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  1. Article ; Online: The dsRBP and Inactive Editor ADR-1 Utilizes dsRNA Binding to Regulate A-to-I RNA Editing across the C. elegans Transcriptome

    Michael C. Washburn / Boyko Kakaradov / Balaji Sundararaman / Emily Wheeler / Shawn Hoon / Gene W. Yeo / Heather A. Hundley

    Cell Reports, Vol 6, Iss 4, Pp 599-

    2014  Volume 607

    Abstract: Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the ... ...

    Abstract Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the theoretically catalytically inactive ADR-1. Using high-throughput RNA sequencing of wild-type and adr mutant worms, we expand the repertoire of C. elegans edited transcripts over 5-fold and confirm that ADR-2 is the only active deaminase in vivo. Despite lacking deaminase function, ADR-1 affects editing of over 60 adenosines within the 3′ UTRs of 16 different mRNAs. Furthermore, ADR-1 interacts directly with ADR-2 substrates, even in the absence of ADR-2, and mutations within its double-stranded RNA (dsRNA) binding domains abolish both binding and editing regulation. We conclude that ADR-1 acts as a major regulator of editing by binding ADR-2 substrates in vivo. These results raise the possibility that other dsRNA binding proteins, including the inactive human ADARs, regulate RNA editing through deaminase-independent mechanisms.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2014-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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

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

    Genome Biology, Vol 21, Iss 1, Pp 1-

    2020  Volume 26

    Abstract: 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 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 eCLIP ; CLIP-seq ; RNA binding protein ; RNA processing ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 004
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival

    Anne E. Conway / Eric L. Van Nostrand / Gabriel A. Pratt / Stefan Aigner / Melissa L. Wilbert / Balaji Sundararaman / Peter Freese / Nicole J. Lambert / Shashank Sathe / Tiffany Y. Liang / Anthony Essex / Severine Landais / Christopher B. Burge / D. Leanne Jones / Gene W. Yeo

    Cell Reports, Vol 15, Iss 3, Pp 666-

    2016  Volume 679

    Abstract: Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of ... ...

    Abstract Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region and binding site levels, IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3′ UTR-enriched targets. RNA Bind-N-seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and increase in cell death. For cell adhesion, we find IMP1 maintains levels of integrin mRNA specifically regulating RNA stability of ITGB5 in hPSCs. Additionally, we show that IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles.
    Keywords Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2016-04-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  4. Article ; Online: Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses

    Katannya Kapeli / Gabriel A. Pratt / Anthony Q. Vu / Kasey R. Hutt / Fernando J. Martinez / Balaji Sundararaman / Ranjan Batra / Peter Freese / Nicole J. Lambert / Stephanie C. Huelga / Seung J. Chun / Tiffany Y. Liang / Jeremy Chang / John P. Donohue / Lily Shiue / Jiayu Zhang / Haining Zhu / Franca Cambi / Edward Kasarskis /
    Shawn Hoon / Manuel Ares Jr. / Christopher B. Burge / John Ravits / Frank Rigo / Gene W. Yeo

    Nature Communications, Vol 7, Iss 1, Pp 1-

    2016  Volume 14

    Abstract: Abnormal functions of RNA-binding proteins TAF15, FUS and TDP43 are associated with amyotrophic lateral sclerosis. Here, Kapeli et al. characterize the RNA targets of TAF15 and identify points of convergence and divergence between the targets of TAF15, ... ...

    Abstract Abnormal functions of RNA-binding proteins TAF15, FUS and TDP43 are associated with amyotrophic lateral sclerosis. Here, Kapeli et al. characterize the RNA targets of TAF15 and identify points of convergence and divergence between the targets of TAF15, FUS and TDP43 in several neuronal systems.
    Keywords Science ; Q
    Language English
    Publishing date 2016-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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