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  1. Article: Recent Advances in RNA m

    Verghese, Michelle / Wilkinson, Emma / He, Yu-Ying

    Cancer treatment and research

    2024  Volume 190, Page(s) 95–142

    Abstract: An analogous field to epigenetics is referred to as epitranscriptomics, which focuses on the study of post-transcriptional chemical modifications in RNA. RNA molecules, including mRNA, tRNA, rRNA, and other non-coding RNA molecules, can be edited with ... ...

    Abstract An analogous field to epigenetics is referred to as epitranscriptomics, which focuses on the study of post-transcriptional chemical modifications in RNA. RNA molecules, including mRNA, tRNA, rRNA, and other non-coding RNA molecules, can be edited with numerous modifications. The most prevalent modification in eukaryotic mRNA is N6-methyladenosine (m
    MeSH term(s) Humans ; RNA/metabolism ; Methylation ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA Methylation ; Neoplasms/genetics ; Neoplasms/therapy
    Chemical Substances RNA (63231-63-0) ; RNA, Messenger
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Journal Article
    ISSN 0927-3042
    ISSN 0927-3042
    DOI 10.1007/978-3-031-45654-1_4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The m

    Yang, Zizhao / Verghese, Michelle / Yang, Seungwon / Shah, Palak / He, Yu-Ying

    Photochemistry and photobiology

    2024  

    Abstract: Ultraviolet B (UVB) radiation represents a major carcinogen for the development of all skin cancer types. Mechanistically, UVB induces damage to DNA in the form of lesions, including cyclobutane pyrimidine dimers (CPDs). Disruption of the functional ... ...

    Abstract Ultraviolet B (UVB) radiation represents a major carcinogen for the development of all skin cancer types. Mechanistically, UVB induces damage to DNA in the form of lesions, including cyclobutane pyrimidine dimers (CPDs). Disruption of the functional repair processes, such as nucleotide excision repair (NER), allows persistence of DNA damage and contributes to skin carcinogenesis. Recent work has implicated m
    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 123540-0
    ISSN 1751-1097 ; 0031-8655
    ISSN (online) 1751-1097
    ISSN 0031-8655
    DOI 10.1111/php.13904
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1686: Show issues Location:
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  3. Article: Roles of RNA Modifications in Diverse Cellular Functions.

    Wilkinson, Emma / Cui, Yan-Hong / He, Yu-Ying

    Frontiers in cell and developmental biology

    2022  Volume 10, Page(s) 828683

    Abstract: Chemical modifications of RNA molecules regulate both RNA metabolism and fate. The deposition and function of these modifications are mediated by the actions of writer, reader, and eraser proteins. At the cellular level, RNA modifications regulate ... ...

    Abstract Chemical modifications of RNA molecules regulate both RNA metabolism and fate. The deposition and function of these modifications are mediated by the actions of writer, reader, and eraser proteins. At the cellular level, RNA modifications regulate several cellular processes including cell death, proliferation, senescence, differentiation, migration, metabolism, autophagy, the DNA damage response, and liquid-liquid phase separation. Emerging evidence demonstrates that RNA modifications play active roles in the physiology and etiology of multiple diseases due to their pervasive roles in cellular functions. Here, we will summarize recent advances in the regulatory and functional role of RNA modifications in these cellular functions, emphasizing the context-specific roles of RNA modifications in mammalian systems. As m
    Language English
    Publishing date 2022-03-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2022.828683
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  4. Article ; Online: Role of RNA modifications in carcinogenesis and carcinogen damage response.

    Verghese, Michelle / Wilkinson, Emma / He, Yu-Ying

    Molecular carcinogenesis

    2022  Volume 62, Issue 1, Page(s) 24–37

    Abstract: The field of epitranscriptomics encompasses the study of post-transcriptional RNA modifications and their regulatory enzymes. Among the numerous RNA modifications, ... ...

    Abstract The field of epitranscriptomics encompasses the study of post-transcriptional RNA modifications and their regulatory enzymes. Among the numerous RNA modifications, N
    MeSH term(s) Humans ; Carcinogens/toxicity ; Adenosine ; Methylation ; Carcinogenesis/chemically induced ; Carcinogenesis/genetics ; RNA, Messenger/genetics ; RNA
    Chemical Substances Carcinogens ; Adenosine (K72T3FS567) ; RNA, Messenger ; RNA (63231-63-0)
    Language English
    Publishing date 2022-05-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1004029-8
    ISSN 1098-2744 ; 0899-1987
    ISSN (online) 1098-2744
    ISSN 0899-1987
    DOI 10.1002/mc.23418
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  5. Article: ALKBH4 Stabilization Is Required for Arsenic-Induced 6mA DNA Methylation Inhibition, Keratinocyte Malignant Transformation, and Tumorigenicity.

