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SnoRNP is essential for thermospermine-mediated development in Arabidopsis thaliana

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Science China(Life Sciences) 2023年第1期66卷 2-11页

作者： Xilong Li Zongyun Yan Meiling Zhang Jiayin Wang Peiyong xin Shujing Cheng Liquan Kou Xiaoting Zhang Songlin Wu Jinfang Chu chengqi Yi Keqiong Ye Bing Wang Jiayang Li State Key Laboratory of Plant Genomics and National Center for Plant Gene Research(Beijing) Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China Key Laboratory of RNA Biology CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100039China Hainan Yazhou Bay Seed Laboratory Sanya 572025China

Polyamines have been discovered for hundreds of years and once considered as a class of phytohormones.Polyamines play critical roles in a range of developmental processes.However,the molecular mechanisms of polyamine signaling pathways remain poorly understood.Here,we measured the contents of main types of polyamines,and found that endogenous level of thermospermine(T-Spm)in Arabidopsis thaliana is comparable to those of classic phytohormones and is significantly lower than those of putrescine(Put),spermidine(Spd),and spermine(Spm).We further found a nodule-like structure around the junction area connecting the shoot and root of the T-Spm biosynthetic mutant acl5 and obtained more than 50 suppressors of acl5 nodule structure(san)through suppressor screening.An in-depth study of two san suppressors revealed that NAP57 and NOP56,core components of box H/ACA and C/D snoRNPs,were essential for T-Spm-mediated nodule-like structure formation and plant height.Furthermore,analyses of rRNA modifications showed that the overall levels of pseudouridylation and 2′-O-methylation were compromised in san1 and san2 respectively.Taken together,these results establish a strong genetic relationship between rRNA modification and T-Spm-mediated growth and development,which was previously undiscovered in all organisms.

关键词： polyamines thermospermine snoRNP pseudouridylation 2’-O-methylation Arabidopsis thaliana

Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans

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Genomics, Proteomics & Bioinformatics 2010年第2期8卷 92-102页

作者： Kaifu Chen Lei Wang Meng Yang Jiucheng Liu chengqi xin Songnian Hu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China.

Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine （AG） gradient from the 5＇-end to the 3＂-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model （HMM） algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures.

关键词： nucleosome positioning sequence signature periodicity HMM

面向可靠性设计的发动机材料超高周疲劳强度估计方法

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航空动力学报 2022年第8期37卷 1761-1770页

作者：陈新何玉怀许巍孙成奇中国航空发动机集团有限公司北京航空材料研究院北京100095 中国航空发动机集团有限公司北京航空材料研究院航空材料检测与评价北京市重点实验室北京100095 中国科学院力学研究所非线性力学国家重点实验室北京100190

提出了一种面向可靠性设计的四参数随机疲劳极限模型,可针对小样本数据实现超高周疲劳(VHCF)应力-寿命(S-N)曲线处理。通过对航空用钛合金常规样本数超高周疲劳数据的拟合分析和对比验证了模型的准确性。同时,以某型航空发动机压气机叶... 详细信息

提出了一种面向可靠性设计的四参数随机疲劳极限模型,可针对小样本数据实现超高周疲劳(VHCF)应力-寿命(S-N)曲线处理。通过对航空用钛合金常规样本数超高周疲劳数据的拟合分析和对比验证了模型的准确性。同时,以某型航空发动机压气机叶片用TC17钛合金为研究对象,分别对室温(RT)和400℃小样本超高周疲劳数据进行了处理,得到了典型置信度和可靠度条件下的超高周疲劳强度估计值。结果表明:本文提出的四参数随机疲劳极限模型,能够通过少量的长寿命区试验数据获得材料超高周范围内发动机设计所需的疲劳强度估计值;相较于常用的升降法,基于本模型进行试验安排可大幅降低68%的试验量,为发动机材料的超高周疲劳强度评价提供方法支持。

关键词：超高周疲劳(VHCF) 随机疲劳极限(RFL)模型概率-应力-寿命(P-S-N)曲线疲劳数据处理钛合金

Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development

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Genomics, Proteomics & Bioinformatics 2014年第3期12卷 111-119页

