Genetic Adaptation to Untranslated Region-Mediated Enterovirus Growth Deficits by Mutations in the Nonstructural Proteins 3AB and 3CD

ABSTRACT Both untranslated regions (UTRs) of plus-strand RNA virus genomes jointly control translation and replication of viral genomes. In the case of the Enterovirus genus of the Picornaviridae family, the 5′UTR consists of a cloverleaf-like terminus preceding the internal ribosomal entry site (IRES) and the 3′ terminus is composed of a structured 3′UTR and poly(A). The IRES and poly(A) have been implicated in translation control, and all UTR structures, in addition to cis-acting genetic elements mapping to the open reading frame, have been assigned roles in RNA replication. Viral UTRs are recognized by viral and host cell RNA-binding proteins that may codetermine genome stability, translation, plus- and minus-strand RNA replication, and scaffolding of viral replication complexes within host cell substructures. In this report, we describe experiments with coxsackie B viruses with a cell type-specific propagation deficit in Sk-N-Mc neuroblastoma cells conferred by the combination of a heterologous IRES and altered 3′UTR. Serial passage of these constructs in Sk-N-Mc cells yielded genetic adaptation by mutations within the viral nonstructural proteins 3A and 3C. Our data implicate 3A and/or 3C or their precursors 3AB and/or 3CD in a functional complex with the IRES and 3′UTR that drives viral propagation. Adaptation to neuroblastoma cells suggests an involvement of cell type-specific host factors or the host cell cytoplasmic milieu in this phenomenon.

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Deep analysis of RNA N6-adenosine methylation (m6A) patterns in human cells

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa007 ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

Jun Wang ◽

Liangjiang Wang

Keyword(s):

Rna Binding ◽

Data Transfer ◽

Rna Binding Proteins ◽

Consensus Sequence ◽

Model Performance ◽

Cell Types ◽

Human Cells ◽

Rna Modification ◽

Cell Type ◽

Cell Type Specific

Abstract N6-adenosine methylation (m6A) is the most abundant internal RNA modification in eukaryotes, and affects RNA metabolism and non-coding RNA function. Previous studies suggest that m6A modifications in mammals occur on the consensus sequence DRACH (D = A/G/U, R = A/G, H = A/C/U). However, only about 10% of such adenosines can be m6A-methylated, and the underlying sequence determinants are still unclear. Notably, the regulation of m6A modifications can be cell-type-specific. In this study, we have developed a deep learning model, called TDm6A, to predict RNA m6A modifications in human cells. For cell types with limited availability of m6A data, transfer learning may be used to enhance TDm6A model performance. We show that TDm6A can learn common and cell-type-specific motifs, some of which are associated with RNA-binding proteins previously reported to be m6A readers or anti-readers. In addition, we have used TDm6A to predict m6A sites on human long non-coding RNAs (lncRNAs) for selection of candidates with high levels of m6A modifications. The results provide new insights into m6A modifications on human protein-coding and non-coding transcripts.

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Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1502849112 ◽

2015 ◽

Vol 112 (11) ◽

pp. 3445-3450 ◽

Cited By ~ 84

Author(s):

Qinghong Yan ◽

Sebastien M. Weyn-Vanhentenryck ◽

Jie Wu ◽

Steven A. Sloan ◽

Ye Zhang ◽

...

Keyword(s):

Rna Binding ◽

Rna Binding Proteins ◽

Splice Variants ◽

Mammalian Brain ◽

Cell Type ◽

Evolutionary Selection ◽

Chromatin Regulators ◽

Brain Transcriptome ◽

Cell Type Specific ◽

Specific Regulation

Alternative splicing (AS) dramatically expands the complexity of the mammalian brain transcriptome, but its atlas remains incomplete. Here we performed deep mRNA sequencing of mouse cortex to discover and characterize alternative exons with potential functional significance. Our analysis expands the list of AS events over 10-fold compared with previous annotations, demonstrating that 72% of multiexon genes express multiple splice variants in this single tissue. To evaluate functionality of the newly discovered AS events, we conducted comprehensive analyses on central nervous system (CNS) cell type-specific splicing, targets of tissue- or cell type-specific RNA binding proteins (RBPs), evolutionary selection pressure, and coupling of AS with nonsense-mediated decay (AS-NMD). We show that newly discovered events account for 23–42% of all cassette exons under tissue- or cell type-specific regulation. Furthermore, over 7,000 cassette exons are under evolutionary selection for regulated AS in mammals, 70% of which are new. Among these are 3,058 highly conserved cassette exons, including 1,014 NMD exons that may function directly to control gene expression levels. These NMD exons are particularly enriched in RBPs including splicing factors and interestingly also regulators for other steps of RNA metabolism. Unexpectedly, a second group of NMD exons reside in genes encoding chromatin regulators. Although the conservation of NMD exons in RBPs frequently extends into lower vertebrates, NMD exons in chromatin regulators are introduced later into the mammalian lineage, implying the emergence of a novel mechanism coupling AS and epigenetics. Our results highlight previously uncharacterized complexity and evolution in the mammalian brain transcriptome.

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Picornavirus Modification of a Host mRNA Decay Protein

mBio ◽

10.1128/mbio.00431-12 ◽

2012 ◽

Vol 3 (6) ◽

Cited By ~ 41

Author(s):

Janet M. Rozovics ◽

Amanda J. Chase ◽

Andrea L. Cathcart ◽

Wayne Chou ◽

Paul D. Gershon ◽

...

Keyword(s):

Host Cell ◽

Mrna Decay ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Rna Binding Protein ◽

Rna Replication ◽

Human Rhinovirus ◽

Genomic Rnas

ABSTRACTDue to the limited coding capacity of picornavirus genomic RNAs, host RNA binding proteins play essential roles during viral translation and RNA replication. Here we describe experiments suggesting that AUF1, a host RNA binding protein involved in mRNA decay, plays a role in the infectious cycle of picornaviruses such as poliovirus and human rhinovirus. We observed cleavage of AUF1 during poliovirus or human rhinovirus infection, as well as interaction of this protein with the 5′ noncoding regions of these viral genomes. Additionally, the picornavirus proteinase 3CD, encoded by poliovirus or human rhinovirus genomic RNAs, was shown to cleave all four isoforms of recombinant AUF1 at a specific N-terminal sitein vitro. Finally, endogenous AUF1 was found to relocalize from the nucleus to the cytoplasm in poliovirus-infected HeLa cells to sites adjacent to (but distinct from) putative viral RNA replication complexes.IMPORTANCEThis study derives its significance from reporting how picornaviruses like poliovirus and human rhinovirus proteolytically cleave a key player (AUF1) in host mRNA decay pathways during viral infection. Beyond cleavage of AUF1 by the major viral proteinase encoded in picornavirus genomes, infection by poliovirus results in the relocalization of this host cell RNA binding protein from the nucleus to the cytoplasm. The alteration of both the physical state of AUF1 and its cellular location illuminates how small RNA viruses manipulate the activities of host cell RNA binding proteins to ensure a faithful intracellular replication cycle.

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Comparative Analysis of Alternative Splicing Profiles in Th Cell Subsets Reveals Extensive Cell Type–Specific Effects Modulated by a Network of Transcription Factors and RNA-Binding Proteins

ImmunoHorizons ◽

10.4049/immunohorizons.2100060 ◽

2021 ◽

Vol 5 (9) ◽

pp. 760-771

Author(s):

Quoseena Mir ◽

Deepak K. Lakshmipati ◽

Benjamin J. Ulrich ◽

Mark H. Kaplan ◽

Sarath Chandra Janga

Keyword(s):

Transcription Factors ◽

Comparative Analysis ◽

Alternative Splicing ◽

Rna Binding ◽

Rna Binding Proteins ◽

Cell Type ◽

Specific Effects ◽

Th Cell ◽

Extensive Cell ◽

Cell Type Specific

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RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability

Cell Research ◽

10.1038/s41422-021-00515-8 ◽

2021 ◽

Cited By ~ 1

Author(s):

Feng Xiong ◽

Ruoyu Wang ◽

Joo-Hyung Lee ◽

Shenglan Li ◽

Shin-Fu Chen ◽

...

Keyword(s):

Matrix Protein ◽

Rna Binding ◽

Rna Binding Proteins ◽

Regulatory Elements ◽

Host Interaction ◽

Damage Repair ◽

Novel Host ◽

Cell Type Specific ◽

Human Fetal Tissues ◽

Long Genes

AbstractThe molecular basis underlying the interaction between retrotransposable elements (RTEs) and the human genome remains poorly understood. Here, we profiled N6-methyladenosine (m6A) deposition on nascent RNAs in human cells by developing a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m6A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes, and are bound by a dozen RNA binding proteins (RBPs) that are putative novel readers of m6A-modified RNAs, including a nuclear matrix protein SAFB. Notably, m6A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes with critical roles in DNA damage repair and sometimes in L1 suppression per se, where they act as transcriptional “roadblocks” to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m6A-L1s to reduce their levels, and to safeguard hosting gene transcription. Remarkably, our analysis identified thousands of MILs in multiple human fetal tissues, enlisting them as a novel category of cell-type-specific regulatory elements that often compromise transcription of long genes and confer their vulnerability in neurodevelopmental disorders. We propose that this m6A-orchestrated L1–host interaction plays widespread roles in gene regulation, genome integrity, human development and diseases.

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Identification of mRNAs Associated with αCP2-Containing RNP Complexes

Molecular and Cellular Biology ◽

10.1128/mcb.23.19.7055-7067.2003 ◽

2003 ◽

Vol 23 (19) ◽

pp. 7055-7067 ◽

Cited By ~ 45

Author(s):

Shelly A. Waggoner ◽

Stephen A. Liebhaber

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Cell Function ◽

Rna Binding Proteins ◽

Translation Control ◽

Viral Mrnas ◽

Posttranscriptional Gene Regulation ◽

Direct Binding

ABSTRACT Posttranscriptional controls in higher eukaryotes are central to cell differentiation and developmental programs. These controls reflect sequence-specific interactions of mRNAs with one or more RNA binding proteins. The α-globin poly(C) binding proteins (αCPs) comprise a highly abundant subset of K homology (KH) domain RNA binding proteins and have a characteristic preference for binding single-stranded C-rich motifs. αCPs have been implicated in translation control and stabilization of multiple cellular and viral mRNAs. To explore the full contribution of αCPs to cell function, we have identified a set of mRNAs that associate in vivo with the major αCP2 isoforms. One hundred sixty mRNA species were consistently identified in three independent analyses of αCP2-RNP complexes immunopurified from a human hematopoietic cell line (K562). These mRNAs could be grouped into subsets encoding cytoskeletal components, transcription factors, proto-oncogenes, and cell signaling factors. Two mRNAs were linked to ceroid lipofuscinosis, indicating a potential role for αCP2 in this infantile neurodegenerative disease. Surprisingly, αCP2 mRNA itself was represented in αCP2-RNP complexes, suggesting autoregulatory control of αCP2 expression. In vitro analyses of representative target mRNAs confirmed direct binding of αCP2 within their 3′ untranslated regions. These data expand the list of mRNAs that associate with αCP2 in vivo and establish a foundation for modeling its role in coordinating pathways of posttranscriptional gene regulation.

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Functional annotation of human long noncoding RNAs using chromatin conformation data

10.1101/2021.01.13.426305 ◽

2021 ◽

Author(s):

Saumya Agrawal ◽

Tanvir Alam ◽

Masaru Koido ◽

Ivan V. Kulakovskiy ◽

Jessica Severin ◽

...

Keyword(s):

Functional Annotation ◽

Rna Binding ◽

Functional Characterization ◽

Cell Types ◽

Chromatin Interaction ◽

Spatial Proximity ◽

Chromatin Conformation ◽

Cell Type ◽

Cell Type Specific ◽

Rna Domains

AbstractTranscription of the human genome yields mostly long non-coding RNAs (lncRNAs). Systematic functional annotation of lncRNAs is challenging due to their low expression level, cell type-specific occurrence, poor sequence conservation between orthologs, and lack of information about RNA domains. Currently, 95% of human lncRNAs have no functional characterization. Using chromatin conformation and Cap Analysis of Gene Expression (CAGE) data in 18 human cell types, we systematically located genomic regions in spatial proximity to lncRNA genes and identified functional clusters of interacting protein-coding genes, lncRNAs and enhancers. Using these clusters we provide a cell type-specific functional annotation for 7,651 out of 14,198 (53.88%) lncRNAs. LncRNAs tend to have specialized roles in the cell type in which it is first expressed, and to incorporate more general functions as its expression is acquired by multiple cell types during evolution. By analyzing RNA-binding protein and RNA-chromatin interaction data in the context of the spatial genomic interaction map, we explored mechanisms by which these lncRNAs can act.

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Picornaviruses and RNA Metabolism: Local and Global Effects of Infection

Journal of Virology ◽

10.1128/jvi.02088-17 ◽

2019 ◽

Vol 93 (21) ◽

Cited By ~ 3

Author(s):

Autumn C. Holmes ◽

Bert L. Semler

Keyword(s):

Host Cell ◽

Rna Binding ◽

Rna Binding Proteins ◽

Foot And Mouth Disease ◽

Rna Metabolism ◽

Cell Nuclei ◽

Cell Functions ◽

Mouth Disease Virus ◽

Wide Range ◽

Positive Strand Rna

ABSTRACT Due to the limiting coding capacity for members of the Picornaviridae family of positive-strand RNA viruses, their successful replication cycles require complex interactions with host cell functions. These interactions span from the down-modulation of many aspects of cellular metabolism to the hijacking of specific host functions used during viral translation, RNA replication, and other steps of infection by picornaviruses, such as human rhinovirus, coxsackievirus, poliovirus, foot-and-mouth disease virus, enterovirus D-68, and a wide range of other human and nonhuman viruses. Although picornaviruses replicate exclusively in the cytoplasm of infected cells, they have extensive interactions with host cell nuclei and the proteins and RNAs that normally reside in this compartment of the cell. This review will highlight some of the more recent studies that have revealed how picornavirus infections impact the RNA metabolism of the host cell posttranscriptionally and how they usurp and modify host RNA binding proteins as well as microRNAs to potentiate viral replication.

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LARP6 proteins in plants

Biochemical Society Transactions ◽

10.1042/bst20200715 ◽

2021 ◽

Author(s):

Cécile Bousquet-Antonelli

Keyword(s):

Vascular Plants ◽

Rna Binding ◽

Rna Binding Proteins ◽

Plant Evolution ◽

Male Reproduction ◽

Translation Regulation ◽

Translation Control ◽

Binding Properties ◽

Crop Species ◽

Species Specific

RNA binding proteins, through control of mRNA fate and expression, are key players of organism development. The LARP family of RBPs sharing the La motif, are largely present in eukaryotes. They classify into five subfamilies which members acquired specific additional domains, including the RRM1 moiety which teams up with the La motif to form a versatile RNA binding unit. The LARP6 subfamily has had a peculiar history during plant evolution. While containing a single LARP6 in algae and non-vascular plants, they expanded and neofunctionalized into three subclusters in vascular plants. Studies from Arabidopsis thaliana, support that they acquired specific RNA binding properties and physiological roles. In particular LARP6C participates, through spatiotemporal control of translation, to male fertilization, a role seemingly conserved in maize. Interestingly, human LARP6 also acts in translation control and mRNA transport and similarly to LARP6C which is required for pollen tube guided elongation, is necessary to cell migration, through protrusion extension. This opens the possibility that some cellular and molecular functions of LARP6 were retained across eukaryote evolution. With their peculiar evolutionary history, plants provide a unique opportunity to uncover how La-module RNA binding properties evolved and identify species specific and basal roles of the LARP6 function. Deciphering of how LARP6, in particular LARP6C, acts at the molecular level, will foster novel knowledge on translation regulation and dynamics in changing cellular contexts. Considering the seemingly conserved function of LARP6C in male reproduction, it should fuel studies aimed at deriving crop species with improved seed yields.

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