, Jian-Jun Zhang, Lan Yang, Xin Wang, Xiao-Jue Peng, Dong Wang, You-Lin Zhu, Shao-Bo Li
PLANT MOLECULAR BIOLOGY
(2019)
Article
Genetics & Heredity
Xin Wang, Jie Chen, Changai Liu, Junling Luo, Xin Yan, Aihua Ai, Yaohui Cai, Hongwei Xie, Xia Ding, Xiaojue Peng
Article
Biochemistry & Molecular Biology
Xin Wang, Chao Yu, Yi Liu, Lu Yang, Yang Li, Wen Yao, Yicong Cai, Xin Yan, Shaobo Li, Yaohui Cai, Shaoqing Li, Xiaojue Peng
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Agriculture, Multidisciplinary
Xin Wang, Xin Yan, Xiaoxiao Tian, Zongfei Zhang, Weiwei Wu, Junjun Shang, Jiexiu Ouyang, Wen Yao, Shaobo Li
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Xiaojing Liu, Xin Wang, Xin Yan, Shaobo Li, Hui Peng
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Plant Sciences
Kun Liu, Xin Wang, Hengchen Liu, Jiarui Wu, Feng Liang, Shaobo Li, Jianjun Zhang, Xinxiang Peng
Summary: The OsAT1 gene plays an important role in rice yield and starch accumulation. Knocking down the OsAT1 gene can increase rice yield and weight, while reducing copper accumulation. These findings provide valuable insights for rice breeding programs.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Agriculture, Multidisciplinary
Zongfei Zhang, Jiaxin Tan, Yuting Chen, Zhangyuqi Sun, Xin Yan, Jiexiu Ouyang, Shaobo Li, Xin Wang
Summary: A new fructokinase, OsFRK3, was identified and its knockou mutants, osfrk3-1 and osfrk3-2, were created using CRISPR/Cas9 technology. The mutants showed decreased 1000-grain weight, grain width, grain thickness, endosperm filling rate, and seed total starch content, while the levels of sucrose and fructose were increased. The expression levels of OsGBSS1, OsBEIIb, OsPFP1 beta, and OsAGPL1 were significantly decreased in the mutants. These results suggest that OsFRK3 positively regulates starch accumulation by influencing sugar metabolism.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Plant Sciences
Huihui Wang, Jiexiu Ouyang, Wenjia Jian, Meng Li, Jiancong Zhong, Xin Yan, Jiadong Gao, Xin Wang, Shaobo Li
Summary: miR5504 is involved in the regulation of plant height by affecting cell expansion and division in rice.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Biochemistry & Molecular Biology
Xin Wang, Zongfei Zhang, Wei Peng, Jinqiu Huang, Xin Yan, Wen Yao, Jiexiu Ouyang, Shaobo Li
Summary: The functions of OsIPCSs were analyzed by CRISPR/Cas9 technology, lipidomics analysis, and transcriptomics analysis. Single-gene mutation resulted in dwarf phenotype, with osipcs3 mutant showing more severe phenotype. Multi-gene mutation led to more severe phenotypes, indicating the additive effects of OsIPCSs. A significant decrease in epidermal cell elongation and content of IPC was observed in the mutants. The results of RNA-seq showed numerous DEGs associated with cellular component organization, anatomical structure morphogenesis, and cell growth. Overall, OsIPCSs may regulate plant height through affecting cell growth and sphingolipid metabolism in rice.
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.
