Most of the mammalian genome does not encode for working proteins. However, much of this non-coding DNA is still transcribed, often to produce RNA products that have a role in development. Some of these molecules are called long non-coding RNAs (lncRNAs) because they contain more than 200 base pairs: these transcripts fine-tune gene expression by interacting with chromatin and the transcription machinery inside cells (Ponting et al., 2009). The brain expresses more lncRNAs than any other part of the body (Derrien et al., 2012), but we know relatively little about the roles these molecules play in this organ (D'haene et al., 2016; Aprea et al., 2013). Learning more about lncRNAs will be essential if we are to understand both the typical and the atypical brain.
In intellectual disabilities or autism spectrum disorders, defects in cognitive abilities, such as social interaction and communication, can appear early in development and persist into adulthood. These neurodevelopmental disorders involve abnormal changes in the way genetic information is expressed (Rennert and Ziats, 2017). Several lncRNAs are associated with these conditions, sometimes being transcribed atypically (reviewed in van de Vondervoort et al., 2013). For instance, certain lncRNAs are expressed differently in patients on the autism spectrum (Ziats and Rennert, 2013).
Now, in eLife, Anand Srivastava, Marius Wernig, Howard Chang and colleagues – including Cheen Ang, Qing Ma and Orly Wapinski, all from Stanford University, as joint first authors – report that several lncRNAs that are involved in the formation of neurons are mutated or disrupted in children with autism spectrum disorder and intellectual disabilities (Ang et al., 2019).
Ang et al. started by reprogramming mouse cells called embryonic fibroblasts into neurons; this experiment helped them to identify 35 candidate lncRNAs that are both upregulated when neurons form and close to neuronal genes. Amongst those, 28 were present on the same chromosomes in humans and in mice. The group then tried to identify whether these 28 human candidates were mutated in disease by overlapping the lncRNAs sequences onto a map of mutations found in children with neurodevelopmental disorders and congenital defects. This analysis highlighted five lncRNAs that were often mutated in affected individuals, and which happened to also be expressed during human brain development. One of them, called lnc-NR2F1, was adjacent to NR2F, a gene which encodes a transcription factor that helps neurons form and wire together (Borello et al., 2014).
The team, which is based at Stanford, Clemson University, the University of Washington, the Greenwood Genetic Center, and the Austrian Academy of Sciences, found patients with developmental delays who expressed normal levels of the coding NR2F1 gene but presented a unique disruption of the lnc-NR2F1 gene. Most of the brain lncRNAs are located near genes that code for proteins, and it is believed that both lncRNAs and protein-coding genes are expressed at the same time (Ponjavic et al., 2009). However, the work by Ang et al. potentially indicates that lnc-NR2F1, rather than NR2F1, might contribute to the clinical symptoms associated with neurodevelopmental disorders. If so, this would strengthen the hypothesis that lncRNAs are independent transcriptional units that activate gene expression in the brain.
Then, Ang et al. discovered that, in mouse cells, lnc-Nr2f1 enhanced the transcription of genes that create and guide the structures which allow neurons to connect. Deleting or overexpressing lnc-Nr2f1 changed how these genes were expressed, and how the cells looked and worked. In addition, lnc-Nr2f1 was shown to attach to the genes, suggesting that it binds chromatin to regulate gene expression (Figure 1). While we still do not fully understand the physiological changes that accompany neurodevelopmental disorders, the results by Ang et al. suggest that lncRNAs themselves may contribute to these conditions, or that they drive the expression of disease-associated genes.
Mouse embryonic fibroblasts (orange) were reprogrammed into neurons (top right) using transcription factors called BAM factors. This led to an increase in the expression of neuronal genes (green …
How mutations in protein-coding genes contribute to disease is widely studied, yet most mutations are found in regions that do not code for proteins. Understanding how lncRNAs regulate genes during brain development provides a way to tie genetic variation with changes in gene expression in neurodevelopmental disorders. Building on the findings by Ang et al., it may be possible to examine how clinical phenotypes, cellular responses and lncRNAs are connected in these conditions, potential unearthing new targets for therapeutic intervention.
© 2019, Lozano-Ureña and Ferrón
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Polyamines are biologically ubiquitous cations that bind to nucleic acids, ribosomes, and phospholipids and, thereby, modulate numerous processes, including surface motility in Escherichia coli. We characterized the metabolic pathways that contribute to polyamine-dependent control of surface motility in the commonly used strain W3110 and the transcriptome of a mutant lacking a putrescine synthetic pathway that was required for surface motility. Genetic analysis showed that surface motility required type 1 pili, the simultaneous presence of two independent putrescine anabolic pathways, and modulation by putrescine transport and catabolism. An immunological assay for FimA—the major pili subunit, reverse transcription quantitative PCR of fimA, and transmission electron microscopy confirmed that pili synthesis required putrescine. Comparative RNAseq analysis of a wild type and ΔspeB mutant which exhibits impaired pili synthesis showed that the latter had fewer transcripts for pili structural genes and for fimB which codes for the phase variation recombinase that orients the fim operon promoter in the ON phase, although loss of speB did not affect the promoter orientation. Results from the RNAseq analysis also suggested (a) changes in transcripts for several transcription factor genes that affect fim operon expression, (b) compensatory mechanisms for low putrescine which implies a putrescine homeostatic network, and (c) decreased transcripts of genes for oxidative energy metabolism and iron transport which a previous genetic analysis suggests may be sufficient to account for the pili defect in putrescine synthesis mutants. We conclude that pili synthesis requires putrescine and putrescine concentration is controlled by a complex homeostatic network that includes the genes of oxidative energy metabolism.
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