The Experts below are selected from a list of 210 Experts worldwide ranked by ideXlab platform
Jonathan S Weissman - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide annotation and quantitation of translation by ribosome profiling.
Current protocols in molecular biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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Current Protocols in Molecular Biology - Genome‐Wide Annotation and Quantitation of Translation by Ribosome Profiling
Current Protocols in Molecular Biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Nature Protocols, 2012Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. In addition, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pretreating cells with Harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5–7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4–5 days.
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ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
Cell, 2011Co-Authors: Nicholas T Ingolia, Liana F Lareau, Jonathan S WeissmanAbstract:The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of Harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.
Nicholas T Ingolia - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide annotation and quantitation of translation by ribosome profiling.
Current protocols in molecular biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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Current Protocols in Molecular Biology - Genome‐Wide Annotation and Quantitation of Translation by Ribosome Profiling
Current Protocols in Molecular Biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Nature Protocols, 2012Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. In addition, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pretreating cells with Harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5–7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4–5 days.
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ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
Cell, 2011Co-Authors: Nicholas T Ingolia, Liana F Lareau, Jonathan S WeissmanAbstract:The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of Harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.
Changling Niu - One of the best experts on this subject based on the ideXlab platform.
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Construction of Chiral Tertiary Alcohol Stereocenters via the [2,3]- Meisenheimer Rearrangement: Enantioselective Synthesis of the Side-Chain Acids of HomoHarringtonine and Harringtonine
2013Co-Authors: Hua Yang, Moran Sun, Shuguang Zhao, Ming Zhu, Yangla Xie, Changling NiuAbstract:For the first time, the [2,3]-Meisenheimer rearrangement has been developed into a general strategy for the construction of chiral tertiary alcohols. The effectiveness and practicality of this methodology are illustrated by the successful synthesis of (R)-20 and (R)-30, the side chain acids of homoHarringtonine and Harringtonine, respectively
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Construction of chiral tertiary alcohol stereocenters via the [2,3]-Meisenheimer rearrangement: enantioselective synthesis of the side-chain acids of homoHarringtonine and Harringtonine.
The Journal of organic chemistry, 2012Co-Authors: Hua Yang, Moran Sun, Shuguang Zhao, Ming Zhu, Yangla Xie, Changling NiuAbstract:For the first time, the [2,3]-Meisenheimer rearrangement has been developed into a general strategy for the construction of chiral tertiary alcohols. The effectiveness and practicality of this methodology are illustrated by the successful synthesis of (R)-20 and (R)-30, the side chain acids of homoHarringtonine and Harringtonine, respectively.
Gloria A Brar - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide annotation and quantitation of translation by ribosome profiling.
Current protocols in molecular biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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Current Protocols in Molecular Biology - Genome‐Wide Annotation and Quantitation of Translation by Ribosome Profiling
Current Protocols in Molecular Biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Nature Protocols, 2012Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. In addition, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pretreating cells with Harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5–7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4–5 days.
Silvia Rouskin - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide annotation and quantitation of translation by ribosome profiling.
Current protocols in molecular biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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Current Protocols in Molecular Biology - Genome‐Wide Annotation and Quantitation of Translation by Ribosome Profiling
Current Protocols in Molecular Biology, 2013Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. This ribosome-profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with Harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days.
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The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Nature Protocols, 2012Co-Authors: Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M Mcgeachy, Jonathan S WeissmanAbstract:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. In addition, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pretreating cells with Harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5–7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4–5 days.
