The Experts below are selected from a list of 39 Experts worldwide ranked by ideXlab platform

Oliver Mühlemann - One of the best experts on this subject based on the ideXlab platform.

  • alternative splicing induced by nonsense mutations in the immunoglobulin mu VDJ Exon is independent of truncation of the open reading frame
    RNA, 2005
    Co-Authors: Marc Bühler, Oliver Mühlemann
    Abstract:

    In addition to triggering nonsense-mediated mRNA decay (NMD), premature translation-termination codons (PTCs) frequently induce alternative splicing, an observation referred to as nonsense-associated alternative splicing (NAS). In many cases, NAS is induced because the nonsense mutation alters a splicing signal, such as inactivating an Exonic splicing enhancer. However, for a few genes, NAS was reported to be PTC specific, implying that a translation signal could influence splicing. Here, we investigated whether production of a previously undetected alternatively spliced transcript from immunoglobulin mu (Ig-mu) depends on premature termination of the open reading frame. We show that PTCs at different positions in the VDJ Exon of an Ig-mu minigene activate usage of an alternative 3' splice site, generating an alternative transcript that lacks the initial PTC and a previously identified NMD-promoting element (NPE), but contains new PTCs because of a frame shift. Corroborating the importance of the NPE for maximal NMD response, the alternative transcript is only moderately down-regulated by NMD. We further demonstrate that NAS of Ig-mu minigene transcripts is not PTC specific. This finding, together with our results that contradict the previously reported frame dependence of TCR-beta NAS, challenges the idea that cells might possess mechanisms that would allow regulation of splice site selection in response to premature termination of the ORF.

  • Alternative splicing induced by nonsense mutations in the immunoglobulin mu VDJ Exon is independent of truncation of the open reading frame.
    RNA, 2004
    Co-Authors: Marc Bühler, Oliver Mühlemann
    Abstract:

    In addition to triggering nonsense-mediated mRNA decay (NMD), premature translation-termination codons (PTCs) frequently induce alternative splicing, an observation referred to as nonsense-associated alternative splicing (NAS). In many cases, NAS is induced because the nonsense mutation alters a splicing signal, such as inactivating an Exonic splicing enhancer. However, for a few genes, NAS was reported to be PTC specific, implying that a translation signal could influence splicing. Here, we investigated whether production of a previously undetected alternatively spliced transcript from immunoglobulin μ (Ig-μ) depends on premature termination of the open reading frame. We show that PTCs at different positions in the VDJ Exon of an Ig-μ minigene activate usage of an alternative 3′ splice site, generating an alternative transcript that lacks the initial PTC and a previously identified NMD-promoting element (NPE), but contains new PTCs because of a frame shift. Corroborating the importance of the NPE for maximal NMD response, the alternative transcript is only moderately down-regulated by NMD. We further demonstrate that NAS of Ig-μ minigene transcripts is not PTC specific. This finding, together with our results that contradict the previously reported frame dependence of TCR-β NAS, challenges the idea that cells might possess mechanisms that would allow regulation of splice site selection in response to premature termination of the ORF.

  • Efficient downregulation of immunoglobulin μ mRNA with premature translation-termination codons requires the 5'-half of the VDJ Exon
    Nucleic Acids Research, 2004
    Co-Authors: Marc Bühler, Alexandra Paillusson, Oliver Mühlemann
    Abstract:

    Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V–D junction in the VDJ Exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (

  • efficient downregulation of immunoglobulin μ mrna with premature translation termination codons requires the 5 half of the VDJ Exon
    Nucleic Acids Research, 2004
    Co-Authors: Marc Bühler, Alexandra Paillusson, Oliver Mühlemann
    Abstract:

    Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V–D junction in the VDJ Exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (<50 nt from the 3′-most 5′ splice site) still resulted in reduced mRNA levels. Using a set of hybrid constructs comprised of Ig-μ and an inefficient substrate for NMD, we identified a 177 nt long element in the V segment that is necessary for efficient downregulation of PTC-containing hybrid transcripts. Moreover, deletion of this NMD-promoting element from the Ig-μ minigene results in loss of strong NMD.

Marc Bühler - One of the best experts on this subject based on the ideXlab platform.

  • alternative splicing induced by nonsense mutations in the immunoglobulin mu VDJ Exon is independent of truncation of the open reading frame
    RNA, 2005
    Co-Authors: Marc Bühler, Oliver Mühlemann
    Abstract:

    In addition to triggering nonsense-mediated mRNA decay (NMD), premature translation-termination codons (PTCs) frequently induce alternative splicing, an observation referred to as nonsense-associated alternative splicing (NAS). In many cases, NAS is induced because the nonsense mutation alters a splicing signal, such as inactivating an Exonic splicing enhancer. However, for a few genes, NAS was reported to be PTC specific, implying that a translation signal could influence splicing. Here, we investigated whether production of a previously undetected alternatively spliced transcript from immunoglobulin mu (Ig-mu) depends on premature termination of the open reading frame. We show that PTCs at different positions in the VDJ Exon of an Ig-mu minigene activate usage of an alternative 3' splice site, generating an alternative transcript that lacks the initial PTC and a previously identified NMD-promoting element (NPE), but contains new PTCs because of a frame shift. Corroborating the importance of the NPE for maximal NMD response, the alternative transcript is only moderately down-regulated by NMD. We further demonstrate that NAS of Ig-mu minigene transcripts is not PTC specific. This finding, together with our results that contradict the previously reported frame dependence of TCR-beta NAS, challenges the idea that cells might possess mechanisms that would allow regulation of splice site selection in response to premature termination of the ORF.

