LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 5 of total 5

Search options

  1. Article ; 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  Volume 51, Issue 12, Page(s) 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 term(s) 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
    Chemical Substances Glutamates ; Lysine (K3Z4F929H6) ; Pyruvate Kinase (EC 2.7.1.40)
    Language English
    Publishing date 2023-05-24
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; 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  Volume 21, Issue 1, Page(s) 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 term(s) 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
    Chemical Substances RNA, Ribosomal ; RNA-Binding Proteins ; Retroelements ; RNA (63231-63-0)
    Language English
    Publishing date 2020-04-06
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article: 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.
    Keywords RNA-binding proteins ; crosslinking ; mechanism of action ; messenger RNA ; models ; precipitin tests ; ribosomal RNA ; spliceosomes
    Language English
    Dates of publication 2020-12
    Size p. 90.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6906
    ISSN (online) 1474-760X
    ISSN 1465-6906
    DOI 10.1186/s13059-020-01982-9
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; 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  Volume 589, Issue 7842, Page(s) E5

    Language English
    Publishing date 2021-01-05
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: 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)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; 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  Volume 583, Issue 7818, Page(s) 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 term(s) 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
    Chemical Substances Chromatin ; RNA, Messenger ; RNA-Binding Proteins
    Keywords covid19
    Language English
    Publishing date 2020-07-29
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: 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)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top