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Article ; Online: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application.

Sun, Yu-Meng / Chen, Yue-Qin

2020 Volume 13, Issue 1, Page(s) 109

Abstract: Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of ... ...

Abstract	Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis.
MeSH term(s)	Chromatin/genetics ; Databases, Genetic ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Humans ; Microarray Analysis ; Models, Genetic ; Neoplasms/genetics ; Neoplasms/metabolism ; Open Reading Frames/genetics ; Organ Specificity ; Protein Biosynthesis ; RNA, Neoplasm/genetics ; RNA, Neoplasm/physiology ; RNA, Untranslated/classification ; RNA, Untranslated/genetics ; RNA, Untranslated/isolation & purification ; RNA, Untranslated/physiology ; RNA-Seq ; Ribosomes/metabolism ; Single-Cell Analysis ; Subcellular Fractions/chemistry ; Transcription, Genetic
Chemical Substances	Chromatin ; RNA, Neoplasm ; RNA, Untranslated
Keywords	covid19
Language	English
Publishing date	2020-08-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2429631-4
ISSN	1756-8722 ; 1756-8722
ISSN (online)	1756-8722
ISSN	1756-8722
DOI	10.1186/s13045-020-00945-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identification and Characterization of Plant Circular RNAs.

Zhou, Yan-Fei / Sun, Yu-Meng / Chen, Yue-Qin

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2362, Page(s) 1–19

Abstract: Recent studies have reported that circular RNAs (circRNAs) are a newly discovered type of ubiquitous, abundant and stable noncoding RNAs (ncRNAs) that play important roles in various biological processes in eukaryotic organisms. However, the biological ... ...

Abstract	Recent studies have reported that circular RNAs (circRNAs) are a newly discovered type of ubiquitous, abundant and stable noncoding RNAs (ncRNAs) that play important roles in various biological processes in eukaryotic organisms. However, the biological functions of circRNAs in plants remain largely unknown and need further studies. Identification of plant circRNAs from plant circRNA database or sequencing analysis is a first step to investigate their functions. Here, we provide a series of protocols for circRNA identification including circular forms, composition features and location even in plant tissues which are rich in polysaccharides and polyphenols and difficult to extract RNAs.
MeSH term(s)	RNA/genetics ; RNA, Circular/genetics
Chemical Substances	RNA, Circular ; RNA (63231-63-0)
Language	English
Publishing date	2021-03-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1645-1_1
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Article: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

Sun, Yu-Meng / Chen, Yue-Qin

J Hematol Oncol

Abstract	Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #708432
Database	COVID19

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Article ; Online: Insights into the roles of long noncoding RNAs in the communication between plants and the environment.

Yuan, Chao / He, Rui-Rui / Zhao, Wen-Long / Chen, Yue-Qin / Zhang, Yu-Chan

The plant genome

2022 Volume 16, Issue 4, Page(s) e20277

Abstract: In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant ... ...

Abstract	In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant biological processes has markedly increased. These lncRNA roles involve plant vegetative and reproductive growth and responses to biotic and abiotic stresses. In this review, we examine the classification, mechanisms, and functions of lncRNAs and then emphasize the roles played by these lncRNAs in the communication between plants and the environment mainly with respect to the following environmental factors: temperature, light, water, salt stress, and nutrient deficiencies. We also discuss the consensus among researchers and the remaining challenges and underscore the exciting ways lncRNAs may affect the biology of plants.
MeSH term(s)	RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Stress, Physiological/genetics ; Stress, Physiological/physiology ; Plant Physiological Phenomena/genetics ; Ecosystem ; Environment
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2022-11-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2375444-8
ISSN	1940-3372 ; 0011-183X
ISSN (online)	1940-3372
ISSN	0011-183X
DOI	10.1002/tpg2.20277
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Article: New insight into circRNAs: characterization, strategies, and biomedical applications.

Feng, Xin-Yi / Zhu, Shun-Xin / Pu, Ke-Jia / Huang, Heng-Jing / Chen, Yue-Qin / Wang, Wen-Tao

Experimental hematology & oncology

2023 Volume 12, Issue 1, Page(s) 91

Abstract: Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled ... ...

Abstract	Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled the extensive identification and characterization of circRNAs, such as novel types of biogenesis, tissue-specific and cell-specific expression patterns, epigenetic regulation, translation potential, localization and metabolism. Increasing evidence has revealed that circRNAs participate in diverse cellular processes, and their dysregulation is involved in the pathogenesis of various diseases, particularly cancer. In this review, we systematically discuss the characterization of circRNAs, databases, challenges for circRNA discovery, new insight into strategies used in circRNA studies and biomedical applications. Although recent studies have advanced the understanding of circRNAs, advanced knowledge and approaches for circRNA annotation, functional characterization and biomedical applications are continuously needed to provide new insights into circRNAs. The emergence of circRNA-based protein translation strategy will be a promising direction in the field of biomedicine.
Language	English
Publishing date	2023-10-12
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2669066-4
ISSN	2162-3619
ISSN	2162-3619
DOI	10.1186/s40164-023-00451-w
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Article: Blockade of the lncRNA-DOT1L-LAMP5 axis enhances autophagy and promotes degradation of MLL fusion proteins.

