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  1. Artikel ; Online: Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.

    Kejiou, Nevraj S / Ilan, Lena / Aigner, Stefan / Luo, Enching / Tonn, Tori / Ozadam, Hakan / Lee, Muyoung / Cole, Gregory B / Rabano, Ines / Rajakulendran, Nishani / Yee, Brian A / Najafabadi, Hamed S / Moraes, Trevor F / Angers, Stephane / Yeo, Gene W / Cenik, Can / Palazzo, Alexander F

    Nucleic acids research

    2023  Band 51, Heft 12, Seite(n) 6461–6478

    Abstract: In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey ...

    Abstract In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we identified the glycolytic enzyme Pyruvate Kinase M (PKM) as a cytosolic (i.e. ER-excluded) polysome interactor and investigated how it influences mRNA translation. We discovered that the PKM-polysome interaction is directly regulated by ADP levels-providing a link between carbohydrate metabolism and mRNA translation. By performing enhanced crosslinking immunoprecipitation-sequencing (eCLIP-seq), we found that PKM crosslinks to mRNA sequences that are immediately downstream of regions that encode lysine- and glutamate-enriched tracts. Using ribosome footprint protection sequencing, we found that PKM binding to ribosomes causes translational stalling near lysine and glutamate encoding sequences. Lastly, we observed that PKM recruitment to polysomes is dependent on poly-ADP ribosylation activity (PARylation)-and may depend on co-translational PARylation of lysine and glutamate residues of nascent polypeptide chains. Overall, our study uncovers a novel role for PKM in post-transcriptional gene regulation, linking cellular metabolism and mRNA translation.
    Mesh-Begriff(e) Humans ; Glutamates/analysis ; Glutamates/genetics ; Glutamates/metabolism ; Lysine/metabolism ; Poly ADP Ribosylation ; Protein Biosynthesis ; Proteomics ; Pyruvate Kinase/genetics ; Pyruvate Kinase/analysis ; Pyruvate Kinase/metabolism ; Ribosomes/metabolism
    Chemische Substanzen Glutamates ; Lysine (K3Z4F929H6) ; Pyruvate Kinase (EC 2.7.1.40)
    Sprache Englisch
    Erscheinungsdatum 2023-05-24
    Erscheinungsland England
    Dokumenttyp Journal Article ; 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/gkad440
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

    Van Nostrand, Eric L / Pratt, Gabriel A / Yee, Brian A / Wheeler, Emily C / Blue, Steven M / Mueller, Jasmine / Park, Samuel S / Garcia, Keri E / Gelboin-Burkhart, Chelsea / Nguyen, Thai B / Rabano, Ines / Stanton, Rebecca / Sundararaman, Balaji / Wang, Ruth / Fu, Xiang-Dong / Graveley, Brenton R / Yeo, Gene W

    Genome biology

    2020  Band 21, Heft 1, Seite(n) 90

    Abstract: Background: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but ... ...

    Abstract Background: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types.
    Results: Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3' splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs.
    Conclusions: This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.
    Mesh-Begriff(e) Binding Sites ; Hep G2 Cells ; Humans ; Immunoprecipitation ; Introns ; K562 Cells ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA, Ribosomal/metabolism ; RNA-Binding Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Spliceosomes/metabolism
    Chemische Substanzen RNA, Ribosomal ; RNA-Binding Proteins ; Retroelements ; RNA (63231-63-0)
    Sprache Englisch
    Erscheinungsdatum 2020-04-06
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-020-01982-9
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

    Van Nostrand, Eric L / Pratt, Gabriel A / Yee, Brian A / Wheeler, Emily C / Blue, Steven M / Mueller, Jasmine / Park, Samuel S / Garcia, Keri E / Gelboin-Burkhart, Chelsea / Nguyen, Thai B / Rabano, Ines / Stanton, Rebecca / Sundararaman, Balaji / Wang, Ruth / Fu, Xiang-Dong / Graveley, Brenton R / Yeo, Gene W

    Genome biology. 2020 Dec., v. 21, no. 1

    2020  

    Abstract: BACKGROUND: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but ... ...

