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Oocyte-associated transcription factors in reprogramming after somatic cell nuclear transfer: a review

Fengxia YIN,Hui LIU,Shorgan BOU,Guangpeng LI

《农业科学与工程前沿（英文）》 2014年 第1卷 第2期   页码 104-113 doi: 10.15302/J-FASE-2014003

摘要： Oocytes are unique cells with the inherent capability to reprogram nuclei. The reprogramming of the somatic nucleus from its original cellular state to a totipotent state is essential for term development after somatic cell nuclear transfer. The nuclear-associated factors contained within oocytes are critical for normal fertilization by sperm or for somatic cell nuclear reprogramming. The chromatin of somatic nuclei can be reprogrammed by factors in the egg cytoplasm whose natural function is to reprogram sperm chromatin. The oocyte first obtains its reprogramming capability in the early fetal follicle, and then its capacity is enriched in the late growth phase and reaches its highest capability for reprogramming as fully-grown germinal vesicle oocytes. The cytoplasmic milieu most likely contains all of the specific transcription and/or reprogramming factors necessary for cellular reprogramming. Certain transcription factors in the cytoplast may be critical as has been demonstrated for induced pluripotent stem cells. The maternal pronucleus exerts a predominant, transcription-dependent effect on embryo cytofragmentation, with a lesser effect imposed by the ooplasm and the paternal pronucleus. With deep analysis of transcriptomics in oocytes and early developmental stage embryos more maternal transcription factors inducing cellular reprogramming will be identified.

关键词： nuclear reprogramming     somatic cell     transcription factors     transcriptomics    

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Role of the forkhead transcription factor FOXO-FOXM1 axis in cancer and drug resistance

null

《医学前沿（英文）》 2012年 第6卷 第4期   页码 376-380 doi: 10.1007/s11684-012-0228-0

摘要：

The forkhead transcription factors FOXO and FOXM1 have pivotal roles in tumorigenesis and in mediating chemotherapy sensitivity and resistance. Recent research shows that the forkhead transcription factor FOXM1 is a direct transcriptional target repressed by the forkhead protein FOXO3a, a vital downstream effector of the PI3K-AKT-FOXO signaling pathway. Intriguingly, FOXM1 and FOXO3a also compete for binding to the same gene targets, which have a role in chemotherapeutic drug action and sensitivity. An understanding of the role and regulation of the FOXO-FOXM1 axis will impact directly on our knowledge of chemotherapeutic drug action and resistance in patients, and provide new insights into the design of novel therapeutic strategy and reliable biomarkers for prediction of drug sensitivity.

关键词： FOXO3a     FOXM1     transcription factor     cancer     drug resistance     tumorigenesis    

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The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis

null

《医学前沿（英文）》 2018年 第12卷 第4期   页码 412-425 doi: 10.1007/s11684-018-0650-z

摘要：

Transcription factor networks have evolved in order to control, coordinate, and separate, the functions of distinct network modules spatially and temporally. In this review we focus on the MYC network (also known as the MAX-MLX Network), a highly conserved super-family of related basic-helix-loop-helix-zipper (bHLHZ) proteins that functions to integrate extracellular and intracellular signals and modulate global gene expression. Importantly the MYC network has been shown to be deeply involved in a broad spectrum of human and other animal cancers. Here we summarize molecular and biological properties of the network modules with emphasis on functional interactions among network members. We suggest that these network interactions serve to modulate growth and metabolism at the transcriptional level in order to balance nutrient demand with supply, to maintain growth homeostasis, and to influence cell fate. Moreover, oncogenic activation of MYC and/or loss of a MYC antagonist, results in an imbalance in the activity of the network as a whole, leading to tumor initiation, progression and maintenance.

