Modified RNA molecules have recently been shown to regulate nervous system functions. This mini-review and associated mini-symposium provide an overview of the types and known functions of novel ...modified RNAs in the nervous system, including covalently modified RNAs, edited RNAs, and circular RNAs. We discuss basic molecular mechanisms involving RNA modifications as well as the impact of modified RNAs and their regulation on neuronal processes and disorders, including neural fate specification, intellectual disability, neurodegeneration, dopamine neuron function, and substance use disorders.
N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the ...brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are incompletely understood. RBM45 acts as an m6A-binding protein that is highly expressed during neurodevelopment. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings show a role for RBM45 in controlling mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA.
Display omitted
•RBM45 preferentially binds to m6A-containing RNA•RBM45 binds thousands of RNAs in mouse and human cells•RBM45 regulates splicing through both m6A-dependent and m6A-independent mechanisms•RBM45 is necessary for proliferation and differentiation of SH-SY5Y cells
Choi et al. identify RBM45 as an m6A-binding protein enriched in the developing brain. RBM45 binds to thousands of cellular RNAs, primarily within introns, and regulates constitutive splicing of target transcripts. Loss of RBM45 causes altered expression of neurodevelopmental genes and defects in the proliferation and differentiation of neuroblastoma cells.
Vertebrate DNA is subjected to epigenetic base modifications that have been thought to be limited to methylated and other modified forms of cytidine. A recent study shows that methylation of adenine ...to form N (6)-methyladenine is a rare but readily detectable modification that can be mapped to distinct genomic sites in vertebrates.
N(6)-methyladenosine (m(6)A) is a modified base that has long been known to be present in non-coding RNAs, ribosomal RNA, polyadenylated RNA and at least one mammalian mRNA. However, our ...understanding of the prevalence of this modification has been fundamentally redefined by transcriptome-wide m(6)A mapping studies, which have shown that m(6)A is present in a large subset of the transcriptome in specific regions of mRNA. This suggests that mRNA may undergo post-transcriptional methylation to regulate its fate and function, which is analogous to methyl modifications in DNA. Thus, the pattern of methylation constitutes an mRNA 'epitranscriptome'. The identification of adenosine methyltransferases ('writers'), m(6)A demethylating enzymes ('erasers') and m(6)A-binding proteins ('readers') is helping to define cellular pathways for the post-transcriptional regulation of mRNAs.
Abstract
N
6
-Methyladenosine (m
6
A) is an abundant post-transcriptional RNA modification that influences multiple aspects of gene expression. In addition to recruiting proteins, m
6
A can modulate ...RNA function by destabilizing base pairing. Here, we show that when neighbored by a 5ʹ bulge, m
6
A stabilizes m
6
A–U base pairs, and global RNA structure by ~1 kcal mol
−1
. The bulge most likely provides the flexibility needed to allow optimal stacking between the methyl group and 3ʹ neighbor through a conformation that is stabilized by Mg
2+
. A bias toward this motif can help explain the global impact of methylation on RNA structure in transcriptome-wide studies. While m
6
A embedded in duplex RNA is poorly recognized by the YTH domain reader protein and m
6
A antibodies, both readily recognize m
6
A in this newly identified motif. The results uncover potentially abundant and functional m
6
A motifs that can modulate the epitranscriptomic structure landscape with important implications for the interpretation of transcriptome-wide data.
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, ...dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
Protein translation typically begins with the recruitment of the 43S ribosomal complex to the 5′ cap of mRNAs by a cap-binding complex. However, some transcripts are translated in a cap-independent ...manner through poorly understood mechanisms. Here, we show that mRNAs containing N6-methyladenosine (m6A) in their 5′ UTR can be translated in a cap-independent manner. A single 5′ UTR m6A directly binds eukaryotic initiation factor 3 (eIF3), which is sufficient to recruit the 43S complex to initiate translation in the absence of the cap-binding factor eIF4E. Inhibition of adenosine methylation selectively reduces translation of mRNAs containing 5′UTR m6A. Additionally, increased m6A levels in the Hsp70 mRNA regulate its cap-independent translation following heat shock. Notably, we find that diverse cellular stresses induce a transcriptome-wide redistribution of m6A, resulting in increased numbers of mRNAs with 5′ UTR m6A. These data show that 5′ UTR m6A bypasses 5′ cap-binding proteins to promote translation under stresses.
Display omitted
•m6A residues within the 5′ UTR promote cap-independent translation•Translation of cellular mRNAs is increased by the presence of m6A within the 5′ UTR•Heat shock induces Hsp70 translation in an m6A-dependent manner•Diverse cellular stresses increase 5′ UTR adenosine methylation
N6-methyladenosine (m6A) residues within the 5′ UTR of mRNAs promote translation initiation through a mechanism that does not require the 5′ cap or cap-binding proteins. Diverse cellular stresses selectively increase the levels of m6A within 5′ UTRs, suggesting that 5′ UTR m6A is important for mediating stress-induced translational responses.
Degraded floodplains and valley floors are restored with the goal of enhancing habitat for native fish and aquatic-riparian biota and the protection or improvement of water quality. Recent years have ...seen a shift toward “process-based restoration” that is intended to reestablish compromised ecogeomorphic processes resulting from site- or watershed-scale degradation. One form of process-based restoration has developed in the Pacific Northwest, United States, that is intended to reconnect rivers to their floodplains by slowing down flows of sediment, water, and nutrients to encourage lateral and vertical connectivity at base flows, facilitating development of dynamic, self-forming, and self-sustaining river-wetland corridors. Synergies between applied practices and the theoretical work of Cluer and Thorne in 2014 have led this form of restoration to be referred to regionally as restoration to a Stage 0 condition. This approach to rehabilitation is valley scale, rendering traditional monitoring strategies that target single-thread channels inadequate to capture pre- and post-project site conditions, thus motivating the development of novel monitoring approaches. We present a specific definition of this new type of rehabilitation that was developed in collaborative workshops with practitioners of the approach. Further, we present an initial synthesis of results from monitoring activities that provide a foundation for understanding the effects of this approach of river rehabilitation on substrate composition, depth to groundwater, water temperature, macroinvertebrate richness and abundance, secondary macroinvertebrate production, vegetation conditions, wood loading and configuration, water inundation, flow velocity, modeled juvenile salmonid habitat, and aquatic biodiversity.
N.sup.6-methyladenosine (m.sup.6A) is a widespread RNA modification that influences nearly every aspect of the messenger RNA lifecycle. Our understanding of m.sup.6A has been facilitated by the ...development of global m.sup.6A mapping methods, which use antibodies to immunoprecipitate methylated RNA. However, these methods have several limitations, including high input RNA requirements and cross-reactivity to other RNA modifications. Here, we present DART-seq (deamination adjacent to RNA modification targets), an antibody-free method for detecting m.sup.6A sites. In DART-seq, the cytidine deaminase APOBEC1 is fused to the m.sup.6A-binding YTH domain. APOBEC1-YTH expression in cells induces C-to-U deamination at sites adjacent to m.sup.6A residues, which are detected using standard RNA-seq. DART-seq identifies thousands of m.sup.6A sites in cells from as little as 10 ng of total RNA and can detect m.sup.6A accumulation in cells over time. Additionally, we use long-read DART-seq to gain insights into m.sup.6A distribution along the length of individual transcripts. Getting around the limitations of antibody-based N.sup.6-methyladenosine (m.sup.6A) pulldown, such as high input requirements and cross-reactivity, DART-seq profiles transcriptome-wide m.sup.6A occurrences from RNA amounts equivalent to the RNA obtained from 1,000 cells.
In recent years,
Disrupted-In-Schizophrenia 1 (
DISC1) has emerged as one of the most promising candidate genes whose disruption confers an increased risk for schizophrenia. Cell biology studies have ...implicated DISC1 in key neurodevelopmental processes including neurite outgrowth and neuronal migration.
In situ hybridization analysis has revealed that
Disc1 is expressed in the hypothalamus, olfactory bulbs, the developing cerebral cortex and the hippocampus. The hippocampus is of particular interest because abnormalities in hippocampal volume and function have been consistently reported in schizophrenics. Moreover,
DISC1 mutations have been associated with abnormal activation of the hippocampus in humans. Given the involvement of the hippocampus in the pathophysiology of schizophrenia, there is an intriguing possibility that disruption of DISC1 may increase schizophrenia susceptibility by altering the normal development and function of the hippocampus. In order to contribute to our understanding of DISC1’s role in the hippocampus, we have performed a detailed analysis of the Disc1 expression pattern in the mouse hippocampus throughout development. We report that Disc1 is expressed throughout the hippocampus during embryonic development, with expression becoming increasingly specialized in Ammon’s horn and dentate gyrus granule cells within the first postnatal week. This expression pattern remains consistent into adulthood, with a noted decrease in Disc1 expression in the adult CA1. Disc1 is also expressed in proliferating cells in the adult subgranular zone, as well as in a subset of GABAergic interneurons. Our results are the first report of a detailed immunohistochemical analysis of the ontogeny of Disc1 expression within the hippocampus.
PDF
