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  1. Book: Chimeric RNA

    Li, Hui / Elfman, Justin

    methods and protocols

    (Methods in molecular biology ; 2079 ; Springer protocols)

    2020  

    Author's details edited by Hui Li, Justin Elfman
    Series title Methods in molecular biology ; 2079
    Springer protocols
    Collection
    Language English
    Size xii, 262 Seiten, Illustrationen
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT020305969
    ISBN 978-1-4939-9903-3 ; 9781493999040 ; 1-4939-9903-6 ; 1493999044
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -2079- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction.

    Elfman, Justin / Goins, Lynette / Heller, Tessa / Singh, Sandeep / Wang, Yuh-Hwa / Li, Hui

    Nucleic acids research

    2024  Volume 52, Issue 8, Page(s) 4409–4421

    Abstract: Gene fusions and their chimeric products are commonly linked with cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. Large-scale efforts to annotate structural variations have identified gene fusions ... ...

    Abstract Gene fusions and their chimeric products are commonly linked with cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. Large-scale efforts to annotate structural variations have identified gene fusions capable of generating chimeric transcripts even in normal tissues. In this study, we present a bottom-up approach targeting population-specific chimeric RNAs, identifying 58 such instances in the GTEx cohort, including notable cases such as SUZ12P1-CRLF3, TFG-ADGRG7 and TRPM4-PPFIA3, which possess distinct patterns across different ancestry groups. We provide direct evidence for an additional 29 polymorphic chimeric RNAs with associated structural variants, revealing 13 novel rare structural variants. Additionally, we utilize the All of Us dataset and a large cohort of clinical samples to characterize the association of the SUZ12P1-CRLF3-causing variant with patient phenotypes. Our study showcases SUZ12P1-CRLF3 as a representative example, illustrating the identification of elusive structural variants by focusing on those producing population-specific fusion transcripts.
    MeSH term(s) Humans ; Gene Fusion ; Neoplasm Proteins/genetics ; Polymorphism, Genetic ; Oncogene Proteins, Fusion/genetics ; Polycomb Repressive Complex 2/genetics ; Polycomb Repressive Complex 2/metabolism ; RNA/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism ; TRPM Cation Channels/genetics ; Neoplasms/genetics
    Chemical Substances Neoplasm Proteins ; Oncogene Proteins, Fusion ; SUZ12 protein, human ; Polycomb Repressive Complex 2 (EC 2.1.1.43) ; RNA (63231-63-0) ; Transcription Factors ; TRPM Cation Channels
    Language English
    Publishing date 2024-05-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae258
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Detection and Measurement of Chimeric RNAs by RT-PCR.

    Elfman, Justin / Li, Hui

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

    2019  Volume 2079, Page(s) 83–94

    Abstract: Reverse-transcription polymerase chain reaction (RT-PCR) is a powerful combination of assays useful in detection and measurement of expressed RNA transcripts. RT-PCR consists of RNA isolation and reverse transcription into complementary DNA (cDNA), which ...

    Abstract Reverse-transcription polymerase chain reaction (RT-PCR) is a powerful combination of assays useful in detection and measurement of expressed RNA transcripts. RT-PCR consists of RNA isolation and reverse transcription into complementary DNA (cDNA), which can then be used as input to a variety of PCR-based procedures such as standard PCR, real-time or quantitative PCR (qPCR or qRT-PCR), or TaqMan PCR procedures. These assays are useful in detection of chimeric transcripts, especially when careful consideration is applied to experimental design. In this chapter, we provide guidelines and procedures for use of RT-PCR in detection and measurement of chimeric RNA expression.
    MeSH term(s) Gene Fusion ; Gene Rearrangement ; RNA/genetics ; Real-Time Polymerase Chain Reaction/methods ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Sensitivity and Specificity
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2019-11-11
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9904-0_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction.

    Elfman, Justin / Goins, Lynette / Heller, Tessa / Singh, Sandeep / Wang, Yuh-Hwa / Li, Hui

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have ...

    Abstract Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, including
    Key points: - Discovery of 57 polymorphic chimeric RNAs- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions.
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.02.526864
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Chimeric RNA in Cancer and Stem Cell Differentiation.

    Elfman, Justin / Li, Hui

    Stem cells international

    2018  Volume 2018, Page(s) 3178789

    Abstract: Gene fusions are considered hallmarks of cancer which can be produced by chromosomal rearrangements. These DNA-level fusion events may result in the expression of chimeric RNAs; however, chimeric RNAs can be also produced by intergenic splicing events. ... ...

