Selective translational usage of TSS and core promoters revealed by translatome sequencing

Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and...
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Autor*in:	Li, Hua [verfasserIn] Bai, Ling Li, Hongmei Li, Xinhui Kang, Yani Zhang, Ningbo Sun, Jielin Shao, Zhifeng

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	CAGE Translatome sequencing TSS profiling Core promoter Polysome selection

Anmerkung:	© The Author(s). 2019

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 20(2019), 1 vom: 11. Apr.
Übergeordnetes Werk:	volume:20 ; year:2019 ; number:1 ; day:11 ; month:04

Links:	Volltext

DOI / URN:	10.1186/s12864-019-5650-0

Katalog-ID:	SPR027152804

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520			\|a Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression.
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700	1		\|a Shao, Zhifeng \|4 aut
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Indexfelder

author_variant	h l hl l b lb h l hl x l xl y k yk n z nz j s js z s zs
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publishDate	2019
allfields	10.1186/s12864-019-5650-0 doi (DE-627)SPR027152804 (SPR)s12864-019-5650-0-e DE-627 ger DE-627 rakwb eng Li, Hua verfasserin (orcid)0000-0003-2153-2500 aut Selective translational usage of TSS and core promoters revealed by translatome sequencing 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. CAGE (dpeaa)DE-He213 Translatome sequencing (dpeaa)DE-He213 TSS profiling (dpeaa)DE-He213 Core promoter (dpeaa)DE-He213 Polysome selection (dpeaa)DE-He213 Bai, Ling aut Li, Hongmei aut Li, Xinhui aut Kang, Yani aut Zhang, Ningbo aut Sun, Jielin aut Shao, Zhifeng aut Enthalten in BMC genomics London : BioMed Central, 2000 20(2019), 1 vom: 11. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:20 year:2019 number:1 day:11 month:04 https://dx.doi.org/10.1186/s12864-019-5650-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 11 04
spelling	10.1186/s12864-019-5650-0 doi (DE-627)SPR027152804 (SPR)s12864-019-5650-0-e DE-627 ger DE-627 rakwb eng Li, Hua verfasserin (orcid)0000-0003-2153-2500 aut Selective translational usage of TSS and core promoters revealed by translatome sequencing 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. CAGE (dpeaa)DE-He213 Translatome sequencing (dpeaa)DE-He213 TSS profiling (dpeaa)DE-He213 Core promoter (dpeaa)DE-He213 Polysome selection (dpeaa)DE-He213 Bai, Ling aut Li, Hongmei aut Li, Xinhui aut Kang, Yani aut Zhang, Ningbo aut Sun, Jielin aut Shao, Zhifeng aut Enthalten in BMC genomics London : BioMed Central, 2000 20(2019), 1 vom: 11. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:20 year:2019 number:1 day:11 month:04 https://dx.doi.org/10.1186/s12864-019-5650-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 11 04
allfields_unstemmed	10.1186/s12864-019-5650-0 doi (DE-627)SPR027152804 (SPR)s12864-019-5650-0-e DE-627 ger DE-627 rakwb eng Li, Hua verfasserin (orcid)0000-0003-2153-2500 aut Selective translational usage of TSS and core promoters revealed by translatome sequencing 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. CAGE (dpeaa)DE-He213 Translatome sequencing (dpeaa)DE-He213 TSS profiling (dpeaa)DE-He213 Core promoter (dpeaa)DE-He213 Polysome selection (dpeaa)DE-He213 Bai, Ling aut Li, Hongmei aut Li, Xinhui aut Kang, Yani aut Zhang, Ningbo aut Sun, Jielin aut Shao, Zhifeng aut Enthalten in BMC genomics London : BioMed Central, 2000 20(2019), 1 vom: 11. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:20 year:2019 number:1 day:11 month:04 https://dx.doi.org/10.1186/s12864-019-5650-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 11 04
allfieldsGer	10.1186/s12864-019-5650-0 doi (DE-627)SPR027152804 (SPR)s12864-019-5650-0-e DE-627 ger DE-627 rakwb eng Li, Hua verfasserin (orcid)0000-0003-2153-2500 aut Selective translational usage of TSS and core promoters revealed by translatome sequencing 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. CAGE (dpeaa)DE-He213 Translatome sequencing (dpeaa)DE-He213 TSS profiling (dpeaa)DE-He213 Core promoter (dpeaa)DE-He213 Polysome selection (dpeaa)DE-He213 Bai, Ling aut Li, Hongmei aut Li, Xinhui aut Kang, Yani aut Zhang, Ningbo aut Sun, Jielin aut Shao, Zhifeng aut Enthalten in BMC genomics London : BioMed Central, 2000 20(2019), 1 vom: 11. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:20 year:2019 number:1 day:11 month:04 https://dx.doi.org/10.1186/s12864-019-5650-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 11 04