    Cui, Yan-Hong / Wilkinson, Emma / Peterson, Jack / He, Yu-Ying

    Water

    2022  Volume 14, Issue 22

    Abstract: Inorganic arsenic is one of the well-known human skin carcinogens. However, the molecular mechanism by which arsenic promotes carcinogenesis remains unclear. Previous studies have established that epigenetic changes, including changes in DNA methylation, ...

    Abstract Inorganic arsenic is one of the well-known human skin carcinogens. However, the molecular mechanism by which arsenic promotes carcinogenesis remains unclear. Previous studies have established that epigenetic changes, including changes in DNA methylation, are among the critical mechanisms that drive carcinogenesis.
    Language English
    Publishing date 2022-11-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2521238-2
    ISSN 2073-4441
    ISSN 2073-4441
    DOI 10.3390/w14223595
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  6. Article ; Online: KAS-Analyzer: a novel computational framework for exploring KAS-seq data.

    Lyu, Ruitu / Wu, Tong / Park, Gayoung / He, Yu-Ying / Chen, Mengjie / He, Chuan

    Bioinformatics advances

    2023  Volume 3, Issue 1, Page(s) vbad121

    Abstract: Motivation: Kethoxal-assisted ssDNA sequencing (KAS-seq) is rapidly gaining popularity as a robust and effective approach to study the nascent dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA ( ... ...

    Abstract Motivation: Kethoxal-assisted ssDNA sequencing (KAS-seq) is rapidly gaining popularity as a robust and effective approach to study the nascent dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source computational tools tailored for KAS-seq data are still lacking.
    Results: Here, we introduce KAS-Analyzer, the first comprehensive computational framework aimed at streamlining and enhancing the analysis and interpretation of KAS-seq and spKAS-seq data. In addition to standard analyses, KAS-Analyzer offers many novel tools specifically designed for KAS-seq data, including, but not limited to: calculation of transcription-related metrics, identification of single-stranded transcribing (SST) enhancers, high-resolution mapping of R-loops, and differential RNA polymerase activity analysis. We provided a detailed overview of KAS-seq data and its diverse applications through the implementation of KAS-Analyzer. Using the example time-course KAS-seq datasets, we further showcase the robust capabilities of KAS-Analyzer for investigating dynamic transcriptional regulatory programs in response to UVB radiation.
    Availability and implementation: KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.
    Language English
    Publishing date 2023-09-08
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbad121
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  7. Article ; Online: NAT10 regulates the repair of UVB-induced DNA damage and tumorigenicity.

    Yang, Zizhao / Wilkinson, Emma / Cui, Yan-Hong / Li, Haixia / He, Yu-Ying

    Toxicology and applied pharmacology

    2023  Volume 477, Page(s) 116688

    Abstract: Chemical modifications in messenger RNA (mRNA) regulate gene expression and play critical roles in stress responses and diseases. Recently we have shown that ... ...

    Abstract Chemical modifications in messenger RNA (mRNA) regulate gene expression and play critical roles in stress responses and diseases. Recently we have shown that N
    MeSH term(s) Animals ; Mice ; DNA Damage ; DNA Repair ; Ultraviolet Rays/adverse effects ; Skin Neoplasms/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2023-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 204477-8
    ISSN 1096-0333 ; 0041-008X
    ISSN (online) 1096-0333
    ISSN 0041-008X
    DOI 10.1016/j.taap.2023.116688
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    Zs.B 14: Show issues Location:
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  8. Article ; Online: Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system.

    Li, Meng / Ghonimy, Abdallah / Chen, Dai-Qiang / Li, Ji-Tao / He, Yu-Ying / López Greco, Laura Susana / Dyzenchauz, Fernando / Chang, Zhi-Qiang

    Applied microbiology and biotechnology

    2024  Volume 108, Issue 1, Page(s) 225

    Abstract: The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile ...

    Abstract The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. KEY POINTS: • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture.
    MeSH term(s) Animals ; Gastrointestinal Microbiome ; Agriculture ; Farms ; Microbiota ; Penaeidae ; Water
    Chemical Substances Water (059QF0KO0R)
    Language English
    Publishing date 2024-02-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-024-13046-0
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    Zs.A 2229: Show issues Location:
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  9. Article ; Online: Context-Dependent Roles of RNA Modifications in Stress Responses and Diseases.