作者： Wei Xu chengqi xin Qiang Lin Feng Ding Wei Gong Yuanyuan Zhou Jun Yu Peng Cui Songnian Hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Postnatal cerebral development is a complicated biological process precisely controlled by multiple genes. To understand the molecular mechanism of cerebral development, we compared dynamics of mouse cerebrum transcriptome through three developmental stages using high-throughput RNA-seq technique. Three libraries were generated from the mouse cerebrum at infancy, adolescence and adulthood, respectively. Consequently, 44,557,729 （infancy）, 59,257,530 （adolescence） and 72,729,636 （adulthood） reads were produced, which were assembled into 15,344, 16,048 and 15,775 genes, respectively. We found that the overall gene expression level increased from infancy to adolescence and decreased later on upon reaching adulthood. The adolescence cerebrum has the most active gene expression, with expression of a large number of reg- ulatory genes up-regulated and some crucial pathways activated. Transcription factor （TF） analysis suggested the similar dynamics as expression profiling, especially those TFs functioning in neurogenesis differentiation, oligodendrocyte lineage determination and circadian rhythm regulation. Moreover, our data revealed a drastic increase in myelin basic protein （MBP）-coding gene expression in adolescence and adulthood, suggesting that the brain myelin may be generated since

关键词： Cerebrum Postnatal development Gene expression Transcriptome High-throughput sequencing

High-temperature failure mechanism and defect sensitivity of TC17 titanium alloy in high cycle fatigue

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Journal of Materials Science & Technology 2022年第27期122卷 128-140页

作者： Gen Li chengqi Sun State Key Laboratory of Nonlinear Mechanics Institute of MechanicsChinese Academy of Sciences School of Engineering Science University of Chinese Academy of Sciences

Crack initiation is an essential stage of fatigue process due to its direct effect on fatigue failure.However,for titanium alloys in high-temperature high cycle fatigue(HCF),the crack initiation mechanisms remain unclear and the understanding for the defect sensitivity is also lacking.In this study,a series of fatigue tests and multi-scale microstructure characterizations were conducted to explore the high-temperature failure mechanism,and the coupled effect of temperature and defect on TC17 titanium alloy in HCF.It was found that an oxygen-rich layer(ORL)was produced at specimen surface at elevated temperatures,and brittle fracture of ORL at surface played a critical role for surface crack initiation in HCF.Besides,internal crack initiation with nanograins at high temperatures was a novel finding for the titanium alloy.Based on energy dispersive spectroscopy,electron backscatter diffraction and transmission electron microscope characterizations,the competition between surface and internal crack initiations at high temperatures was related to ORL at surface and dislocation resistance in inner microstructure.The fatigue strengths of smooth specimens decreased at elevated temperatures due to the lower dislocation resistance.While the fatigue strengths of the specimens with defect were not very sensitive to the temperatures.Finally,a fatigue strength model considering the coupled effect of temperature and defect was proposed for TC17titanium alloy.

关键词： TC17 titanium alloy High temperature Defect High cycle fatigue Oxygen-rich layer Rough area

Mechanical and Biotribological Properties of PVA/SB Triple-Network Hydrogel for Biomimetic Artificial Cartilage

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Journal of Bionic Engineering 2023年第3期20卷 1072-1082页

作者： Lingling Cui Junyue Chen chengqi Yan Dangsheng Xiong School of Materials Science and Engineering Nanjing University of Science and TechnologyNanjing210094China

Poly (vinyl alcohol) hydrogel has been perceived as a promising replacement for articular cartilage due to its superior water-absorption ability and excellent biocompatibility, but its mechanical properties are still insufficient. In this study, the poly (vinyl alcohol)/sodium tetraborate triple-network (PVA/SB TN) hydrogel was developed by repeated freeze–thaw method. Scanning electron microscopy images demonstrated that the structure of as-prepared hydrogels was three-dimensional porous network structure similar to that of natural articular cartilage. Compared to the pure PVA hydrogel, the mechanical performance of the PVA/SB TN hydrogels were improved by 116% and 461% in tensile and compressive strengths, respectively. This was mainly because that the complexation reaction between the PVA and SB strengthened the stability of the hydrogel network. Notably, the biotribological performance of PVA hydrogel has also been improved significantly. Even at high load, the friction coefficient of the PVA/SB TN hydrogel was both very low in calf serum or deionized water. This PVA/SB TN hydrogel with good mechanical property and low friction has high application potential in cartilage repair.

关键词： Bionic PVA/SB TN hydrogel Three-dimensional porous network Mechanical performance Biotribological properties

The Association Between H3K4me3 and Antisense Transcription

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Genomics, Proteomics & Bioinformatics 2012年第2期10卷 74-81页

作者： Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Feng Ding chengqi xin Jianing Geng Shuhui Song Fanglin Sun Songnian Hu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100029China Institute of Epigenetics and Cancer Research School of MedicineTsinghua UniversityBeijing 100080China Graduate University of Chinese Academy of Sciences Beijing 100049China

