|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | Retrospective and perspective of plant epigenetics in China显示文摘Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer(two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications(PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato.Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation(RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects.We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms. | Cheng-Guo Duan Jian-Kang Zhu Xiaofeng Cao | 2018 | Journal of Genetics and Genomics2018，45，11： | 14 |
| 2 | Regulation of MYC gene expression by aberrant Wnt/β-catenin signaling in colorectal cancer显示文摘The Wnt/β-catenin signaling pathway controls intestinal homeostasis and mutations in components of this pathway are prevalent in human colorectal cancers(CRCs).These mutations lead to inappropriate expression of genes controlled by Wnt responsive DNA elements(WREs). T-cell factor/Lymphoid enhancer factor transcription factors bind WREs and recruit the β-catenin transcriptional co-activator to activate target gene expression. Deregulated expression of the c-MYC proto-oncogene(MYC) by aberrant Wnt/β-catenin signaling drives colorectal carcinogenesis. In this review,we discuss the current literature pertaining to the identification and characterization of WREs that control oncogenic MYC expression in CRCs. A common theme has emerged whereby these WREs often map distally to the MYC genomic locus and control MYC gene expression through long-range chromatin loops with the MYC proximal promoter. We propose that by determining which of these WREs is critical for CRC pathogenesis,novel strategies can be developed to treat individuals suffering from this disease. | Sherri Rennoll Gregory Yochum | 2015 | World Journal of Biological Chemistry2015，6，4： | 9 |
| 3 | Predicting enhancer-promoter interaction from genomic sequence with deep neural networks显示文摘Background:In the human genome,distal enhancers are involved in regulating target genes through proximal promoters by forming enhancer-promoter interactions.Although recently developed high-throughput experimental approaches have allowed us to recognize potential enhancer-promoter interactions genome-wide,it is still largely unclear to what extent the sequence-level information encoded in our genome help guide such interactions.Methods:Here we report a new computational method (named 'SPEID') using deep learning models to predict enhancer-promoter interactions based on sequence-based features only,when the locations of putative enhancers and promoters in a particular cell type are given.Results:Our results across six different cell types demonstrate that SPEID is effective in predicting enhancerpromoter interactions as compared to state-of-the-art methods that only use information from a single cell type.As a proof-of-principle,we also applied SPEID to identify somatic non-coding mutations in melanoma samples that may have reduced enhancer-promoter interactions in tumor genomes.Conclusions^ This work demonstrates that deep learning models can help reveal that sequence-based features alone are sufficient to reliably predict enhancer-promoter interactions genome-wide. | Shashank Singh Yang Yang Barnabas Poczos Jian Ma | 2019 | Frontiers of Electrical and Electronic Engineering in China2019，7，2： | 8 |
| 4 | Reversible Histone H2B Monoubiquitination Fine-Tunes Abscisic Acid Signaling and Drought Response in Rice显示文摘Histone H2B monoubiquitination (H2Bub1) plays important roles in several physiological and developmental processes, but its roles in the regulation of plant stress responses remain elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found that rice HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, in teracted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, upregulated by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were in creased in the target genes of OsbZIP46 under the drought stress and ABA treat- merits, which were positively correlated with their increased expression levels. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance by mediating OsbZIP46 deactivation and degradation, could reduce the H2Bub1 levels in the target genes of OsbZIP46 by recruiting a putative deubiquitinase OsOTLD1 . Suppression of OsOTLD1in vivo resulted in increased H2Bub1 levels and expression of OsbZIP46 target genes. Collectively, these fin dings established an elaborate mecha nism of histone monoubiquitination in the fine-turning of ABA signaling and drought response by balancing H2Bub1 deposition and removal. | Siqi Ma Ning Tang Xu Li Yongjun Xie Denghao Xiang Jie Fu Jianqiang Shen Jun Yang Haifu Tu Xianghua Li Honghong Hu Lizhong Xiong | 2019 | Molecular Plant2019，12，2： | 7 |
