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  1. Article: siRNA Therapeutics: From Bench Lab. to Clinics.

    Romero-López, Cristina / Berzal-Herranz, Alfredo

    Pharmaceuticals (Basel, Switzerland)

    2024  Volume 17, Issue 4

    Abstract: The discovery of the RNA interference (RNAi) mechanism in 1998 by Andrew Fire and Craig C [ ... ]. ...

    Abstract The discovery of the RNA interference (RNAi) mechanism in 1998 by Andrew Fire and Craig C [...].
    Language English
    Publishing date 2024-03-26
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph17040416
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Aptamers' Potential to Fill Therapeutic and Diagnostic Gaps.

    Berzal-Herranz, Alfredo / Romero-López, Cristina

    Pharmaceuticals (Basel, Switzerland)

    2024  Volume 17, Issue 1

    Abstract: More than 30 years ago, in 1990, three independent research groups published several papers demonstrating that genetics could be performed in vitro in the absence of living organisms or cells [ ... ]. ...

    Abstract More than 30 years ago, in 1990, three independent research groups published several papers demonstrating that genetics could be performed in vitro in the absence of living organisms or cells [...].
    Language English
    Publishing date 2024-01-12
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph17010105
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Recruitment of the 40S ribosomal subunit by the West Nile virus 3' UTR promotes the cross-talk between the viral genomic ends for translation regulation.

    Ramos-Lorente, Sara Esther / Berzal-Herranz, Beatriz / Romero-López, Cristina / Berzal-Herranz, Alfredo

    Virus research

    2024  Volume 343, Page(s) 199340

    Abstract: Flaviviral RNA genomes are composed of discrete RNA structural units arranged in an ordered fashion and grouped into complex folded domains that regulate essential viral functions, e.g. replication and translation. This is achieved by adjusting the ... ...

    Abstract Flaviviral RNA genomes are composed of discrete RNA structural units arranged in an ordered fashion and grouped into complex folded domains that regulate essential viral functions, e.g. replication and translation. This is achieved by adjusting the overall structure of the RNA genome via the establishment of inter- and intramolecular interactions. Translation regulation is likely the main process controlling flaviviral gene expression. Although the genomic 3' UTR is a key player in this regulation, little is known about the molecular mechanisms underlying this role. The present work provides evidence for the specific recruitment of the 40S ribosomal subunit by the 3' UTR of the West Nile virus RNA genome, showing that the joint action of both genomic ends contributes the positioning of the 40S subunit at the 5' end. The combination of structural mapping techniques revealed specific conformational requirements at the 3' UTR for 40S binding, involving the highly conserved SL-III, 5'DB, 3'DB and 3'SL elements, all involved in the translation regulation. These results point to the 40S subunit as a bridge to ensure cross-talk between both genomic ends during viral translation and support a link between 40S recruitment by the 3' UTR and translation control.
    MeSH term(s) West Nile virus/genetics ; 3' Untranslated Regions ; Ribosome Subunits, Small, Eukaryotic/metabolism ; Flavivirus/genetics ; Genomics ; RNA, Viral/metabolism ; Virus Replication
    Chemical Substances 3' Untranslated Regions ; RNA, Viral
    Language English
    Publishing date 2024-02-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2024.199340
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Genomic 3' UTR of Flaviviruses Is a Translation Initiation Enhancer.

    Berzal-Herranz, Alfredo / Berzal-Herranz, Beatriz / Ramos-Lorente, Sara Esther / Romero-López, Cristina

    International journal of molecular sciences

    2022  Volume 23, Issue 15

    Abstract: Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The ... ...

    Abstract Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The genus
    MeSH term(s) 3' Untranslated Regions ; Animals ; Cell Line ; Flavivirus/genetics ; Genomics ; Humans ; Mammals/genetics ; Zika Virus/genetics ; Zika Virus Infection
    Chemical Substances 3' Untranslated Regions
    Language English
    Publishing date 2022-08-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23158604
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  5. Article ; Online: Inter- and Intramolecular RNA-RNA Interactions Modulate the Regulation of Translation Mediated by the 3' UTR in West Nile Virus.