    Wilkinson, Emma / Cui, Yan-Hong / He, Yu-Ying

    International journal of molecular sciences

    2021  Volume 22, Issue 4

    Abstract: RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in ... ...

    Abstract RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in cellular stress responses and disease pathogenesis. In response to stress, RNA modifications are mobilized to activate or inhibit the signaling pathways that combat stresses, including oxidative stress, hypoxia, therapeutic stress, metabolic stress, heat shock, DNA damage, and ER stress. The role of RNA modifications in response to these cellular stressors is context- and cell-type-dependent. Due to their pervasive roles in cell biology, RNA modifications have been implicated in the pathogenesis of different diseases, including cancer, neurologic and developmental disorders and diseases, and metabolic diseases. In this review, we aim to summarize the roles of RNA modifications in molecular and cellular stress responses and diseases.
    MeSH term(s) Animals ; DNA Damage ; Endoplasmic Reticulum Stress ; Heat-Shock Response ; Humans ; Hypoxia/metabolism ; Metabolic Diseases/genetics ; Metabolic Diseases/metabolism ; Neoplasms/genetics ; Neoplasms/metabolism ; Nervous System Diseases/genetics ; Nervous System Diseases/metabolism ; Oxidative Stress ; RNA/genetics ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; Stress, Physiological
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2021-02-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22041949
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  10. Article ; Online: Prevalence and contributing factors of impaired awareness of hypoglycemia in patients with type 2 diabetes: a meta-analysis.

    Li, Xiang-Ning / Kan, Yin-Shi / Liu, Hong-Yuan / Pang, Juan / He, Yu-Ying / Liu, Lin / Zou, Yan / Zhang, Ning / Zhang, Yu

    Acta diabetologica

    2023  Volume 60, Issue 9, Page(s) 1155–1169

    Abstract: Aims: To conduct a systematic review to summarize the definition, measurement tools, prevalence, and contributing factors of impaired awareness of hypoglycemia (IAH) in type 2 diabetes mellitus (T2DM).: Methods: A reproducible search strategy was ... ...

    Abstract Aims: To conduct a systematic review to summarize the definition, measurement tools, prevalence, and contributing factors of impaired awareness of hypoglycemia (IAH) in type 2 diabetes mellitus (T2DM).
    Methods: A reproducible search strategy was used to identify factors affecting IAH in T2DM in PubMed, MEDLINE, EMBASE, Cochrane, PsycINFO, and CINAHL from inception until 2022. Literature screening, quality evaluation, and information extraction were performed independently by 2 investigators. A meta-analysis of prevalence was performed using Stata 17.0.
    Results: The pooled prevalence of IAH in patients with T2DM was 22% (95%CI:14-29%). Measurement tools included the Gold score, Clarke's questionnaire, and the Pedersen-Bjergaard scale. IAH in T2DM was associated with sociodemographic factors (age, BMI, ethnicity, marital status, education level, and type of pharmacy patients visited), clinical disease factors (disease duration, HbAlc, complications, insulin therapy regimen, sulfonylureas use, and the frequency and severity of hypoglycemia), and behavior and lifestyle (smoking and medication adherence).
    Conclusion: The study found a high prevalence of IAH in T2DM, with an increased risk of severe hypoglycemia, suggesting that medical workers should take targeted measures to address sociodemographic factors, clinical disease, and behavior and lifestyle to reduce IAH in T2DM and thus reduce hypoglycemia in patients.
    MeSH term(s) Humans ; Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/drug therapy ; Diabetes Mellitus, Type 2/epidemiology ; Diabetes Mellitus, Type 1/complications ; Prevalence ; Hypoglycemia/epidemiology ; Hypoglycemia/etiology ; Hypoglycemia/diagnosis ; Insulin/therapeutic use ; Hypoglycemic Agents/adverse effects
    Chemical Substances Insulin ; Hypoglycemic Agents
    Language English
    Publishing date 2023-05-18
    Publishing country Germany
    Document type Systematic Review ; Meta-Analysis ; Journal Article ; Review
    ZDB-ID 1097676-0
    ISSN 1432-5233 ; 0940-5429
    ISSN (online) 1432-5233
    ISSN 0940-5429
    DOI 10.1007/s00592-023-02102-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 611: Show issues Location:
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