| 5 | Roles and regulation of bone morphogenetic protein-7 in kidney development and diseases显示文摘The gene encoding bone morphogenetic protein-7(BMP7) is expressed in the developing kidney in embryos and also in the mature organ in adults. During kidney development, expression of BMP7 is essential to determine the final number of nephrons in and proper size of the organ. The secreted BMP7 acts on the nephron progenitor cells to exert its dual functions: To maintain and expand the progenitor population and to provide them with competence to respond to differentiation cues, each relying on distinct signaling pathways. Intriguingly, in the adult organ, BMP7 has been implicated in protection against and regeneration from injury. Exogenous administration of recombinant BMP7 to animal models of kidney diseases has shown promising effects in counteracting inflammation, apoptosis and fibrosis evoked upon injury. Although the expression pattern of BMP7 has been well described, the mechanisms by which it is regulated have remained elusive and the processes by which the secretion sites of BMP7 impinge upon its functions in kidney development and diseases have not yet been assessed. Understanding the regulatory mechanisms will pave the way towards gaining better insight into the roles of BMP7, and to achieving desired control of the gene expression as a therapeutic strategy for kidney diseases. | Taro Tsujimura Mana Idei Masahiro Yoshikawa Osamu Takase Keiichi Hishikawa | 2016 | World Journal of Stem Cells2016，8，9： | 6 |
| 6 | Histone modifications:Targeting head and neck cancer stem cells显示文摘Head and neck squamous cell carcinoma(HNSCC) is the sixth most common cancer worldwide, and is responsible for a quarter of a million deaths annually. The survival rate for HNSCC patients is poor, showing only minor improvement in the last three decades. Despite new surgical techniques and chemotherapy protocols, tumor resistance to chemotherapy remains a significant challenge for HNSCC patients. Numerous mechanisms underlie chemoresistance, including genetic and epigenetic alterations in cancer cells that may be acquired during treatment and activation of mitogenic signaling pathways, such as nuclear factor kappa-light-chain-enhancer-of activated B cell, that cause reduced apoptosis. In addition to dysfunctional molecular signaling, emerging evidence reveals involvement of cancer stem cells(CSCs) in tumor development and in tumor resistance to chemotherapy and radiotherapy. These observations have sparked interest in understanding the mechanisms involved in the control of CSC function and fate. Post-translational modifications of histones dynamically influence gene expression independent of alterations to the DNA sequence. Recent findings from our group have shown that pharmacological induction of posttranslational modifications of tumor histones dynamically modulates CSC plasticity. These findings suggest that a better understanding of the biology of CSCs in response to epigenetic switches and pharmacological inhibitors of histone function may directly translate to the development of a mechanism-based strategy to disrupt CSCs. In this review, we present and discuss current knowledge on epigenetic modifications of HNSCC and CSC response to DNA methylation and histone modifications. In addition, we discuss chromatin modifications and their role in tumor resistance to therapy. | John M Le Cristiane H Squarize Rogerio M Castilho | 2014 | World Journal of Stem Cells2014，6，5： | 6 |
| 7 | Chromatin and epigenetic regulation of the telomerase reverse transcriptase gene显示文摘Telomerase expression and telomere maintenance are critical for long-term cell proliferation and survival,and they play important roles in development,aging,and cancer.Cumulating evidence has indicated that regulation of the rate-limiting subunit of human telomerase reverse transcriptase gene(hTERT)is a complex process in normal cells and many cancer cells.In addition to a number of transcriptional activators and repressors,the chromatin environment and epigenetic status of the endogenous hTERT locus are also pivotal for its regulation in normal human somatic cells and in tumorigenesis. | Jiyue Zhu Yuanjun Zhao Shuwen Wang | 2010 | Protein & Cell2010，1，1： | 5 |