allfieldsSound	10.1186/s12864-019-5650-0 doi (DE-627)SPR027152804 (SPR)s12864-019-5650-0-e DE-627 ger DE-627 rakwb eng Li, Hua verfasserin (orcid)0000-0003-2153-2500 aut Selective translational usage of TSS and core promoters revealed by translatome sequencing 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. CAGE (dpeaa)DE-He213 Translatome sequencing (dpeaa)DE-He213 TSS profiling (dpeaa)DE-He213 Core promoter (dpeaa)DE-He213 Polysome selection (dpeaa)DE-He213 Bai, Ling aut Li, Hongmei aut Li, Xinhui aut Kang, Yani aut Zhang, Ningbo aut Sun, Jielin aut Shao, Zhifeng aut Enthalten in BMC genomics London : BioMed Central, 2000 20(2019), 1 vom: 11. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:20 year:2019 number:1 day:11 month:04 https://dx.doi.org/10.1186/s12864-019-5650-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 1 11 04
language	English
source	Enthalten in BMC genomics 20(2019), 1 vom: 11. Apr. volume:20 year:2019 number:1 day:11 month:04
sourceStr	Enthalten in BMC genomics 20(2019), 1 vom: 11. Apr. volume:20 year:2019 number:1 day:11 month:04
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	CAGE Translatome sequencing TSS profiling Core promoter Polysome selection
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Li, Hua @@aut@@ Bai, Ling @@aut@@ Li, Hongmei @@aut@@ Li, Xinhui @@aut@@ Kang, Yani @@aut@@ Zhang, Ningbo @@aut@@ Sun, Jielin @@aut@@ Shao, Zhifeng @@aut@@
publishDateDaySort_date	2019-04-11T00:00:00Z
hierarchy_top_id	326644954
id	SPR027152804
language_de	englisch
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author	Li, Hua
spellingShingle	Li, Hua misc CAGE misc Translatome sequencing misc TSS profiling misc Core promoter misc Polysome selection Selective translational usage of TSS and core promoters revealed by translatome sequencing
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topic_title	Selective translational usage of TSS and core promoters revealed by translatome sequencing CAGE (dpeaa)DE-He213 Translatome sequencing (dpeaa)DE-He213 TSS profiling (dpeaa)DE-He213 Core promoter (dpeaa)DE-He213 Polysome selection (dpeaa)DE-He213
topic	misc CAGE misc Translatome sequencing misc TSS profiling misc Core promoter misc Polysome selection
topic_unstemmed	misc CAGE misc Translatome sequencing misc TSS profiling misc Core promoter misc Polysome selection
topic_browse	misc CAGE misc Translatome sequencing misc TSS profiling misc Core promoter misc Polysome selection
format_facet	Elektronische Aufsätze Aufsätze Elektronische Ressource
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title	Selective translational usage of TSS and core promoters revealed by translatome sequencing
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title_full	Selective translational usage of TSS and core promoters revealed by translatome sequencing
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author_browse	Li, Hua Bai, Ling Li, Hongmei Li, Xinhui Kang, Yani Zhang, Ningbo Sun, Jielin Shao, Zhifeng
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title_sort	selective translational usage of tss and core promoters revealed by translatome sequencing
title_auth	Selective translational usage of TSS and core promoters revealed by translatome sequencing
abstract	Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. © The Author(s). 2019
abstractGer	Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. © The Author(s). 2019
abstract_unstemmed	Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. © The Author(s). 2019
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title_short	Selective translational usage of TSS and core promoters revealed by translatome sequencing
url	https://dx.doi.org/10.1186/s12864-019-5650-0
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author2	Bai, Ling Li, Hongmei Li, Xinhui Kang, Yani Zhang, Ningbo Sun, Jielin Shao, Zhifeng
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Selective translational usage of TSS and core promoters revealed by translatome sequencing

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