关键词： network     transcription     cancer     MYC     MAX     MLX    

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RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Fruit ripening is a complex developmental process made up of genetically programmed physiological and biochemical activities. It culminates in desirable changes in the structural and textural properties and is governed by a complex regulatory network. Much is known about ethylene, one of the most important metabolites promoting the ripening of climacteric fruits. However, the dynamic interplay between phytohormones also plays an important part. Additional regulatory factors such as transcription factors (TFs) and epigenetic modifications also play vital role in the regulation of climacteric fruit ripening. Here, we review and evaluate the complex regulatory network comprising interactions between hormones and the action of TFs and epigenetic modifications during climacteric fruit ripening.

 

关键词： climacteric fruit ripening / phytohormones / TFs / epigenetic modifications    

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RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

Yinglin JI, Mingyang XU, Aide WANG

《农业科学与工程前沿（英文）》   页码 314-334 doi: 10.15302/J-FASE-2021386

摘要： Fruit ripening is a complex developmental process made up of genetically programmed physiological and biochemical activities. It culminates in desirable changes in the structural and textural properties and is governed by a complex regulatory network. Much is known about ethylene, one of the most important metabolites promoting the ripening of climacteric fruits. However, the dynamic interplay between phytohormones also plays an important part. Additional regulatory factors such as transcription factors (TFs) and epigenetic modifications also play vital role in the regulation of climacteric fruit ripening. Here, we review and evaluate the complex regulatory network comprising interactions between hormones and the action of TFs and epigenetic modifications during climacteric fruit ripening.

关键词： climacteric fruit ripening     phytohormones     TFs     epigenetic modifications    

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Characterization of chromatin accessibility in psoriasis

《医学前沿（英文）》 2022年 第16卷 第3期   页码 483-495 doi: 10.1007/s11684-021-0872-3

摘要： The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.

关键词： psoriasis     ATAC-seq     epigenetics     transcription factor    

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Cloning of human XAF1 gene promoter and assay of its transcription activity in a variety of cell lines

Qiong CHEN, Qing YU, Yuhu SONG, Peiyuan Li, Ying CHANG, Zhijun WANG, Lifeng LIU, Wei WU, Jusheng LIN

《医学前沿（英文）》 2009年 第3卷 第2期   页码 148-152 doi: 10.1007/s11684-009-0032-7

摘要： To investigate the regulation of tumor suppressor XAF1 gene expression in digestive system cancers, we studied XAF1 gene promoter transcription activity and mRNA level in digestive system cancer cell lines (human hepatoma cell line HepG2, human colon cancer cell line LoVo, and human gastric cancer cell line AGS) and nontumor cell lines (human embryonic liver cell line L02 (L02 cells) and human embryonic kidney 293 cells [HEK293 cells]) as controls. 1395-bp-promoter fragment of XAF1 gene was amplified by polymerase chain reaction (PCR) and cloned into pGL3-basic vector and pEGFP-1 vector to assay its promoter transcription activity. The plasmids were transfected into a variety of cell lines by lipofectamine 2000. The promoter transcription activity was determined by dual-luciferase report assay, and enhanced green fluorescent protein (EGFP)-positive cells were detected by fluorescence microscope. The expression of XAF1 mRNA in HEK293 and L02 were significantly higher than that in any of the three digestive system cancer cell lines. The dual-luciferase reporter assay showed that the promoter transcription activity in digestive system tumor cell lines transfected with pGL3-XAF1p promoter was apparently lower than that of both HEK293 and L02 cells. Expression of green fluorescent protein (GFP) under the control of XAF1 promoter in the three digestive system cancer cell lines was lower than that of both HEK293 and L02 cells. The activities of pGL3-XAF1p in the three digestive system cancer cell lines after treatment with heat stress were significantly lower than those in the unstressed cells. The results suggested that remarkably down-regulated XAF1 mRNA expression in digestive system cancer cell lines may be due to loss of transcription activity of XAF1 promoter.