  • Alternative splicing induced by nonsense mutations in the immunoglobulin mu VDJ Exon is independent of truncation of the open reading frame.
    RNA, 2004
    Co-Authors: Marc Bühler, Oliver Mühlemann
    Abstract:

    In addition to triggering nonsense-mediated mRNA decay (NMD), premature translation-termination codons (PTCs) frequently induce alternative splicing, an observation referred to as nonsense-associated alternative splicing (NAS). In many cases, NAS is induced because the nonsense mutation alters a splicing signal, such as inactivating an Exonic splicing enhancer. However, for a few genes, NAS was reported to be PTC specific, implying that a translation signal could influence splicing. Here, we investigated whether production of a previously undetected alternatively spliced transcript from immunoglobulin μ (Ig-μ) depends on premature termination of the open reading frame. We show that PTCs at different positions in the VDJ Exon of an Ig-μ minigene activate usage of an alternative 3′ splice site, generating an alternative transcript that lacks the initial PTC and a previously identified NMD-promoting element (NPE), but contains new PTCs because of a frame shift. Corroborating the importance of the NPE for maximal NMD response, the alternative transcript is only moderately down-regulated by NMD. We further demonstrate that NAS of Ig-μ minigene transcripts is not PTC specific. This finding, together with our results that contradict the previously reported frame dependence of TCR-β NAS, challenges the idea that cells might possess mechanisms that would allow regulation of splice site selection in response to premature termination of the ORF.

  • Efficient downregulation of immunoglobulin μ mRNA with premature translation-termination codons requires the 5'-half of the VDJ Exon
    Nucleic Acids Research, 2004
    Co-Authors: Marc Bühler, Alexandra Paillusson, Oliver Mühlemann
    Abstract:

    Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V–D junction in the VDJ Exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (

  • efficient downregulation of immunoglobulin μ mrna with premature translation termination codons requires the 5 half of the VDJ Exon
    Nucleic Acids Research, 2004
    Co-Authors: Marc Bühler, Alexandra Paillusson, Oliver Mühlemann
    Abstract:

    Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V–D junction in the VDJ Exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (<50 nt from the 3′-most 5′ splice site) still resulted in reduced mRNA levels. Using a set of hybrid constructs comprised of Ig-μ and an inefficient substrate for NMD, we identified a 177 nt long element in the V segment that is necessary for efficient downregulation of PTC-containing hybrid transcripts. Moreover, deletion of this NMD-promoting element from the Ig-μ minigene results in loss of strong NMD.

Alexandra Paillusson - One of the best experts on this subject based on the ideXlab platform.

  • Efficient downregulation of immunoglobulin μ mRNA with premature translation-termination codons requires the 5'-half of the VDJ Exon
    Nucleic Acids Research, 2004
    Co-Authors: Marc Bühler, Alexandra Paillusson, Oliver Mühlemann
    Abstract:

    Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V–D junction in the VDJ Exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (

  • efficient downregulation of immunoglobulin μ mrna with premature translation termination codons requires the 5 half of the VDJ Exon
    Nucleic Acids Research, 2004
    Co-Authors: Marc Bühler, Alexandra Paillusson, Oliver Mühlemann
    Abstract:

    Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V–D junction in the VDJ Exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (<50 nt from the 3′-most 5′ splice site) still resulted in reduced mRNA levels. Using a set of hybrid constructs comprised of Ig-μ and an inefficient substrate for NMD, we identified a 177 nt long element in the V segment that is necessary for efficient downregulation of PTC-containing hybrid transcripts. Moreover, deletion of this NMD-promoting element from the Ig-μ minigene results in loss of strong NMD.

Miles F. Wilkinson - One of the best experts on this subject based on the ideXlab platform.