| 8 | Human pescadillo induces large-scale chromatin unfolding显示文摘The human pescadillo gene encodes a protein with a BRCT domain. Pescadillo plays an important role in DNA synthesis, cell proliferation and transformation. Since BRCT do- mains have been shown to induce chromatin large-scale unfolding, we tested the role of Pesca- dillo in regulation of large-scale chromatin unfolding. To this end, we isolated the coding region of Pescadillo from human mammary MCF10A cells. Compared with the reported sequence, the isolated Pescadillo contains in-frame deletion from amino acid 580 to 582. Targeting the Pesca- dillo to an amplified, lac operator-containing chromosome region in the mammalian genome re- sults in large-scale chromatin decondensation. This unfolding activity maps to the BRCT domain of Pescadillo. These data provide a new clue to understanding the vital role of Pescadillo. | ZHANG Hao FANG Yan HUANG Cuifen YANG Xiao YE Qinong | 2005 | Science China(Life Sciences)2005，48，3： | 4 |
| 9 | Functional impacts of non-coding RNA processing on enhancer activity and target gene expression显示文摘Tight regulation of gene expression is orchestrated by enhancers.Through recent research advancements,it is becoming clear that enhancers are not solely distal regulatory elements harboring transcription factor binding sites and decorated with specific histone marks,but they rather display sign atures of active transcription,showingdistinct degrees oftranscription unit organization.Thereby,a substantial fraction of enhancers give rise to different species of non-coding RNA transcripts with an unprecedented range of potential functions.In this review,we bring together data from recent studies indicating that non-coding RNA transcription from active enhancers,as well as enhancer-produced long non-coding RNA transcripts,may modulate or define the functional regulatory potential ofthe cognate enhancer.In addition,we summarize supporting evidence that RNA processing ofthe enhancer-associated long non-coding RNA transcripts may constitute an additional layer of regulation of enhancer activity,which contributes to the control and final outcome of enhancer-targeted gene expression. | Evgenia Ntini Annalisa Marsico | 2019 | Journal of Molecular Cell Biology2019，11，10： | 4 |
| 10 | Recent advances in the study of Kaposi's sarcoma-associated herpesvirus replication and pathogenesis显示文摘It has now been over twenty years since a novel herpesviral genome was identified in Kaposi's sarcoma biopsies. Since then, the cumulative research effort by molecular biologists, virologists, clinicians, and epidemiologists alike has led to the extensive characterization of this tumor virus, Kaposi's sarcoma-associated herpesvirus(KSHV; also known as human herpesvirus 8(HHV-8)), and its associated diseases. Here we review the current knowledge of KSHV biology and pathogenesis, with a particular emphasis on new and exciting advances in the field of epigenetics. We also discuss the development and practicality of various cell culture and animal model systems to study KSHV replication and pathogenesis. | Denis Avey Brittany Brewers Fanxiu Zhu | 2015 | Virologica Sinica2015，30，2： | 3 |
| 11 | KAPtain in charge of multiple missions: Emerging roles of KAP1显示文摘KAP1/TRIM28/TIF1β was identified nearly twenty years ago as a universal transcriptional co-repressor because it interacts with a large KRAB-containing zinc finger protein(KRAB-ZFP) transcription factor family. Many studies demonstrate that KAP1 affects gene expression by regulating the transcription of KRAB-ZFP-specific loci, trans-repressing as a transcriptional co-repressor or epigenetically modulating chromatin structure. Emerging evidence suggests that KAP1 also functions independent of gene regulation by serving as a SUMO/ubiquitin E3 ligase or signaling scaffold protein to mediate signal transduction. KAP1 is subjected to multiple post-translational modifications(PTMs), including serine/tyrosine phosphorylation, SUMOylation, and acetylation, which coordinately regulate KAP1 function and its protein abundance. KAP1 is involved in multiple aspects of cellular activities, including DNA damage response, virus replication, cytokine production and stem cell pluripotency. Moreover, knockout of KAP1 results in embryonic lethality, indicating that KAP1 is crucial for embryonic development and possibly impacts a wide-range of(patho)physiological manifestations. Indeed, studies from conditional knockout mouse models reveal that KAP1-deficiency significantly impairs vital physiological processes, such as immune maturation, stress vulnerability, hepatic metabolism, gamete development and erythropoiesis. In this review, we summarize and evaluate current literatures involving the biochemical and physiological functions of KAP1. In addition, increasing studies on the clinical relevance of KAP1 in cancer will also be discussed. | Chun-Ting Cheng Ching-Ying Kuo David K Ann | 2014 | World Journal of Biological Chemistry2014，5，3： | 3 |