关键词： gene     X-linked inhibitor of apoptosis protein associated factor-1 (XAF1)     promoter     transcription regulation    

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The genetic regulation of skeletal muscle development: insights from chicken studies

Wen LUO, Bahareldin A. ABDALLA, Qinghua NIE, Xiquan ZHANG

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 295-304 doi: 10.15302/J-FASE-2017159

摘要： Skeletal muscle development is a complex multi-process trait regulated by various genetic factors. The chicken embryo is an ideal model system for studying skeletal muscle development. However, only a small proportion of the genetic factors affecting skeletal muscle development have been identified in chicken. The aim of this review is to summarize recent knowledge about the genetic factors involved in the regulation of skeletal muscle development in the chicken, such as gene polymorphisms, epigenetic modification, noncoding RNAs and transcription factors, which can influence skeletal muscle development at the genome, epigenome, transcriptome and proteome levels. Research on the regulation of skeletal muscle development in chicken is not yet comprehensive and most of the candidate genes and single nucleotide polymorphisms related to chicken muscle growth remain to be verified in experimental studies. In addition, the data derived from transcriptome sequencing and genome-wide association studies still require further investigation and analysis and comprehensive studies on the regulation of chicken skeletal muscle development will continue as a major research focus.

关键词： chicken     epigenetic modification     miRNAs     skeletal muscle development     SNP     transcription factor    

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Targeting “undruggable” c-Myc protein by synthetic lethality

Chen Wang, Hui Fang, Jiawei Zhang, Ying Gu

《医学前沿（英文）》 2021年 第15卷 第4期   页码 541-550 doi: 10.1007/s11684-020-0780-y

摘要： Synthetic lethal screening, which exploits the combination of mutations that result in cell death, is a promising method for identifying novel drug targets. This method provides a new avenue for targeting “undruggable” proteins, such as c-Myc. Here, we revisit current methods used to target c-Myc and discuss the important functional nodes related to c-Myc in non-oncogene addicted network, whose inhibition may cause a catastrophe for tumor cell destiny but not for normal cells. We further discuss strategies to identify these functional nodes in the context of synthetic lethality. We review the progress and shortcomings of this research field and look forward to opportunities offered by synthetic lethal screening to treat tumors potently.

关键词： synthetic lethality     undruggable     transcription factor     c-Myc    

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Genetic biosensors for small-molecule products: Design and applications in high-throughput screening

Qingzhuo Wang,Shuang-Yan Tang,Sheng Yang

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 15-26 doi: 10.1007/s11705-017-1629-z

摘要： Overproduction of small-molecule chemicals using engineered microbial cells has greatly reduced the production cost and promoted environmental protection. Notably, the rapid and sensitive evaluation of the concentrations of the desired products greatly facilitates the optimization process of cell factories. For this purpose, many genetic components have been adapted into biosensors of small molecules, which couple the intracellular concentrations of small molecules to easily detectable readouts such as fluorescence, absorbance, and cell growth. Such biosensors allow a high-throughput screening of the small-molecule products, and can be roughly classified as protein-based and RNA-based biosensors. This review summarizes the recent developments in the design and applications of biosensors for small-molecule products.

关键词： biosensor     small molecule product     transcription factor     riboswitch     high-throughput screening    

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Molecular mechanisms of leukemia-associated protein degradation

Ying-Li WU, Guo-Qiang CHEN, Hu-Chen ZHOU,

《医学前沿（英文）》 2010年 第4卷 第4期   页码 363-370 doi: 10.1007/s11684-010-0210-7

摘要： Chemical biology, using small molecules as probes to study the cellular signaling network, has developed rapidly in recent years. The interaction between chemistry and biology not only provides new insight into the understanding of cellular activities, but also generates new lead compounds for the treatment of diseases. Transcription factors and kinases such as retinoic acid receptor-alpha (RARα), acute myeloid leukemia 1 (AML1), CAAT/enhancer-binding protein α (C/EBPα), c-myc, and c-abl play important roles in the differentiation of hematopoietic stem/progenitor cells. Abnormalities in these proteins may cause the dysregulation of hematopoiesis and even the occurrence of leukemia. Ubiquitin-mediated protein degradation represents a critical mechanism in regulating the cellular levels and functions of these proteins. Thus, targeting protein degradation has been emerging as an important strategy to conquer malignant diseases. In this review, we will summarize the recent advances in the understanding of the roles of protein degradation in leukemia, with an emphasis on the mechanisms revealed by small molecules.