    Romero-López, Cristina / Roda-Herreros, Margarita / Berzal-Herranz, Beatriz / Ramos-Lorente, Sara Esther / Berzal-Herranz, Alfredo

    International journal of molecular sciences

    2023  Volume 24, Issue 6

    Abstract: RNA viruses rely on genomic structural elements to accomplish the functions necessary to complete the viral cycle. These elements participate in a dynamic network of RNA-RNA interactions that determine the overall folding of the RNA genome and may be ... ...

    Abstract RNA viruses rely on genomic structural elements to accomplish the functions necessary to complete the viral cycle. These elements participate in a dynamic network of RNA-RNA interactions that determine the overall folding of the RNA genome and may be responsible for the fine regulation of viral replication and translation as well as the transition between them. The genomes of members of the genus
    MeSH term(s) West Nile virus/genetics ; 3' Untranslated Regions ; RNA, Viral/genetics ; RNA, Viral/chemistry ; Flavivirus/genetics ; Virus Replication/genetics
    Chemical Substances 3' Untranslated Regions ; RNA, Viral
    Language English
    Publishing date 2023-03-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24065337
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  6. Article ; Online: The Genomic 3′ UTR of Flaviviruses Is a Translation Initiation Enhancer

    Alfredo Berzal-Herranz / Beatriz Berzal-Herranz / Sara Esther Ramos-Lorente / Cristina Romero-López

    International Journal of Molecular Sciences, Vol 23, Iss 15, p

    2022  Volume 8604

    Abstract: Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The genus Flavivirus is a large group of positive, single-stranded ... ...

    Abstract Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The genus Flavivirus is a large group of positive, single-stranded RNA viruses that includes several important human pathogens, such as West Nile, Dengue and Zika virus. The genome of flaviviruses bears a type 1 cap structure at its 5′ end, needed for the main translation initiation mechanism. Several members of the genus also use a cap-independent translation mechanism. The present work provides evidence that the WNV 5′ end also promotes a cap-independent translation initiation mechanism in mammalian and insect cells, reinforcing the hypothesis that this might be a general strategy of flaviviruses. In agreement with previous reports, we show that this mechanism depends on the presence of the viral genomic 3′ UTR. The results also show that the 3′ UTR of the WNV genome enhances translation of the cap-dependent mechanism. Interestingly, WNV 3′ UTR can be replaced by the 3′ UTR of other flaviviruses and the translation enhancing effect is maintained, suggesting a molecular mechanism that does not involve direct RNA-RNA interactions to be at work. In addition, the deletion of specific structural elements of the WNV 3′ UTR leads to increased cap-dependent and cap-independent translation. These findings suggest the 3′ UTR to be involved in a fine-tuned translation regulation mechanism.
    Keywords West Nile Virus ; WNV ; flavivirus ; regulation of translation ; 3′ UTR ; cap-independent translation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 616
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Inter- and Intramolecular RNA–RNA Interactions Modulate the Regulation of Translation Mediated by the 3′ UTR in West Nile Virus

    Cristina Romero-López / Margarita Roda-Herreros / Beatriz Berzal-Herranz / Sara Esther Ramos-Lorente / Alfredo Berzal-Herranz

    International Journal of Molecular Sciences, Vol 24, Iss 5337, p

    2023  Volume 5337

    Abstract: RNA viruses rely on genomic structural elements to accomplish the functions necessary to complete the viral cycle. These elements participate in a dynamic network of RNA–RNA interactions that determine the overall folding of the RNA genome and may be ... ...