| 12 | Epigenetics and chromatin plasticity in embryonic stem cells显示文摘The study of embryonic stem cells is in the spotlight in many laboratories that study the structure and function of chromatin and epigenetic processes. The key properties of embryonic stem cells are their capacity for selfrenewal and their pluripotency. Pluripotent stem cells are able to differentiate into the cells of all three germ layers, and because of this property they represent a promising therapeutic tool in the treatment of diseases such as Parkinson's disease and diabetes, or in the healing of lesions after heart attack. As the basic nuclear unit, chromatin is responsible for the regulation of the functional status of cells, including pluripotency and differentiation. Therefore, in this review we discuss the functional changes in chromatin during differentiation and the correlation between epigenetics events and the differentiation potential of embryonic stem cells. In particular we focus on post-translational histone modification, DNA methylation and the heterochromatin protein HP1 and its unique function in mouse and human embryonic stem cells. | Terézia Pikrylová Jií Pacherník Stanislav Kozubek Eva Bártová | 2013 | World Journal of Stem Cells2013，5，3： | 3 |
| 13 | Clinical and molecular spectrum of Wiedemann-Steiner syndrome, an emerging member of the chromatinopathy family显示文摘Wiedemann-Steiner syndrome(OMIM#605130)is a rare congenital malformation syndrome characterized by hypertrichosis cubiti associated with short stature;consistent facial features,including long eyelashes,thick or arched eyebrows with a lateral flare,wide nasal bridge,and downslanting and vertically narrow palpebral fissures;mild to moderate intellectual disability;behavioral difficulties;and hypertrichosis on the back.It is caused by heterozygous pathogenic variants in KMT2A.This gene has an established role in histone methylation,which explains the overlap of Wiedemann-Steiner syndrome with other chromatinopathies,a heterogeneous group of syndromic conditions that share a common trigger:The disruption of one of the genes involved in chromatin modification,leading to dysfunction of the epigenetic machinery. | Paolo Fontana Francesco Fioravanti Passaretti Marianna Maioli Giuseppina Cantalupo Francesca Scarano Fortunato Lonardo | 2020 | World Journal of Medical Genetics2020，9，1： | 2 |
| 14 | Ultramicroscopic Characterization of Mature Pollen Grains of Habenaria sagittifera显示文摘Transmission electron microscopy was conducted to characterize the mature pollen grains in the massulae of Habenaria sagittifera at anthesis to understand its ultramicroscopic features of mature pollen grains of this species. I found that(a) pollen walls on the surface of the massula consisted of several layers, which included the tectum, baculum, nexine-1, nexine-2, and intine, whereas pollen walls within the massula were comprised of less layers, lacking tectum and baculum;(b) both vegetative and generative nuclei in mature pollen grains were predominated by highly condensed chromatin, which occupied over half of the nuclear volume; and(c) the pollen grains did not contain lipid droplets, starch grains,or storage proteins, indicative of the absence of macromolecular storage reserves. In summary, the structural difference between walls on the surface of the massula and walls within the massula, the highly condensed status of the vegetative nucleus, and the absence of macromolecular storage reserves were the most noticeable ultramicroscopic characteristics of mature pollen grains of H. sagittifera. | LIU Lin | 2016 | Horticultural Plant Journal2016，2，1： | 2 |
| 15 | Dynamics of the higher-order structure of chromatin显示文摘Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA,such as DNA replication and DNA repair.Many factors,including histone variants,histone modification,DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin.Although the structure of nucleosomes,the fundamental repeating unit of chromatin,is clear,there is still much discussion on the higher-order levels of chromatin structure.Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities.Here,we review studies on the dynamics of chromatin higherorder structure and its relationship with gene transcription. | Ping Chen Guohong Li | 2010 | Protein & Cell2010，1，11： | 2 |
| 16 | 染色体外DNA促进癌基因高表达和肿瘤异质性的研究进展显示文摘染色体外DNA(extrachromosomal DNA,ecDNA)是存在于肿瘤细胞中、可在有丝分裂中期被光镜观察到的游离于染色体外的环形DNA。ecDNA不仅携带高拷贝的癌基因,而且转录活跃,是癌基因表达的主要来源;另外其还是形成肿瘤异质性的关键。本文将就上述ecDNA对肿瘤的作用机制进行概述,并提出关于该领域的研究展望。 | 徐博文 李楠 | 2020 | 中国肿瘤生物治疗杂志2020，27，3： | 2 |