    Abstract Gene fusions are considered hallmarks of cancer which can be produced by chromosomal rearrangements. These DNA-level fusion events may result in the expression of chimeric RNAs; however, chimeric RNAs can be also produced by intergenic splicing events. Chimeric transcripts created by the latter mechanism are regulated at the transcriptional level and thus present additional modes of action and regulation. They have demonstrated importance in normal cell physiology, and their dysregulation can induce oncogenesis and impact cell differentiation. In this review, we outline proven mechanisms through which intergenically spliced chimeric RNAs are involved in carcinogenesis. We highlight their similarity to canonical chimeric RNAs resulting from gene fusions as well as their unique qualities. Additionally, we review known roles of chimeric RNA in cell differentiation and propose means through which chimeric RNAs may be valuable as stage-specific markers or as targets for expression profiling.
    Language English
    Publishing date 2018-10-28
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2573856-2
    ISSN 1687-9678 ; 1687-966X
    ISSN (online) 1687-9678
    ISSN 1687-966X
    DOI 10.1155/2018/3178789
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The relationship between chimeric RNAs and gene fusions: Potential implications of reciprocity in cancer.

    Elfman, Justin / Pham, Lam-Phong / Li, Hui

    Journal of genetics and genomics = Yi chuan xue bao

    2020  Volume 47, Issue 7, Page(s) 341–348

    MeSH term(s) Co-Repressor Proteins/genetics ; DNA-Binding Proteins/genetics ; Gene Fusion/genetics ; Humans ; Neoplasm Proteins/genetics ; Neoplasms/genetics ; Neoplasms/pathology ; Oncogene Proteins, Fusion/genetics ; Paired Box Transcription Factors/genetics ; RNA/genetics ; Transcription Factors/genetics
    Chemical Substances Co-Repressor Proteins ; DNA-Binding Proteins ; JAZF1 protein, human ; Neoplasm Proteins ; Oncogene Proteins, Fusion ; PAX3-FOXO1A fusion protein, human ; Paired Box Transcription Factors ; SUZ12 protein, human ; Transcription Factors ; RNA (63231-63-0)
    Language English
    Publishing date 2020-06-14
    Publishing country China
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2374568-X
    ISSN 1873-5533 ; 1673-8527
    ISSN (online) 1873-5533
    ISSN 1673-8527
    DOI 10.1016/j.jgg.2020.04.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: RNase Protection Assay.

    Zhao, Jianzhu / Tang, Jun / Elfman, Justin / Li, Hui

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

    2019  Volume 2079, Page(s) 109–116

    Abstract: Unbound, single-stranded RNA can be digested by RNase (A or T1) to ribonucleotides, whereas double-stranded RNA is not digested by RNase. Based on this principle, the RNase Protection Assay (RPA) is used to validate chimeric RNAs. Importantly, this assay ...

    Abstract Unbound, single-stranded RNA can be digested by RNase (A or T1) to ribonucleotides, whereas double-stranded RNA is not digested by RNase. Based on this principle, the RNase Protection Assay (RPA) is used to validate chimeric RNAs. Importantly, this assay does not employ reverse transcription (RT), thus avoiding potential false-positive results which could occur during RT such as template-switching. We first generate RNA probes with
    MeSH term(s) Autoradiography ; Binding Sites ; Electrophoresis, Polyacrylamide Gel/methods ; Isotope Labeling ; Molecular Probes ; Nucleic Acid Hybridization ; Protein Binding ; RNA/chemistry ; RNA/metabolism ; RNA, Double-Stranded ; RNA-Binding Proteins/metabolism ; Ribonucleases
    Chemical Substances Molecular Probes ; RNA, Double-Stranded ; RNA-Binding Proteins ; RNA (63231-63-0) ; Ribonucleases (EC 3.1.-)
    Language English
    Publishing date 2019-11-11
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9904-0_8
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  8. Article: UBA1-CDK16

    Shi, Xinrui / Facemire, Loryn / Singh, Sandeep / Kumar, Shailesh / Cornelison, Robert / Liang, Chen / Qin, Fujun / Liu, Aiqun / Lin, Shitong / Tang, Yue / Elfman, Justin / Manley, Thomas / Bullock, Timothy / Haverstick, Doris M / Wu, Peng / Li, Hui

    bioRxiv : the preprint server for biology

    2024  

    Abstract: RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing ... ...

    Abstract RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing a large set of RNA-Seq data and validating results in over 1,200 blood samples, we identified
    Language English
    Publishing date 2024-02-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.13.580120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The landscape of chimeric RNAs in non-diseased tissues and cells.

    Singh, Sandeep / Qin, Fujun / Kumar, Shailesh / Elfman, Justin / Lin, Emily / Pham, Lam-Phong / Yang, Amy / Li, Hui

    Nucleic acids research

    2020  Volume 48, Issue 4, Page(s) 1764–1778

    Abstract: Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non- ... ...

    Abstract Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.
    MeSH term(s) Biomarkers ; Chimera/classification ; Chimera/genetics ; Humans ; Neoplasms/genetics ; RNA/chemistry ; RNA/classification ; RNA/genetics
    Chemical Substances Biomarkers ; RNA (63231-63-0)
    Language English
    Publishing date 2020-01-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkz1223
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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