Histone H3 lysine 4 trimethylation （H3K4me3） is well known to occur in the promoter region of genes for transcription activation. How- ever, when investigating the H3K4me3 profiles in the mouse cerebrum and testis, we discovered that H3K4me3 also has a significant enrichment at the 3＇ end of actively transcribed （sense） genes, named as 3＇-H3K4me3. 3＇-H3K4me3 is associated with ~15% of pro- tein-coding genes in both tissues. In addition, we examined the transcriptional initiation signals including RNA polymerase II （RNAPII） binding sites and Y-CAGE-tag that marks transcriptional start sites. Interestingly, we found that 3＇-H3K4me3 is associated with the ini- tiation of antisense transcription. Furthermore, 3＇-H3K4me3 modification levels correlate positively with the antisense expression levels of the associated sense genes, implying that 3＇-H3K4me3 is involved in the activation of antisense transcription. Taken together, our findings suggest that H3K4me3 may be involved in the regulation of antisense transcription that initiates from the 3＇ end of sense genes. In addition, a positive correlation was also observed between the expression of antisense and the associated sense genes with 3＇-H3K4me3 modification. More importantly, we observed the 3＇-H3K4me3 enrichment among genes in human, fruitfly and Arabidopsis, and found that the sequences of 3＇-H3K4me3-marked regions are highly conserved and essentially indistinguishable from known promoters in ver- tebrate. Therefore, we speculate that these 3＇-H3K4me3-marked regions may serve as potential promoters for antisense transcription and 3＇-H3K4me3 appear to be a universal epigenetic feature in eukaryotes. Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription.

关键词： Antisense initiation and activation Antisense transcription H3K4me3

Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis

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Genomics, Proteomics & Bioinformatics 2012年第2期10卷 82-93页

作者： Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Daoyong Zhang Feng Ding chengqi xin Zhang Zhang Shuhui Song Fanglin Sun Jun Yu Songnian Hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100029China Institute of Epigenetics and Cancer Research School of MedicineTsinghua UniversityBeijing 100080China Computational Bioscience Research Center 4700 King Abdullah University of Science and TechnologyThuwa123955-6900Kingdom of Saudi Arabia Graduate University of Chinese Academy of Sciences Beijing 100049China

The global features of H3K4 and H3K27 trimethylations （H3K4me3 and H3K27me3） have been well studied in recent years, but most of these studies were performed in mammalian cell lines. In this work, we generated the genorne-wide maps of H3K4me3 and H3K27me3 of mouse cerebrum and testis using ChlP-seq and their high-coverage transcriptomes using ribominus RNA-seq with SOLID technology. We examined the global patterns of H3K4me3 and H3K27me3 in both tissues and found that modifications are closely-associated with tissue-specific expression, function and development. Moreover, we revealed that H3K4me3 and H3K27me3 rarely occur in silent genes, which contradicts the findings in previous studies. Finally, we observed that bivalent domains, with both H3K4me3 and H3K27me3, existed ubiquitously in both tissues and demonstrated an invariable preference for the regulation of developmentally-related genes. How- ever, the bivalent domains tend towards a ＂winner-takes-all＂ approach to regulate the expression of associated genes. We also verified the above results in mouse ES cells. As expected, the results in ES cells are consistent with those in cerebrum and testis. In conclusion, we present two very important findings. One is that H3K4me3 and H3K27me3 rarely occur in silent genes. The other is that bivalent domains may adopt a ＂winner-takes-all＂ principle to regulate gene expression.

关键词： H3K4me3 H3K27me3 Mouse

Phase separation,transcriptional elongation control,and human diseases

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Journal of Molecular Cell Biology 2021年第4期13卷 314-318页

作者： Chenghao Guo Zhuojuan Luo chengqi Lin School of Life Science and Technology Key Laboratory of Developmental Genes and Human DiseaseSoutheast UniversityNanjing 210096China Co-innovation Center of Neuroregeneration Nantong UniversityNantong 226019China

Precise regulation of gene transcription is of great importance to development and diseases.Promoter-proximal transcriptional pause is a key and general mechanism to precisely control transcription in metazoans.Subsequent to transcription initiation and synthesis of a short RNA,RNA polymerase Ⅱ(Pol Ⅱ)usually pauses at the promoter-proximal regions,standing by for further signals to be released into the productive elongation stage.Fine regulation of Pol Ⅱ pausing and release is achieved by the concerted action of many negative and positive elongation factors,including the super elongation complex(SEC).Recent studies suggested that phase-separated assemblies of transcription regulatory complexes could provide a general biophysical basis for the dynamic regulation of transcription in response to various cellular needs,though direct evidence at endogenous level in living cells is still largely lacking.Here,we summarize and discuss latest advances in understanding how phase separation contributes to RNA polymerase ll-mediated transcription,with a focus on transcriptional pause and release.

关键词： separation release elongation