LIVIVO - Search results -

Search results

Result 1 - 10 of total 33

Search options

Article ; Online: Toward a systematic understanding of translational regulatory elements in human and viruses.

Weingarten-Gabbay, Shira / Segal, Eran

RNA biology

2016 Volume 13, Issue 10, Page(s) 927–933

Abstract: Translational regulation is a critical step in the production of proteins from genomic material in both human and viruses. However, unlike other steps of the central dogma, such as transcriptional regulation, little is known about the cis-regulatory ... ...

Abstract	Translational regulation is a critical step in the production of proteins from genomic material in both human and viruses. However, unlike other steps of the central dogma, such as transcriptional regulation, little is known about the cis-regulatory elements involved. In a recent study we devised a high-throughput bicistronic reporter assay for the discovery and the characterization of thousands of novel Internal Ribosome Entry Sites (IRESs) in human and hundreds of viral genomes. Our results provide insights into the landscape of IRES elements in human and viral transcripts and the cis-regulatory sequences underlying their activity. Here, we discuss these results as well as emerging insights from other studies, providing new views about translational regulation in human and viruses. In addition, we highlight recent high-throughput technologies in the field and discuss how combining insights from high- and low-throughput approaches can illuminate yet uncovered mechanisms of translational regulation.
Language	English
Publishing date	2016-10-02
Publishing country	United States
Document type	Journal Article
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2016.1212802
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

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.

Article: Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling.

Weingarten-Gabbay, Shira / Bauer, Matthew R / Stanton, Alexandra C / Klaeger, Susan / Verzani, Eva K / López, Daniel / Clauser, Karl R / Carr, Steven A / Abelin, Jennifer G / Rice, Charles M / Sabeti, Pardis C

bioRxiv : the preprint server for biology

2023

Abstract: Unveiling the complete proteome of viruses is crucial to our understanding of the viral life cycle and interaction with the host. We developed Massively Parallel Ribosome Profiling (MPRP) to experimentally determine open reading frames (ORFs) in 20,170 ... ...

Abstract	Unveiling the complete proteome of viruses is crucial to our understanding of the viral life cycle and interaction with the host. We developed Massively Parallel Ribosome Profiling (MPRP) to experimentally determine open reading frames (ORFs) in 20,170 designed oligonucleotides across 679 human-associated viral genomes. We identified 5,381 ORFs, including 4,208 non-canonical ORFs, and show successful detection of both annotated coding sequences (CDSs) and reported non-canonical ORFs. By examining immunopeptidome datasets of infected cells, we found class I human leukocyte antigen (HLA-I) peptides originating from non-canonical ORFs identified through MPRP. By inspecting ribosome occupancies on the 5'UTR and CDS regions of annotated viral genes, we identified hundreds of upstream ORFs (uORFs) that negatively regulate the synthesis of canonical viral proteins. The unprecedented source of viral ORFs across a wide range of viral families, including highly pathogenic viruses, expands the repertoire of vaccine targets and exposes new cis-regulatory sequences in viral genomes.
Language	English
Publishing date	2023-09-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.26.559641
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

Details ▾

Article ; Online: Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes.

Hernández, Greco / García, Alejandra / Weingarten-Gabbay, Shira / Mishra, Rishi Kumar / Hussain, Tanweer / Amiri, Mehdi / Moreno-Hagelsieb, Gabriel / Montiel-Dávalos, Angélica / Lasko, Paul / Sonenberg, Nahum

Nucleic acids research

2023 Volume 52, Issue 3, Page(s) 1064–1079

Abstract: mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at -3 and a G at + ... ...

Abstract	mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at -3 and a G at +4 (where A of the AUG initiator codon is numbered + 1), promote TIS recognition. However, the TIS context in other eukaryotes has been poorly experimentally analyzed. We analyzed in vitro the influence of the -3, -2, -1 and + 4 positions of the TIS context in rabbit, Drosophila, wheat, and yeast. We observed that -3A conferred the best translational efficiency across these species. However, we found variability at the + 4 position for optimal translation. In addition, the Kozak motif that was defined from mammalian cells was only weakly predictive for wheat and essentially non-predictive for yeast. We discovered eight conserved sequences that significantly disfavored translation. Due to the big differences in translational efficiency observed among weak TIS context sequences, we define a novel category that we termed 'barren AUG context sequences (BACS)', which represent sequences disfavoring translation. Analysis of mRNA-ribosomal complexes structures provided insights into the function of BACS. The gene ontology of the BACS-containing mRNAs is presented.
MeSH term(s)	Animals ; Rabbits ; Codon, Initiator/genetics ; Conserved Sequence ; Mammals/genetics ; Peptide Chain Initiation, Translational ; Protein Biosynthesis ; RNA, Messenger/metabolism ; Yeasts ; Eukaryota/genetics ; Eukaryota/metabolism
Chemical Substances	Codon, Initiator ; RNA, Messenger
Language	English
Publishing date	2023-12-01
Publishing country	England
Document type	Journal Article
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/gkad1152
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: A shared architecture for promoters and enhancers.

