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Allelic reprogramming of chromatin states in human early embryos

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National Science Review 2024年第03期11卷 58-71页

作者： Shenli Yuan Lei Gao Wenrong Tao Jianhong Zhan Gang Lu Jingye Zhang Chuanxin Zhang Lizhi Yi Zhenbo Liu Zhenzhen Hou Min Dai Han Zhao Zi-Jiang Chen Jiang Liu Keliang Wu Center for reproductive Medicine Shandong University CAS Key Laboratory of Genome sciences and Information Collaborative Innovation Center of Genetics and Development Beijing Institute of Genomicsand China National Center for BioinformationChinese Academy of Sciences University of Chinese Academy of sciences CUHK-SDU Joint Laboratory on reproductive Genetics School of Biomedical Sciences the Chinese University of Hong Kong Key Laboratory of reproductive Endocrinology of the Ministry of Education Shandong University Center for reproductive Medicine Ren Ji Hospital School of Medicine Shanghai Jiao Tong University CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

The reprogramming of parental epigenomes in human early embryos remains elusive. To what extent the characteristics of parental epigenomes are conserved between humans and mice is currently unknown. Here,we mapped parental haploid epigenomes using human parthenogenetic and androgenetic embryos. Human embryos have a larger portion of genome with parentally specific epigenetic states than mouse *** allelic patterns of epigenetic states for orthologous regions are not conserved between humans and mice. Nevertheless, it is conserved that maternal DNA methylation and paternal H3K27me3 are associated with the repression of two alleles in humans and mice. In addition, for DNA-methylation-dependent imprinting, we report 19 novel imprinted genes and their associated germline differentially methylated regions. Unlike in mice, H3K27me3-dependent imprinting is not observed in human early ***, allele-specific epigenomic reprogramming is different in humans and mice.

关键词： human embryo epigenetics reprogramming DNA methylation H3K27me3 chromatin accessibility

GreenPhos,a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility

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Molecular Plant 2024年第1期17卷 199-213页

作者： Xiaoxiao Duan Yuanya Zhang Xiahe Huang Xiao Ma Hui Gao Yan Wang Zhen Xiao Chengcheng Huang Zhongshu Wang Bolong Li Wenqiang Yang Yingchun Wang State Key Laboratory of Molecular developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBejing 100101China University of Chinese Academy of sciences Bejing 100049China Key Laboratory of Photobiology Instute of BotanyChinese Academy of SciencesBejing 100093China

Protein phosphorylation regulates a variety of important cellular and physiological processes in ***-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal *** is largely due to the need to improve protein extraction efficiency from plant cells,which have a dense cell wall,and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry *** this end,we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis,rice,tomato,and Chlamydomonas reinhardtii,enabling in-depth identification with high quantitative reproducibility of about 11000 phosphosites,the greatest depth achieved so far with single liquid chromatography-mass spectrometry(LC-MS)runs operated in a data-dependent acquisition(DDA)*** mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time-and *** method,named GreenPhos,combined with single-shot LC-MS,enabled in-depth quantitative identification of Arabidopsis phosphoproteins,including differentially phosphorylated spliceosomal proteins,at multiple time points during salt stress and a number of kinase substrate *** is expected to serve as a universal method for purification of plant phosphopeptides,which,if samples are further fractionated and analyzed by multiple LC-MS runs,could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.

关键词： plant phosphoproteomics phosphopeptides LC–MS Arabidopsis salt stress

Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat

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Science China(Life sciences) 2024年第7期67卷 1479-1488页

作者： Congyang Yi Qian Liu Yuhong Huang Chang Liu Xianrui Guo Chaolan Fan Kaibiao Zhang Yang Liu Fangpu Han Institute of Genetics and developmental Biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China

Non-B-form DNA differs from the classic B-DNA double helix structure and plays a crucial regulatory role in replication and ***,the role of non-B-form DNA in centromeres,especially in polyploid wheat,remains ***,we systematically analyzed seven non-B-form DNA motif profiles(A-phased DNA repeat,direct repeat,G-quadruplex,inverted repeat,mirror repeat,short tandem repeat,and Z-DNA)in hexaploid *** found that three of these non-B-form DNA motifs were enriched at centromeric regions,especially at the CENH3-binding sites,suggesting that non-B-form DNA may create a favorable loading environment for the CENH3 *** investigate the dynamics of centromeric non-B form DNA during the alloploidization process,we analyzed DNA secondary structure using CENH3 ChIP-seq data from newly formed allotetraploid wheat and its two diploid *** found that newly formed allotetraploid wheat formed more non-B-form DNA in centromeric regions compared with their parents,suggesting that non-B-form DNA is related to the localization of the centromeric regions in newly formed ***,non-B-form DNA enriched in the centromeric regions was found to preferentially form on young LTR retrotransposons,explaining CENH3's tendency to bind to younger ***,our study describes the landscape of non-B-form DNA in the wheat genome,and sheds light on its potential role in the evolution of polyploid centromeres.

关键词： non-B-form DNA polyploid wheat centromere retrotransposon

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Modern phenomics to empower holistic crop science, agronomy, and breeding research

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Journal of Genetics and Genomics 2024年第8期51卷 790-800页

作者： Ni Jiang Xin-Guang Zhu Institute of Genetics and developmental Biology Chinese Academy of SciencesBeijing 100101China Center of Excellence for Molecular Plant sciences Chinese Academy of SciencesShanghai 200032China

Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional *** modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal *** multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop *** challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.