| 17 | Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication显示文摘The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression.However,it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication(WGD)in plants.In this study,high-resolution interaction maps were generated using high-throughput chromatin conformation capture(Hi-C)techniques for two poplar species,Populus euphratica and Populus alba var.pyramidalis,which diverged~14 Mya after a common WGD.We examined the similarities and differences in the hierarchical chromatin organization between the two species,including A/B compartment regions and topologically associating domains(TADs),as well as in their DNA methylation and gene expression patterns.We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity,yet the conservation of hierarchical chromatin organization across the two species was low.The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions,and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels.Thus,the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process.This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD. | Le Zhang Jingtian Zhao Hao Bi Xiangyu Yang Zhiyang Zhang Yutao Su Zhenghao Li Lei Zhang Brian J.Sanderson Jianquan Liu Tao Ma | 2021 | Horticulture Research2021，8，1： | 2 |
| 18 | Ikaros in hematopoiesis and leukemia显示文摘Ikaros is a gene whose activity is essential for normal hematopoiesis.Ikaros acts as a master regulator of lymphoid and myeloid development as well as a tumor suppressor.In cells,Ikaros regulates gene expression via chromatin remodeling.During the past 15 years tremendous advances have been made in understanding the role of Ikaros in hematopoiesis and leukemogenesis.In this Topic Highlights series of reviews,several groups of international experts in this field summarize the experimental data that is shaping the emerging picture of Ikaros function at the biochemical and cellular levels.The articles provide detailed analyses of recent scientific advancements and present models that will serve as a basis for future studies aimed at developing a better understanding of normal hematopoiesis and hematological malignancies and at accelerating the application of this knowledge in clinical practice. | Sinisa Dovat | 2011 | World Journal of Biological Chemistry2011，2，6： | 1 |
| 19 | Genomic data reveal high conservation but divergent evolutionary pattern of Polycomb/Trithorax group genes in arthropods显示文摘Eplgenetlc gene control is maintained by chromatln-assoclated Polycomb group (PcG)and Trithorax group (TrxG)genes,which act antagonistically via the interplay between PcG and TrxG regulation to generate silenced or permissive transcriptional states. In this study,we searched for PcG/TrxG genes in 180 arthropod genomes,covering all the sequenced arthropod genomes at the time of conducting this study,to perform a global investigation of PcG/TrxG genes in a phylogenetic frame.Results of ancestral state reconstruction analysis revealed that the ancestor of arthropod species has an almost complete repertoire of PcG/TrxG genes,and most of these genes were seldom lost above order level. The domain diversity analysis indicated that the PcG/TrxG genes show variable extent of domain structure changes;some of these changes could be associated with lineage-specific events.The likelihood ratio tests for selection pressure detected a number of PcG/TrxG genes which underwent episodic positive selection on the branch leading to the insects with holometabolous development.These results suggest that,despite their high conservation across arthropod species,different members of PcG/TrxG genes showed considerable differences in domain structure and sequence divergence in arthropod evolution.Our cross species comparisons using large-scale genomic data provide insights into divergent evolutionary pattern on highly conserved genes in arthropods. | Feng Jiang Qing Liu Xiang Liu Xian-Hui Wang Le Kang | 2019 | Insect Science2019，26，1： | 1 |
| 20 | Identification of target genes of transcription factor CEBPB in acute promyelocytic leukemia cells induced by all-trans retinoic acid显示文摘Objective:To indentify target genes of transcription factor CCA AT enhancer-binding protein P(CEBPB) in acute proinyelocytie leukemia cells induced by all-tram retinoie acid.Methods: A new strategy for high—throughput identification of direct target genes was established by combining chromatin immunoprecipitation(ChIP) with in vitro selection.Then,106 potential CKBPB binding fragments from the genome of the all-trans retinoie acid(ATRA)-treated NB4 cells were identified.Results:Of them,82 were mapped in proximity to known or previously predicted genes;7 were randomly picked up for further confirmation by ChlP-PCR and 3 genes (CALM,1TPR2 and 0RM2) were found to be specificaUy up-regulated in the ATRA-treated NB4 cells,indicating that they might lie the down-stream target genes of ATKA.Conclusions:Our results provided new insight into the mechanisms of ATRA-induced granulocytic differentiation. | Lei Yu Yang-De Zhang Jun Zhou De-Ming Yao Xiang Li | 2013 | Asian Pacific Journal of Tropical Medicine2013，6，6： | 1 |
您所在的机构暂未开通此部分的功能，请联系管理员