Weingarten-Gabbay, Shira / Segal, Eran

Nature genetics

2014 Volume 46, Issue 12, Page(s) 1253–1254

Abstract: A new study detects unstable nascent RNAs and uncovers thousands of transcription initiation sites in promoters and enhancers. Detailed analysis shows that these initiation sites have a similar architecture and that they are differentiated by post- ... ...

Abstract	A new study detects unstable nascent RNAs and uncovers thousands of transcription initiation sites in promoters and enhancers. Detailed analysis shows that these initiation sites have a similar architecture and that they are differentiated by post-transcriptional regulation rather than transcription initiation.
MeSH term(s)	Enhancer Elements, Genetic ; Humans ; Promoter Regions, Genetic ; RNA/genetics
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2014-12
Publishing country	United States
Document type	Comment ; Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/ng.3152
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3613: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 46: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: The grammar of transcriptional regulation.

Weingarten-Gabbay, Shira / Segal, Eran

Human genetics

2014 Volume 133, Issue 6, Page(s) 701–711

Abstract: Eukaryotes employ combinatorial strategies to generate a variety of expression patterns from a relatively small set of regulatory DNA elements. As in any other language, deciphering the mapping between DNA and expression requires an understanding of the ... ...

Abstract	Eukaryotes employ combinatorial strategies to generate a variety of expression patterns from a relatively small set of regulatory DNA elements. As in any other language, deciphering the mapping between DNA and expression requires an understanding of the set of rules that govern basic principles in transcriptional regulation, the functional elements involved, and the ways in which they combine to orchestrate a transcriptional output. Here, we review the current understanding of various grammatical rules, including the effect on expression of the number of transcription factor binding sites, their location, orientation, affinity and activity; co-association with different factors; and intrinsic nucleosome organization. We review different methods that are used to study the grammar of transcription regulation, highlight gaps in current understanding, and discuss how recent technological advances may be utilized to bridge them.
MeSH term(s)	Binding Sites ; DNA/genetics ; DNA/metabolism ; Gene Expression Regulation ; Humans ; Protein Binding ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Regulatory Elements, Transcriptional ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
Chemical Substances	RNA, Messenger ; Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2014-01-05
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	223009-4
ISSN	1432-1203 ; 0340-6717
ISSN (online)	1432-1203
ISSN	0340-6717
DOI	10.1007/s00439-013-1413-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 256: 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

Details ▾

Article ; Online: MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies.

Taylor, Hannah B / Klaeger, Susan / Clauser, Karl R / Sarkizova, Siranush / Weingarten-Gabbay, Shira / Graham, Daniel B / Carr, Steven A / Abelin, Jennifer G

Molecular & cellular proteomics : MCP

2021 Volume 20, Page(s) 100116

Abstract: Immunotherapies have emerged to treat diseases by selectively modulating a patient's immune response. Although the roles of T and B cells in adaptive immunity have been well studied, it remains difficult to select targets for immunotherapeutic strategies. ...

Abstract	Immunotherapies have emerged to treat diseases by selectively modulating a patient's immune response. Although the roles of T and B cells in adaptive immunity have been well studied, it remains difficult to select targets for immunotherapeutic strategies. Because human leukocyte antigen class II (HLA-II) peptides activate CD4+ T cells and regulate B cell activation, proliferation, and differentiation, these peptide antigens represent a class of potential immunotherapy targets and biomarkers. To better understand the molecular basis of how HLA-II antigen presentation is involved in disease progression and treatment, systematic HLA-II peptidomics combined with multiomic analyses of diverse cell types in healthy and diseased states is required. For this reason, MS-based innovations that facilitate investigations into the interplay between disease pathologies and the presentation of HLA-II peptides to CD4+ T cells will aid in the development of patient-focused immunotherapies.
MeSH term(s)	Animals ; Antigen Presentation ; Genomics ; Histocompatibility Antigens Class II/genetics ; Histocompatibility Antigens Class II/immunology ; Humans ; Immunotherapy ; Mass Spectrometry ; Peptides/genetics ; Peptides/immunology
Chemical Substances	Histocompatibility Antigens Class II ; Peptides
Language	English
Publishing date	2021-06-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2021.100116
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5599: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: The HLA-II immunopeptidome of SARS-CoV-2