关键词： Crop phenomics High-throughput phenotyping Traits Crop designer breeding Agronomy

Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez Laura M.Jensen Raluca G.Mateescu Peter J.Hansen Department of Animal sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied Systems Biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef *** Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were *** In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations

关键词： Beef cattle Fertility GWAS QTL

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Emerging roles and therapeutic potentials of sphingolipids in pathophysiology:emphasis on fatty acyl heterogeneity

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Journal of Genetics and Genomics 2024年第3期51卷 268-278页

作者： Jinming Mu Sin Man Lam Guanghou Shui State Key Laboratory of Molecular developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100101China Lipidall Technologies Company Limited ChangzhouJiangsu 213000China

Sphingolipids not only exert structural roles in cellular membranes,but also act as signaling molecules in various physiological and pathological processes.A myriad of studies have shown that abnormal levels of sphingolipids and their metabolic enzymes are associated with a variety of human ***,blood sphingolipids can also be used as biomarkers for disease *** review summarizes the biosynthesis,metabolism,and pathological roles of sphingolipids,with emphasis on the biosynthesis of ceramide,the precursor for the biosynthesis of complex sphingolipids with different fatty acyl *** possibility of using sphingolipids for disease prediction,diagnosis,and treatment is also *** endogenous ceramides and complex sphingolipids along with their specific fatty acyl chain to promote future drug development will also be discussed.

关键词： Sphingolipids Ceramide Therapeutic targets Microdomain Biomarker

Pyruvate kinase M in germ cells is essential for sperm motility and male fertility but not spermatogenesis

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Asian Journal of Andrology 2024年第2期26卷 212-219页

作者： Gao-Qing Qian Xiao-Chen Wang Xi Zhang Bin Shen Qiang Liu State Key Laboratory of reproductive Medicine and Offspring Health Nanjing Medical UniversityNanjing 211166China Shanghai Key Laboratory of reproductive Medicine Department of HistoembryologyGenetics and Developmental BiologyShanghai Jiao Tong University School of MedicineShanghai 200025China State Key Laboratory of Molecular Biology Shanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai 200031China

Male germ cells employ specific metabolic pathways throughout their developmental *** a previous study,we discovered heightened expression of pyruvate kinase M(PKM),a pivotal glycolytic enzyme,in spermatogonia and *** gain deeper insights into PKM's roles in spermatogenesis,sperm function,and male fertility,we engineered a conditional-knockout mouse model(Pkm-vkO mice)to selectively disrupt the Pkm gene within germ *** maintaining regular testicular histology and sperm morphology,the male Pkm-vko mice were infertility,characterized by significant impairments in sperm motility and adenosine triphosphate(ATP)*** addition,Pkm-null spermatozoa exhibited similar deficits in protein tyrosine phosphorylation linked to capacitation,as well as compromised performance in in vitro fertilization *** conclude,PKM's presence is not obligatory for the entirety of spermatogenesis in male germ cells;however,it emerges as a critical factor influencing sperm motility and overall male fertility.

关键词： glycolysis male fertility pyruvate kinase M sperm motility spermatogenesis

Central cell:the key to determine persistent pollen tube attraction or termination

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Science China(Life sciences) 2024年第9期67卷 2030-2032页

作者： Jiang-Guo Meng Shi-Zhen Li Hong-Ju Li Center for developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation Integrative Science Center of Germplasm Creation Western China(Chongqing)Science CitySchool of Life SciencesSouthwest UniversityChongqing400715 China Key Laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Center for Molecular Agrobiology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Most eukaryotic species depend on sexual reproduction,characterized by fertilization,to produce a new *** process requires the transfer of sperm(male gamete),containing half of the genetic information,from the male to the egg cell(female gamete),which holds half of the maternal genome,within the female reproductive *** strategies have been evolved to ensure fertilization success in plants.

关键词： organs termination holds

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The transgenerational effects of maternal low-protein diet during lactation on offspring

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Journal of Genetics and Genomics 2024年第8期51卷 824-835页

作者： Lin-Jian Gu Li Li Qian-Nan Li Ke Xu Wei Yue Jing-Yi Qiao Tie-Gang Meng Ming-Zhe Dong Wen-Long Lei Jia-Ni Guo Zhen-Bo Wang Qing-Yuan Sun State Key Laboratory of Stem Cell and reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China Institute of Laboratory Animal sciences CAMS&PUMCBeijing 100021China Guangzhou Key Laboratory of Metabolic Diseases and reproductive Health Guangdong-Hong Kong Metabolism&Reproduction Joint LaboratoryReproductive Medicine CenterGuangdong Second Provincial General HospitalGuangzhouGuangdong 510317China

Environmental factors such as diet and lifestyle can influence the health of both mothers and ***,its transgenerational transmission and underlying mechanisms remain largely ***,using a maternal lactation-period low-protein diet(LPD)mouse model,we show that maternal LPD during lactation causes decreased survival and stunted growth,significantly reduces ovulation and litter size,and alters the gut microbiome in the female LPD-F1 *** transcriptome of LPD-F1 metaphase II(MII)oocytes shows that differentially expressed genes are enriched in female pregnancy and multiple metabolic ***,maternal LPD causes early stunted growth and impairs metabolic health,which is transmitted over two *** methylome alteration of LPD-F1 oocytes can be partly transmitted to the F2 ***,our results reveal that LPD during lactation transgenerationally affects offspring health,probably via oocyte epigenetic changes.

关键词： Lactationdiet Maternal low-proteindiet DNAmethylation Transgenerational effect Oocyte