关键词： protein degradation     leukemia     chemical biology     transcription factors     oncoprotein    

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Expression and clinical implication of PRL-1 and PRL-3 in transitional cell carcinoma of bladder

Bin HAO, Changwei LIU, Huixiang LI

《医学前沿（英文）》 2009年 第3卷 第2期   页码 197-203 doi: 10.1007/s11684-009-0036-3

摘要： The mRNA and protein expression of phosphatase of regenerating liver 1 (PRL-1) and phosphatase of regenerating liver 3 (PRL-3) in transitional cell carcinoma of bladder (BTCC) and normal epithelia of bladder was investigated, and the relationship between the BTCC and pathological changes was clarified. The expression of PRL-1 and PRL-3 mRNA was detected by using reverse transcription polymerase chain reaction (RT-PCR) in 30 cases of BTCC and 10 cases of normal bladder, and the expression of PRL-1 and PRL-3 protein was checked by using immunohistochemistry in 30 cases of BTCC and 15 cases of normal bladder. The expression levels of PRL-1 and PRL-3 mRNA and protein were higher in BTCC than those in normal bladder epithelia ( <0.05). The increased expression of PRL-1 and PRL-3 mRNA and protein was detectable in deep invasion and metastasis of BTCC ( <0.05). There was no correlation between the expression of PRL-1 and PRL-3 and gender, age or recurrence of BTCC (all >0.05). A significantly positive correlation was found between PRL-1 and PRL-3 in BTCC ( <0.05). PRL-1 and PRL-3 are expressed consistently and may contribute to the growth, differentiation, invasion and metastasis of BTCC.

关键词： transitional cell carcinoma of bladder     phosphatase of regenerating liver 1     phosphatase of regenerating liver 3     reverse transcription polymerase chain reaction     immunohistochemistry    

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SALL4 maintains self-renewal of porcine pluripotent stem cells through downregulation of OTX2

Ning WANG, Sile WANG, Yaxian WANG, Yuanxing CAI, Fan YANG, Huayan WANG

《农业科学与工程前沿（英文）》 2019年 第6卷 第1期   页码 81-92 doi: 10.15302/J-FASE-2017180

摘要：

Sall4 as one of the spalt family members contains several alternative splicing variants, which are differentially expressed and has a key role in maintaining pluripotent stem cells. However, the molecular features and function of SALL4 have not been well elucidated in porcine induced pluripotent stem cells (piPSCs). In this study, we identified splice variants and found two splicing variants through analysis of the porcine transcriptome data derived from piPSCs. SALL4A was only detected in piPSCs but SALL4B was globally expressed in porcine tissues and piPSCs. The level of SALL4B was significantly reduced when piPSCs differentiation occurred, however, the expression of SALL4A was not affected, indicating that SALL4B may be essential for the maintenance of piPSCs self-renewal. Overexpression of SALL4A and SALL4B in PEF cells could significantly stimulated expression of endogenous pluripotent genes, when SALL4B significantly promoted OCT4 expression. Conversely, SALL4A significantly promoted KLF4 expression. Additionally, both SALL4A and SALL4B could repress promoter activity in a dose-dependent manner. Conversely, OTX2 also negatively regulated SALL4 expression. These observations indicate that a negative feedback regulatory mechanism may exist between SALL4 and OTX2, which is useful for the maintenance of the self-renewal of piPSCs.

关键词： OTX2     pluripotency     pig     SALL4     transcription regulation    

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Effect of lanthanum chloride on growth of breast cancer cells and regulation of transcription

Xue LI MM , Ping HE MM , Jie XIA MM , Shiwei SONG BS , Jinhai LU BM , Yunde LIU MM ,

《医学前沿（英文）》 2009年 第3卷 第3期   页码 336-340 doi: 10.1007/s11684-009-0053-2

摘要： Lanthanum salt is a prescription drug, but its underlying functions and mechanisms are not fully understood currently. To explore the potential therapeutic value of , cytotoxicity test was applied to investigate its effects on cell proliferation. Furthermore, we observed its influence on pro-oncogene by reverse transcription polymerase chain reaction (RT-PCR). In MCF-7 cell line, repressed cell proliferation at high concentration but had no significant inhibition effect on cell growth at low concentration. However, we observed that repressed transcription at a low concentration. This may suggest that is a potent drug to inhibit the high expression of in carcinoma cells and play a clue for inhibiting the growth and invasion of tumor.