    Abstract BACKGROUND: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types. RESULTS: Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3′ splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs. CONCLUSIONS: This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.
    Schlagwörter RNA-binding proteins ; crosslinking ; mechanism of action ; messenger RNA ; models ; precipitin tests ; ribosomal RNA ; spliceosomes
    Sprache Englisch
    Erscheinungsverlauf 2020-12
    Umfang p. 90.
    Erscheinungsort BioMed Central
    Dokumenttyp Artikel
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6906
    ISSN (online) 1474-760X
    ISSN 1465-6906
    DOI 10.1186/s13059-020-01982-9
    Datenquelle NAL Katalog (AGRICOLA)

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  4. Artikel ; Online: Author Correction: A large-scale binding and functional map of human RNA-binding proteins.

    Van Nostrand, Eric L / Freese, Peter / Pratt, Gabriel A / Wang, Xiaofeng / Wei, Xintao / Xiao, Rui / Blue, Steven M / Chen, Jia-Yu / Cody, Neal A L / Dominguez, Daniel / Olson, Sara / Sundararaman, Balaji / Zhan, Lijun / Bazile, Cassandra / Bouvrette, Louis Philip Benoit / Bergalet, Julie / Duff, Michael O / Garcia, Keri E / Gelboin-Burkhart, Chelsea /
    Hochman, Myles / Lambert, Nicole J / Li, Hairi / McGurk, Michael P / Nguyen, Thai B / Palden, Tsultrim / Rabano, Ines / Sathe, Shashank / Stanton, Rebecca / Su, Amanda / Wang, Ruth / Yee, Brian A / Zhou, Bing / Louie, Ashley L / Aigner, Stefan / Fu, Xiang-Dong / Lécuyer, Eric / Burge, Christopher B / Graveley, Brenton R / Yeo, Gene W

    Nature

    2021  Band 589, Heft 7842, Seite(n) E5

    Sprache Englisch
    Erscheinungsdatum 2021-01-05
    Erscheinungsland England
    Dokumenttyp Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-03067-w
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: A large-scale binding and functional map of human RNA-binding proteins.

    Van Nostrand, Eric L / Freese, Peter / Pratt, Gabriel A / Wang, Xiaofeng / Wei, Xintao / Xiao, Rui / Blue, Steven M / Chen, Jia-Yu / Cody, Neal A L / Dominguez, Daniel / Olson, Sara / Sundararaman, Balaji / Zhan, Lijun / Bazile, Cassandra / Bouvrette, Louis Philip Benoit / Bergalet, Julie / Duff, Michael O / Garcia, Keri E / Gelboin-Burkhart, Chelsea /
    Hochman, Myles / Lambert, Nicole J / Li, Hairi / McGurk, Michael P / Nguyen, Thai B / Palden, Tsultrim / Rabano, Ines / Sathe, Shashank / Stanton, Rebecca / Su, Amanda / Wang, Ruth / Yee, Brian A / Zhou, Bing / Louie, Ashley L / Aigner, Stefan / Fu, Xiang-Dong / Lécuyer, Eric / Burge, Christopher B / Graveley, Brenton R / Yeo, Gene W

    Nature

    2020  Band 583, Heft 7818, Seite(n) 711–719

    Abstract: Many proteins regulate the expression of genes by binding to specific regions encoded in the ... ...

    Abstract Many proteins regulate the expression of genes by binding to specific regions encoded in the genome
    Mesh-Begriff(e) Alternative Splicing/genetics ; Base Sequence ; Binding Sites ; Cell Line ; Chromatin/genetics ; Chromatin/metabolism ; Databases, Genetic ; Female ; Gene Knockdown Techniques ; Humans ; Intracellular Space/genetics ; Male ; Protein Binding ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA-Binding Proteins/chemistry ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Substrate Specificity ; Transcriptome/genetics
    Chemische Substanzen Chromatin ; RNA, Messenger ; RNA-Binding Proteins
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-07-29
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-2077-3
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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