    Abstract RNA viruses rely on genomic structural elements to accomplish the functions necessary to complete the viral cycle. These elements participate in a dynamic network of RNA–RNA interactions that determine the overall folding of the RNA genome and may be responsible for the fine regulation of viral replication and translation as well as the transition between them. The genomes of members of the genus Flavivirus are characterized by a complexly folded 3′ UTR with a number of RNA structural elements that are conserved across isolates of each species. The present work provides evidence of intra- and intermolecular RNA–RNA interactions involving RNA structural elements in the 3′ UTR of the West Nile virus genome. The intermolecular interactions can be visualized in vitro by the formation of molecular dimers involving the participation of at least the SLI and 3′DB elements. Certainly, the 3′ UTR of dengue virus, which lacks the SLI element, forms molecular dimers in lower quantities via a single interaction site, probably 3′DB. The functional analysis of sequence or deletion mutants revealed an inverse relationship between 3′ UTR dimerization and viral translation efficiency in cell cultures. A network of RNA–RNA interactions involving 3′ UTR structural elements might therefore exist, helping to regulate viral translation.
    Keywords RNA–RNA interactions ; West Nile virus ; flavivirus translation ; 3′ UTR ; RNA virus ; RNA dimerization ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence.

    Ramos-Lorente, Sara / Romero-López, Cristina / Berzal-Herranz, Alfredo

    International journal of molecular sciences

    2021  Volume 22, Issue 7

    Abstract: ... The ... ...

    Abstract The genus
    MeSH term(s) Animals ; Flavivirus/genetics ; Flavivirus/metabolism ; Genome, Viral/physiology ; Humans ; RNA Folding/physiology ; RNA Stability ; RNA, Viral/genetics ; RNA, Viral/metabolism
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2021-04-03
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22073738
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  9. Article: Two Examples of RNA Aptamers with Antiviral Activity. Are Aptamers the Wished Antiviral Drugs?

    Berzal-Herranz, Alfredo / Romero-López, Cristina

    Pharmaceuticals (Basel, Switzerland)

    2020  Volume 13, Issue 8

    Abstract: The current Covid-19 pandemic has pointed out some major deficiencies of the even most advanced societies to fight against viral RNA infections. Once more, it has been demonstrated that there is a lack of efficient drugs to control RNA viruses. Aptamers ... ...

    Abstract The current Covid-19 pandemic has pointed out some major deficiencies of the even most advanced societies to fight against viral RNA infections. Once more, it has been demonstrated that there is a lack of efficient drugs to control RNA viruses. Aptamers are efficient ligands of a great variety of molecules including proteins and nucleic acids. Their specificity and mechanism of action make them very promising molecules for interfering with the function encoded in viral RNA genomes. RNA viruses store essential information in conserved structural genomic RNA elements that promote important steps for the consecution of the infective cycle. This work describes two well documented examples of RNA aptamers with antiviral activity against highly conserved structural domains of the HIV-1 and HCV RNA genome, respectively, performed in our laboratory. They are two good examples that illustrate the potential of the aptamers to fill the therapeutic gaps in the fight against RNA viruses.
    Keywords covid19
    Language English
    Publishing date 2020-07-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph13080157
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  10. Article ; Online: The Role of the RNA-RNA Interactome in the Hepatitis C Virus Life Cycle.

    Romero-López, Cristina / Berzal-Herranz, Alfredo

    International journal of molecular sciences

    2020  Volume 21, Issue 4

    Abstract: RNA virus genomes are multifunctional entities endowed with conserved structural elements that control translation, replication and encapsidation, among other processes. The preservation of these structural RNA elements constraints the genomic sequence ... ...

    Abstract RNA virus genomes are multifunctional entities endowed with conserved structural elements that control translation, replication and encapsidation, among other processes. The preservation of these structural RNA elements constraints the genomic sequence variability. The hepatitis C virus (HCV) genome is a positive, single-stranded RNA molecule with numerous conserved structural elements that manage different steps during the infection cycle. Their function is ensured by the association of protein factors, but also by the establishment of complex, active, long-range RNA-RNA interaction networks-the so-called HCV RNA interactome. This review describes the RNA genome functions mediated via RNA-RNA contacts, and revisits some canonical ideas regarding the role of functional high-order structures during the HCV infective cycle. By outlining the roles of long-range RNA-RNA interactions from translation to virion budding, and the functional domains involved, this work provides an overview of the HCV genome as a dynamic device that manages the course of viral infection.
    MeSH term(s) Genome, Viral/physiology ; Hepacivirus/physiology ; Hepatitis C/genetics ; Hepatitis C/metabolism ; Humans ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Virus Assembly/physiology ; Virus Replication/physiology
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2020-02-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms21041479
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