关键词： proliferation     c-met     invasion     lanthanum chloride    

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论智能起源中的简约与自洽原则 Position Paper

马毅1,曹颖2,沈向洋3

《信息与电子工程前沿（英文）》 2022年 第23卷 第9期   页码 1298-1323 doi: 10.1631/FITEE.2200297

摘要： 深度学习重振人工智能十年后的今天，我们提出一个理论框架来帮助理解深度神经网络在整个智能系统里面扮演的角色。我们引入两个基本原则：简约与自洽；分别解释智能系统要学习什么以及如何学习。我们认为这两个原则是人工智能和自然智能之所以产生和发展的基石。虽然这两个原则的雏形早已出现在前人的经典工作里，但是我们对这些原则的重新表述使得它们变得可以精准度量与计算。确切地说，简约与自洽这两个原则能自然地演绎出一个高效计算框架：压缩闭环转录。这个框架统一并解释了现代深度神经网络以及众多人工智能实践的演变和进化。尽管本文主要用视觉数据建模作为例子，我们相信这两个原则将会有助于统一对各种自动智能系统的理解，并且提供一个帮助理解大脑工作机理的框架。

关键词： 智能；简约；自洽；编码率减少；深度网络；闭环转录    

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标题 作者 时间 类型 操作

Oocyte-associated transcription factors in reprogramming after somatic cell nuclear transfer: a review

Fengxia YIN,Hui LIU,Shorgan BOU,Guangpeng LI

期刊论文

Role of the forkhead transcription factor FOXO-FOXM1 axis in cancer and drug resistance

null

期刊论文

The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis

null

期刊论文

RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

期刊论文

RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING: HORMONE, TRANSCRIPTION FACTOR AND EPIGENETIC

Yinglin JI, Mingyang XU, Aide WANG

期刊论文

Characterization of chromatin accessibility in psoriasis

期刊论文

Cloning of human XAF1 gene promoter and assay of its transcription activity in a variety of cell lines

Qiong CHEN, Qing YU, Yuhu SONG, Peiyuan Li, Ying CHANG, Zhijun WANG, Lifeng LIU, Wei WU, Jusheng LIN

期刊论文

The genetic regulation of skeletal muscle development: insights from chicken studies

Wen LUO, Bahareldin A. ABDALLA, Qinghua NIE, Xiquan ZHANG

期刊论文

Targeting “undruggable” c-Myc protein by synthetic lethality

Chen Wang, Hui Fang, Jiawei Zhang, Ying Gu

期刊论文

Genetic biosensors for small-molecule products: Design and applications in high-throughput screening

Qingzhuo Wang,Shuang-Yan Tang,Sheng Yang

期刊论文

Molecular mechanisms of leukemia-associated protein degradation

Ying-Li WU, Guo-Qiang CHEN, Hu-Chen ZHOU,

期刊论文

Expression and clinical implication of PRL-1 and PRL-3 in transitional cell carcinoma of bladder

Bin HAO, Changwei LIU, Huixiang LI

期刊论文

SALL4 maintains self-renewal of porcine pluripotent stem cells through downregulation of OTX2

Ning WANG, Sile WANG, Yaxian WANG, Yuanxing CAI, Fan YANG, Huayan WANG

期刊论文

Effect of lanthanum chloride on growth of breast cancer cells and regulation of transcription

Xue LI MM , Ping HE MM , Jie XIA MM , Shiwei SONG BS , Jinhai LU BM , Yunde LIU MM ,

期刊论文

论智能起源中的简约与自洽原则

马毅1,曹颖2,沈向洋3

期刊论文