Chen, Tian-Qi / Huang, Heng-Jing / Zhu, Shun-Xin / Chen, Xiao-Tong / Pu, Ke-Jia / Wang, Dan / An, Yan / Lian, Jun-Yi / Sun, Yu-Meng / Chen, Yue-Qin / Wang, Wen-Tao

Experimental hematology & oncology

2024 Volume 13, Issue 1, Page(s) 18

Abstract: Background: Mixed-lineage leukemia (MLL) fusion gene caused by chromosomal rearrangement is a dominant oncogenic driver in leukemia. Due to having diverse MLL rearrangements and complex characteristics, MLL leukemia treated by currently available ... ...

Abstract	Background: Mixed-lineage leukemia (MLL) fusion gene caused by chromosomal rearrangement is a dominant oncogenic driver in leukemia. Due to having diverse MLL rearrangements and complex characteristics, MLL leukemia treated by currently available strategies is frequently associated with a poor outcome. Therefore, there is an urgent need to identify novel therapeutic targets for hematological malignancies with MLL rearrangements. Methods: qRT-PCR, western blot, and spearman correction analysis were used to validate the regulation of LAMP5-AS1 on LAMP5 expression. In vitro and in vivo experiments were conducted to assess the functional relevance of LAMP5-AS1 in MLL leukemia cell survival. We utilized chromatin isolation by RNA purification (ChIRP) assay, RNA pull-down assay, chromatin immunoprecipitation (ChIP), RNA fluorescence in situ hybridization (FISH), and immunofluorescence to elucidate the relationship among LAMP5-AS1, DOT1L, and the LAMP5 locus. Autophagy regulation by LAMP5-AS1 was evaluated through LC3B puncta, autolysosome observation via transmission electron microscopy (TEM), and mRFP-GFP-LC3 puncta in autophagic flux. Results: The study shows the crucial role of LAMP5-AS1 in promoting MLL leukemia cell survival. LAMP5-AS1 acts as a novel autophagic suppressor, safeguarding MLL fusion proteins from autophagic degradation. Knocking down LAMP5-AS1 significantly induced apoptosis in MLL leukemia cell lines and primary cells and extended the survival of mice in vivo. Mechanistically, LAMP5-AS1 recruits the H3K79 histone methyltransferase DOT1L to LAMP5 locus, directly activating LAMP5 expression. Importantly, blockade of LAMP5-AS1-LAMP5 axis can represses MLL fusion proteins by enhancing their degradation. Conclusions: The findings underscore the significance of LAMP5-AS1 in MLL leukemia progression through the regulation of the autophagy pathway. Additionally, this study unveils the novel lncRNA-DOT1L-LAMP5 axis as promising therapeutic targets for degrading MLL fusion proteins.
Language	English
Publishing date	2024-02-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2669066-4
ISSN	2162-3619
ISSN	2162-3619
DOI	10.1186/s40164-024-00488-5
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Article ; Online: N6-methyladenosine methyltransferases: functions, regulation, and clinical potential.

Huang, Wei / Chen, Tian-Qi / Fang, Ke / Zeng, Zhan-Cheng / Ye, Hua / Chen, Yue-Qin

Journal of hematology & oncology

2021 Volume 14, Issue 1, Page(s) 117

Abstract: N6-methyladenosine (m6A) has emerged as an abundant modification throughout the transcriptome with widespread functions in protein-coding and noncoding RNAs. It affects the fates of modified RNAs, including their stability, splicing, and/or translation, ... ...

Abstract	N6-methyladenosine (m6A) has emerged as an abundant modification throughout the transcriptome with widespread functions in protein-coding and noncoding RNAs. It affects the fates of modified RNAs, including their stability, splicing, and/or translation, and thus plays important roles in posttranscriptional regulation. To date, m6A methyltransferases have been reported to execute m6A deposition on distinct RNAs by their own or forming different complexes with additional partner proteins. In this review, we summarize the function of these m6A methyltransferases or complexes in regulating the key genes and pathways of cancer biology. We also highlight the progress in the use of m6A methyltransferases in mediating therapy resistance, including chemotherapy, targeted therapy, immunotherapy and radiotherapy. Finally, we discuss the current approaches and clinical potential of m6A methyltransferase-targeting strategies.
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/genetics ; Adenosine/metabolism ; Animals ; Gene Expression Regulation, Neoplastic ; Humans ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Molecular Targeted Therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/therapy ; Signal Transduction
Chemical Substances	N-methyladenosine (CLE6G00625) ; 6-methyladenine mRNA methyltransferase (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2021-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2429631-4
ISSN	1756-8722 ; 1756-8722
ISSN (online)	1756-8722
ISSN	1756-8722
DOI	10.1186/s13045-021-01129-8
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Article ; Online: Circulating miRNAs in cancer: from detection to therapy.