Shira Weingarten-Gabbay / Da-Yuan Chen / Siranush Sarkizova / Hannah B. Taylor / Matteo Gentili / Gabrielle M. Hernandez / Leah R. Pearlman / Matthew R. Bauer / Charles M. Rice / Karl R. Clauser / Nir Hacohen / Steven A. Carr / Jennifer G. Abelin / Mohsan Saeed / Pardis C. Sabeti

Cell Reports, Vol 43, Iss 1, Pp 113596- (2024)

1481

Abstract: Summary: Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 ...

Abstract	Summary: Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4+ T cell epitopes in coronavirus disease 2019 patients, including 2 reported immunodominant regions in the SARS-CoV-2 membrane protein. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and nonstructural and noncanonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize vaccine effectiveness.
Keywords	CP: Microbiology ; CP: Immunology ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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.

Article ; Online: The HLA-II immunopeptidome of SARS-CoV-2.

Weingarten-Gabbay, Shira / Chen, Da-Yuan / Sarkizova, Siranush / Taylor, Hannah B / Gentili, Matteo / Hernandez, Gabrielle M / Pearlman, Leah R / Bauer, Matthew R / Rice, Charles M / Clauser, Karl R / Hacohen, Nir / Carr, Steven A / Abelin, Jennifer G / Saeed, Mohsan / Sabeti, Pardis C

Cell reports

2023 Volume 43, Issue 1, Page(s) 113596

Abstract: Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS- ... ...

Abstract	Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Epitopes, T-Lymphocyte ; Histocompatibility Antigens Class I ; HLA Antigens ; Histocompatibility Antigens ; CD8-Positive T-Lymphocytes ; Peptides
Chemical Substances	Epitopes, T-Lymphocyte ; Histocompatibility Antigens Class I ; HLA Antigens ; Histocompatibility Antigens ; Peptides
Language	English
Publishing date	2023-12-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.113596
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: The HLA-II immunopeptidome of SARS-CoV-2.

Weingarten-Gabbay, Shira / Chen, Da-Yuan / Sarkizova, Siranush / Taylor, Hannah B / Gentili, Matteo / Pearlman, Leah R / Bauer, Matthew R / Rice, Charles M / Clauser, Karl R / Hacohen, Nir / Carr, Steven A / Abelin, Jennifer G / Saeed, Mohsan / Sabeti, Pardis C

bioRxiv : the preprint server for biology

2023

Abstract: Targeted synthetic vaccines have the potential to transform our response to viral outbreaks; yet the design of these vaccines requires a comprehensive knowledge of viral immunogens, including T-cell epitopes. Having previously mapped the SARS-CoV-2 HLA-I ...

Abstract	Targeted synthetic vaccines have the potential to transform our response to viral outbreaks; yet the design of these vaccines requires a comprehensive knowledge of viral immunogens, including T-cell epitopes. Having previously mapped the SARS-CoV-2 HLA-I landscape, here we report viral peptides that are naturally processed and loaded onto HLA-II complexes in infected cells. We identified over 500 unique viral peptides from canonical proteins, as well as from overlapping internal open reading frames (ORFs), revealing, for the first time, the contribution of internal ORFs to the HLA-II peptide repertoire. Most HLA-II peptides co-localized with the known CD4+ T cell epitopes in COVID-19 patients. We also observed that two reported immunodominant regions in the SARS-CoV-2 membrane protein are formed at the level of HLA-II presentation. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and non-structural and non-canonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize the vaccine effectiveness.
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.26.542482
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

Details ▾

Article ; Online: HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses.

Weingarten-Gabbay, Shira / Pearlman, Leah R / Chen, Da-Yuan / Klaeger, Susan / Taylor, Hannah B / Welch, Nicole L / Keskin, Derin B / Carr, Steven A / Abelin, Jennifer G / Saeed, Mohsan / Sabeti, Pardis C

STAR protocols

2022 Volume 3, Issue 4, Page(s) 101910

Abstract: ... execution of this protocol, please refer to Weingarten-Gabbay et al. (2021). ...

Abstract	Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility. For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).
MeSH term(s)	Humans ; Histocompatibility Antigens Class I ; Peptides/chemistry ; Mass Spectrometry ; Viruses
Chemical Substances	Histocompatibility Antigens Class I ; Peptides
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101910
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

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.

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED