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Article ; Online: Special Issue "APOBECs and Virus Restriction".

Chelico, Linda

2021 Volume 13, Issue 8

Abstract: The apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) enzyme family in humans has 11 members with diverse functions in metabolism and immunity [ ... ]. ...

Abstract	The apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) enzyme family in humans has 11 members with diverse functions in metabolism and immunity [...].
MeSH term(s)	APOBEC-1 Deaminase/classification ; APOBEC-1 Deaminase/genetics ; APOBEC-1 Deaminase/metabolism ; Animals ; DNA Viruses/immunology ; DNA Viruses/metabolism ; Humans ; Immunity, Innate ; Mice ; RNA Editing
Chemical Substances	APOBEC-1 Deaminase (EC 3.5.4.36)
Language	English
Publishing date	2021-08-15
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13081613
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Special Issue “APOBECs and Virus Restriction”

Chelico, Linda

Viruses. 2021 Aug. 15, v. 13, no. 8

2021

Abstract: The apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) enzyme family in humans has 11 members with diverse functions in metabolism and immunity [ ... ] ...

Abstract	The apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) enzyme family in humans has 11 members with diverse functions in metabolism and immunity [...]
Keywords	apolipoprotein B ; enzymes ; immunity ; metabolism ; polypeptides ; viruses
Language	English
Dates of publication	2021-0815
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13081613
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells.

Granadillo Rodríguez, Milaid / Wong, Lai / Chelico, Linda

Frontiers in genome editing

2023 Volume 5, Page(s) 1196697

Abstract: APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. ... ...

Abstract	APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and
Language	English
Publishing date	2023-06-01
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-3439
ISSN (online)	2673-3439
DOI	10.3389/fgeed.2023.1196697
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Article ; Online: Stability of APOBEC3F in the Presence of the APOBEC3 Antagonist HIV-1 Vif Increases at the Expense of Co-Expressed APOBEC3H Haplotype I.

Yousefi, Maria / Annan Sudarsan, Arun Kumar / Gaba, Amit / Chelico, Linda

Viruses

2023 Volume 15, Issue 2

Abstract: The seven human APOBEC3 enzymes (APOBEC3A through H, excluding E) are host restriction factors. Most of the APOBEC3 enzymes can restrict HIV-1 replication with different efficiencies. The HIV-1 Vif protein combats APOBEC3-mediated restriction by inducing ...

Abstract	The seven human APOBEC3 enzymes (APOBEC3A through H, excluding E) are host restriction factors. Most of the APOBEC3 enzymes can restrict HIV-1 replication with different efficiencies. The HIV-1 Vif protein combats APOBEC3-mediated restriction by inducing ubiquitination and degradation in the proteasome. APOBEC3F and APOBEC3G can hetero-oligomerize, which increases their restriction capacity and resistance to Vif. Here we determined if APOBEC3C, APOBEC3F, or APOBEC3G could hetero-oligomerize with APOBEC3H haplotype I. APOBEC3H haplotype I has a short half-life in cells due to ubiquitination and degradation by host proteins, but is also resistant to Vif. We hypothesized that hetero-oligomerization with APOBEC3H haplotype I may result in less Vif-mediated degradation of the interacting APOBEC3 and stabilize APOBEC3H haplotype I, resulting in more efficient HIV-1 restriction. Although we found that all three APOBEC3s could interact with APOBEC3H haplotype I, only APOBEC3F affected APOBEC3H haplotype I by surprisingly accelerating its proteasomal degradation. However, this increased APOBEC3F levels in cells and virions in the absence or presence of Vif and enabled APOBEC3F-mediated restriction of HIV-1 in the presence of Vif. Altogether, the data suggest that APOBEC3 enzymes can co-regulate each other at the protein level and that they cooperate to ensure HIV-1 inactivation rather than evolution.
MeSH term(s)	Humans ; HIV-1/genetics ; Haplotypes ; Cytidine Deaminase ; Cytoplasm ; HIV Seropositivity ; vif Gene Products, Human Immunodeficiency Virus/genetics ; Cytosine Deaminase ; APOBEC Deaminases ; Aminohydrolases/genetics
Chemical Substances	APOBEC3A protein, human (EC 3.5.4.5) ; Cytidine Deaminase (EC 3.5.4.5) ; vif protein, Human immunodeficiency virus 1 ; vif Gene Products, Human Immunodeficiency Virus ; APOBEC3F protein, human (EC 3.5.4.1) ; Cytosine Deaminase (EC 3.5.4.1) ; APOBEC3 proteins, human (EC 3.5.4.5) ; APOBEC Deaminases (EC 3.5.4.5) ; vif protein, Human immunodeficiency virus 2 ; APOBEC3H protein, human (EC 3.5.4.-) ; Aminohydrolases (EC 3.5.4.-)
Language	English
Publishing date	2023-02-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15020463
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Competition for DNA binding between the genome protector replication protein A and the genome modifying APOBEC3 single-stranded DNA deaminases.

Wong, Lai / Sami, Alina / Chelico, Linda

Nucleic acids research

2022 Volume 50, Issue 21, Page(s) 12039–12057

Abstract: The human APOBEC family of eleven cytosine deaminases use RNA and single-stranded DNA (ssDNA) as substrates to deaminate cytosine to uracil. This deamination event has roles in lipid metabolism by altering mRNA coding, adaptive immunity by causing ... ...

Abstract	The human APOBEC family of eleven cytosine deaminases use RNA and single-stranded DNA (ssDNA) as substrates to deaminate cytosine to uracil. This deamination event has roles in lipid metabolism by altering mRNA coding, adaptive immunity by causing evolution of antibody genes, and innate immunity through inactivation of viral genomes. These benefits come at a cost where some family members, primarily from the APOBEC3 subfamily (APOBEC3A-H, excluding E), can cause off-target deaminations of cytosine to form uracil on transiently single-stranded genomic DNA, which induces mutations that are associated with cancer evolution. Since uracil is only promutagenic, the mutations observed in cancer genomes originate only when uracil is not removed by uracil DNA glycosylase (UNG) or when the UNG-induced abasic site is erroneously repaired. However, when ssDNA is present, replication protein A (RPA) binds and protects the DNA from nucleases or recruits DNA repair proteins, such as UNG. Thus, APOBEC enzymes must compete with RPA to access their substrate. Certain APOBEC enzymes can displace RPA, bind and scan ssDNA efficiently to search for cytosines, and can become highly overexpressed in tumor cells. Depending on the DNA replication conditions and DNA structure, RPA can either be in excess or deficient. Here we discuss the interplay between these factors and how despite RPA, multiple cancer genomes have a mutation bias at cytosines indicative of APOBEC activity.
MeSH term(s)	Humans ; Replication Protein A/genetics ; Replication Protein A/metabolism ; DNA, Single-Stranded/genetics ; Cytidine Deaminase/genetics ; Cytidine Deaminase/metabolism ; Uracil-DNA Glycosidase/genetics ; Uracil-DNA Glycosidase/metabolism ; DNA Replication/genetics ; Cytosine/metabolism ; DNA/metabolism ; Uracil/metabolism ; APOBEC Deaminases/genetics ; APOBEC Deaminases/metabolism ; Deamination
Chemical Substances	APOBEC3A protein, human (EC 3.5.4.5) ; Replication Protein A ; DNA, Single-Stranded ; Cytidine Deaminase (EC 3.5.4.5) ; Uracil-DNA Glycosidase (EC 3.2.2.-) ; Cytosine (8J337D1HZY) ; DNA (9007-49-2) ; Uracil (56HH86ZVCT) ; APOBEC Deaminases (EC 3.5.4.5) ; APOBEC3 proteins, human (EC 3.5.4.5)
Language	English
Publishing date	2022-11-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
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/gkac1121
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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)

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Article: Summary of an environmental scan of HIV and Hepatitis C programs, projects and initiatives in Saskatchewan.

Cheekireddy, Meghana / Madampage, Claudia / Hammond, Chad / Chelico, Linda / King, Alexandra

Canada communicable disease report = Releve des maladies transmissibles au Canada

2022 Volume 48, Issue 10, Page(s) 424–428

Abstract: Background: In 2019, the human immunodeficiency virus (HIV) and hepatitis C (HCV) diagnosis rates in Saskatchewan (SK) were approximately twice the national rate. To address these high levels, Saskatchewan Stories, a community-based digital database, ... ...

Abstract	Background: In 2019, the human immunodeficiency virus (HIV) and hepatitis C (HCV) diagnosis rates in Saskatchewan (SK) were approximately twice the national rate. To address these high levels, Saskatchewan Stories, a community-based digital database, was developed to make information on Saskatchewan-based HIV and HCV programs, projects and initiatives (PPI) centrally and freely available. To begin populating this database, we conducted an environmental scan representing HIV and HCV PPI from January 1, 1980 to May 31, 2020. Methods: MedLine, ERIC, ProQuest One Literature, Public Health Information database, SCOPUS and CINAHL were searched for both HIV and HCV articles. In addition, Bibliography of Native North Americans was searched for HIV and EMBSE (Ovid) and Indigenous studies portal (iPortal) were searched for HCV articles. Google Canada, Government of Saskatchewan, and Government of Canada websites were also searched. Results: In total, 139 HIV-specific PPI and 29 HCV-specific PPI were found in the environmental scan (n=168). Among HIV PPI, 27% (n=38) were from academic literature while 73% (n=101) were from grey literature. Among HCV PPI, 41% (n=12) were from academic literature, while 59% (n=17) were from grey literature. HIV accounted for 83% of total PPI, compared to 17% for HCV. Conclusion: This environmental scan is an important contribution to evidence-based practice and research in SK. It is particularly useful for organizations, researchers, policymakers and people living with HIV/HCV to develop new evidence-based PPI, to secure funding for PPI and to support individuals and communities in SK affected by HIV and HCV.
Language	English
Publishing date	2022-10-01
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1146585-2
ISSN	1188-4169
ISSN	1188-4169
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 3396: 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)

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Article ; Online: Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses.

Gaba, Amit / Flath, Ben / Chelico, Linda

Viruses

2021 Volume 13, Issue 6

Abstract: The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific ... ...

Abstract	The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific step. In the natural virus host, the restriction factor activity is usually suppressed by a viral antagonist protein, but this is not the case for restriction factors from an unnatural host. However, due to ongoing viral evolution, sometimes the viral antagonist can evolve to suppress restriction factors in a new host, enabling cross-species transmission. Here we examine the classical case of this paradigm by reviewing research on APOBEC3 restriction factors and how they can suppress human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). APOBEC3 enzymes are single-stranded DNA cytidine deaminases that can induce mutagenesis of proviral DNA by catalyzing the conversion of cytidine to promutagenic uridine on single-stranded viral (-)DNA if they escape the HIV/SIV antagonist protein, Vif. APOBEC3 degradation is induced by Vif through the proteasome pathway. SIV has been transmitted between Old World Monkeys and to hominids. Here we examine the adaptations that enabled such events and the ongoing impact of the APOBEC3-Vif interface on HIV in humans.
MeSH term(s)	APOBEC Deaminases/genetics ; Animals ; Gene Products, vif/chemistry ; Gene Products, vif/metabolism ; HIV Infections/genetics ; HIV Infections/transmission ; HIV Infections/virology ; HIV-1/physiology ; Host-Pathogen Interactions/genetics ; Humans ; Lentivirus Infections/genetics ; Lentivirus Infections/transmission ; Lentivirus Infections/virology ; Lentiviruses, Primate/physiology ; Protein Binding ; Protein Isoforms ; Structure-Activity Relationship ; Viral Zoonoses/transmission ; vif Gene Products, Human Immunodeficiency Virus/chemistry ; vif Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	Gene Products, vif ; Protein Isoforms ; vif Gene Products, Human Immunodeficiency Virus ; APOBEC Deaminases (EC 3.5.4.5) ; APOBEC3 proteins, human (EC 3.5.4.5)
Language	English
Publishing date	2021-06-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13061084
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead.

Granadillo Rodríguez, Milaid / Flath, Ben / Chelico, Linda

Open biology

2020 Volume 10, Issue 12, Page(s) 200188

Abstract: Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous ...

Abstract	Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse 'off-target' cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the APOBEC 'off-target' activity are overexpression in a non-normal cell type, nuclear localization and replication stress. The resulting uracil-induced mutations contribute to genomic variation, which may result in neutral, beneficial or harmful consequences for the cancer. This review summarizes the functional and biochemical basis of the APOBEC3 enzyme activity and highlights their relationship with the most well-studied cancers in this particular context such as breast, lung, bladder, and human papillomavirus-associated cancers. We focus on APOBEC3A, APOBEC3B and APOBEC3H haplotype I because they are the leading candidates as sources of somatic mutations in these and other cancers. Also, we discuss the prognostic value of the APOBEC3 expression in drug resistance and response to therapies.
MeSH term(s)	APOBEC Deaminases/chemistry ; APOBEC Deaminases/genetics ; APOBEC Deaminases/metabolism ; Animals ; Biomarkers, Tumor ; Disease Susceptibility ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Neoplastic ; Humans ; Isoenzymes/chemistry ; Isoenzymes/genetics ; Isoenzymes/metabolism ; Mutation ; Neoplasms/etiology ; Neoplasms/metabolism ; Neoplasms/pathology ; Organ Specificity ; Protein Binding ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship
Chemical Substances	Biomarkers, Tumor ; Isoenzymes ; APOBEC Deaminases (EC 3.5.4.5) ; APOBEC3 proteins, human (EC 3.5.4.5)
Language	English
Publishing date	2020-12-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.200188
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Article ; Online: Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.

Jang, Gwendolyn M / Annan Sudarsan, Arun Kumar / Shayeganmehr, Arzhang / Prando Munhoz, Erika / Lao, Reanna / Gaba, Amit / Granadillo Rodríguez, Milaid / Love, Robin P / Polacco, Benjamin J / Zhou, Yuan / Krogan, Nevan J / Kaake, Robyn M / Chelico, Linda

Molecular & cellular proteomics : MCP

2024 , Page(s) 100755

Abstract: Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or ... ...

Abstract	Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence is not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and map a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology. Data are available via ProteomeXchange with identifier PXD044275.
Language	English
Publishing date	2024-03-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2024.100755
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Zs.A 5599: Show issues

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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article: Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.

Jang, Gwendolyn M / Sudarsan, Arun Kumar Annan / Shayeganmehr, Arzhang / Munhoz, Erika Prando / Lao, Reanna / Gaba, Amit / Rodríguez, Milaid Granadillo / Love, Robin P / Polacco, Benjamin J / Zhou, Yuan / Krogan, Nevan J / Kaake, Robyn M / Chelico, Linda

bioRxiv : the preprint server for biology

2024

Abstract	Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence is not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and map a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology.
Language	English
Publishing date	2024-02-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.06.579137
Database	MEDical Literature Analysis and Retrieval System OnLINE

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