Wang, Wen-Tao / Chen, Yue-Qin

Journal of hematology & oncology

2014 Volume 7, Page(s) 86

Abstract: Since the discovery of circulating microRNAs (miRNAs) in body fluids, an increasing number of studies have focused on their potential as non-invasive biomarkers and as therapeutic targets or tools for many diseases, particularly for cancers. Because of ... ...

Abstract	Since the discovery of circulating microRNAs (miRNAs) in body fluids, an increasing number of studies have focused on their potential as non-invasive biomarkers and as therapeutic targets or tools for many diseases, particularly for cancers. Because of their stability, miRNAs are easily detectable in body fluids. Extracellular miRNAs have potential as biomarkers for the prediction and prognosis of cancer. Moreover, they also enable communication between cells within the tumor microenvironment, thereby influencing tumorigenesis. In this review, we summarize the progresses made over the past decade regarding circulating miRNAs, from the development of detection methods to their clinical application as biomarkers and therapeutic tools for cancer. We also discuss the advantages and limitations of different detection methods and the pathways of circulating miRNAs in cell-cell communication, in addition to their clinical pharmacokinetics and toxicity in human organs. Finally, we highlight the potential of circulating miRNAs in clinical applications for cancer.
MeSH term(s)	Animals ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Humans ; MicroRNAs/blood ; MicroRNAs/genetics ; Neoplasms/blood ; Neoplasms/genetics ; Prognosis ; Tumor Microenvironment
Chemical Substances	Biomarkers, Tumor ; MicroRNAs
Language	English
Publishing date	2014-12-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2429631-4
ISSN	1756-8722 ; 1756-8722
ISSN (online)	1756-8722
ISSN	1756-8722
DOI	10.1186/s13045-014-0086-0
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Article ; Online: Author Correction: Reproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice.

Zhang, Yu-Chan / Lei, Meng-Qi / Zhou, Yan-Fei / Yang, Yu-Wei / Lian, Jian-Ping / Yu, Yang / Feng, Yan-Zhao / Zhou, Ke-Ren / He, Rui-Rui / He, Huang / Zhang, Zhi / Yang, Jian-Hua / Chen, Yue-Qin

Nature communications

2023 Volume 14, Issue 1, Page(s) 1584

Language	English
Publishing date	2023-03-22
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-37355-6
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Article ; Online: Calcium-dependent activation of CPK12 facilitates its cytoplasm-to-nucleus translocation to potentiate plant hypoxia sensing by phosphorylating ERF-VII transcription factors.

Fan, Biao / Liao, Ke / Wang, Lin-Na / Shi, Li-Li / Zhang, Yi / Xu, Ling-Jing / Zhou, Ying / Li, Jian-Feng / Chen, Yue-Qin / Chen, Qin-Fang / Xiao, Shi

Molecular plant

2023 Volume 16, Issue 6, Page(s) 979–998

Abstract: Calcium-dependent protein kinases (CDPKs/CPKs) are key regulators of plant stress signaling that translate calcium signals into cellular responses by phosphorylating diverse substrate proteins. However, the molecular mechanism by which plant cells relay ... ...

Abstract	Calcium-dependent protein kinases (CDPKs/CPKs) are key regulators of plant stress signaling that translate calcium signals into cellular responses by phosphorylating diverse substrate proteins. However, the molecular mechanism by which plant cells relay calcium signals in response to hypoxia remains elusive. Here, we show that one member of the CDPK family in Arabidopsis thaliana, CPK12, is rapidly activated during hypoxia through calcium-dependent phosphorylation of its Ser-186 residue. Phosphorylated CPK12 shuttles from the cytoplasm to the nucleus, where it interacts with and phosphorylates the group VII ethylene-responsive transcription factors (ERF-VII) that are core regulators of plant hypoxia sensing, to enhance their stabilities. Consistently, CPK12 knockdown lines show attenuated tolerance of hypoxia, whereas transgenic plants overexpressing CPK12 display improved hypoxia tolerance. Nonethelss, loss of function of five ERF-VII proteins in an erf-vii pentuple mutant could partially suppress the enhanced hypoxia-tolerance phenotype of CPK12-overexpressing lines. Moreover, we also discovered that phosphatidic acid and 14-3-3κ protein serve as positive and negative modulators of the CPK12 cytoplasm-to-nucleus translocation, respectively. Taken together, these findings uncover a CPK12-ERF-VII regulatory module that is key to transducing calcium signals from the cytoplasm into the nucleus to potentiate hypoxia sensing in plants.
MeSH term(s)	Transcription Factors/genetics ; Transcription Factors/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Calcium/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Cell Nucleus/metabolism ; Hypoxia ; Gene Expression Regulation, Plant
Chemical Substances	Transcription Factors ; Arabidopsis Proteins ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-04-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2393618-6
ISSN	1752-9867 ; 1674-2052
ISSN (online)	1752-9867
ISSN	1674-2052
DOI	10.1016/j.molp.2023.04.002
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