  • T-cell receptor sequences that elicit strong down-regulation of premature termination codon-bearing transcripts
    The EMBO Journal, 2002
    Co-Authors: Jayanthi Gudikote, Miles F. Wilkinson
    Abstract:

    The nonsense-mediated decay (NMD) RNA surveillance pathway detects and degrades mRNAs containing premature termination codons (PTCs). T-cell receptor (TCR) and immunoglobulin transcripts, which commonly harbor PTCs as a result of programmed DNA rearrangement during normal development, are down-regulated much more than other known mammalian gene transcripts in response to nonsense codons. Here, we demonstrate that this is not because of promoter or cell type but instead is directed by regulatory sequences within the rearranging VDJ Exon and immediately flanking intron sequences of a Vβ8.1 TCR-β gene. Insertion of these sequences into a heterologous gene elicited strong down-regulation (>30-fold) in response to PTCs, indicating that this region is sufficient to trigger robust down-regulation. The rearranging Vβ5.1 Exon and the flanking intron sequences from another member of the TCR-β family also triggered strong down-regulation, suggesting that down-regulatory-promoting elements are a conserved feature of TCR genes. Importantly, we found that the Vβ8.1 down-regulatory-promoting element was position dependent, such that it failed to function when positioned downstream of a PTC. To our knowledge, this is the first class of down-regulatory elements identified that act upstream of nonsense codons.

  • T-cell receptor sequences that elicit strong down-regulation of premature termination codon-bearing transcripts.
    The EMBO journal, 2002
    Co-Authors: Jayanthi Gudikote, Miles F. Wilkinson
    Abstract:

    The nonsense-mediated decay (NMD) RNA surveillance pathway detects and degrades mRNAs containing premature termination codons (PTCs). T-cell receptor (TCR) and immunoglobulin transcripts, which commonly harbor PTCs as a result of programmed DNA rearrangement during normal development, are down-regulated much more than other known mammalian gene transcripts in response to nonsense codons. Here, we demonstrate that this is not because of promoter or cell type but instead is directed by regulatory sequences within the rearranging VDJ Exon and immediately flanking intron sequences of a Vbeta8.1 TCR-beta gene. Insertion of these sequences into a heterologous gene elicited strong down-regulation (>30-fold) in response to PTCs, indicating that this region is sufficient to trigger robust down-regulation. The rearranging Vbeta5.1 Exon and the flanking intron sequences from another member of the TCR-beta family also triggered strong down-regulation, suggesting that down-regulatory-promoting elements are a conserved feature of TCR genes. Importantly, we found that the Vbeta8.1 down-regulatory-promoting element was position dependent, such that it failed to function when positioned downstream of a PTC. To our knowledge, this is the first class of down-regulatory elements identified that act upstream of nonsense codons.

Jayanthi Gudikote - One of the best experts on this subject based on the ideXlab platform.

  • T-cell receptor sequences that elicit strong down-regulation of premature termination codon-bearing transcripts
    The EMBO Journal, 2002
    Co-Authors: Jayanthi Gudikote, Miles F. Wilkinson
    Abstract:

    The nonsense-mediated decay (NMD) RNA surveillance pathway detects and degrades mRNAs containing premature termination codons (PTCs). T-cell receptor (TCR) and immunoglobulin transcripts, which commonly harbor PTCs as a result of programmed DNA rearrangement during normal development, are down-regulated much more than other known mammalian gene transcripts in response to nonsense codons. Here, we demonstrate that this is not because of promoter or cell type but instead is directed by regulatory sequences within the rearranging VDJ Exon and immediately flanking intron sequences of a Vβ8.1 TCR-β gene. Insertion of these sequences into a heterologous gene elicited strong down-regulation (>30-fold) in response to PTCs, indicating that this region is sufficient to trigger robust down-regulation. The rearranging Vβ5.1 Exon and the flanking intron sequences from another member of the TCR-β family also triggered strong down-regulation, suggesting that down-regulatory-promoting elements are a conserved feature of TCR genes. Importantly, we found that the Vβ8.1 down-regulatory-promoting element was position dependent, such that it failed to function when positioned downstream of a PTC. To our knowledge, this is the first class of down-regulatory elements identified that act upstream of nonsense codons.

  • T-cell receptor sequences that elicit strong down-regulation of premature termination codon-bearing transcripts.
    The EMBO journal, 2002
    Co-Authors: Jayanthi Gudikote, Miles F. Wilkinson
    Abstract:

    The nonsense-mediated decay (NMD) RNA surveillance pathway detects and degrades mRNAs containing premature termination codons (PTCs). T-cell receptor (TCR) and immunoglobulin transcripts, which commonly harbor PTCs as a result of programmed DNA rearrangement during normal development, are down-regulated much more than other known mammalian gene transcripts in response to nonsense codons. Here, we demonstrate that this is not because of promoter or cell type but instead is directed by regulatory sequences within the rearranging VDJ Exon and immediately flanking intron sequences of a Vbeta8.1 TCR-beta gene. Insertion of these sequences into a heterologous gene elicited strong down-regulation (>30-fold) in response to PTCs, indicating that this region is sufficient to trigger robust down-regulation. The rearranging Vbeta5.1 Exon and the flanking intron sequences from another member of the TCR-beta family also triggered strong down-regulation, suggesting that down-regulatory-promoting elements are a conserved feature of TCR genes. Importantly, we found that the Vbeta8.1 down-regulatory-promoting element was position dependent, such that it failed to function when positioned downstream of a PTC. To our knowledge, this is the first class of down-regulatory elements identified that act upstream of nonsense codons.