Nitrous systems, improved aerodynamics, and slick tires on your car may all help to quench your need for speed when you get behind the wheel; however, the need to slow down is just as critical in the world of gene regulation. Recently, a team of researchers has described how the modification of a racy subset of intergenic RNAs known as chromosome-associated regulatory RNAs or carRNAs induces a transcriptional slowdown and a change to the underlying epigenetic state that can modify downstream gene expression.
In the epigenetics lane of the biology highway, the N6-methyladenosine (m6A)-modification of pluripotency-related mRNAs by Mettl3 puts a brake on their transcription by “speeding up” their Ythdf2-driven decay in the cytoplasm of pluripotent stem cells; however, studies have suggested that m6A may also play a nucleus-specific Ythdc1-mediated function in transcriptional regulation. These findings drove a car-pooling research team led by Yawei Gao (Tongji University, Shanghai), Dali Han (Chinese Academy of Sciences, Beijing, China), and Chuan He (University of Chicago, Illinois, USA) to “hit the brakes” on other projects, shift gears, and accelerate an investigation into the transcriptional consequences of m6A in the nucleus of mouse embryonic stem cells (mESCs). Fascinatingly, the team now reports that m6A acts as an epigenetic brake for carRNAs, which include promoter-associated, enhancer, and repeats RNAs, in a mechanism that also impedes downstream gene expression via alterations at the chromatin level.
So, let’s allow Liu, Dou, Chen, and colleagues to take us for an epigenetic ride through their car-efully compiled data:
- Mass spectrometry and methylated RNA immunoprecipitation sequencing (MeRIP-seq) of wild type, Ythdc1 conditional knockout, and Mettl3 knockout mESCs established that Mettl3 deposits m6A modifications on carRNAs located in intergenic regions and Ythdc1 recognizes said RNAs (but not Ythdc2)
- m6A levels negatively correlate with carRNA expression, suggesting that m6A acts to destabilize these RNAs
- Ythdc1 promotes the decay of modified RNA via the nuclear exosome targeting (NEXT) complex, with LINE1 repeat elements constituting the greatest proportion of Mettl3-modified carRNAs affected by Ythdc1
- Time-course RNA-seq of both nascent transcripts and total nuclear RNAs and mammalian native elongating transcript sequencing (mNET-seq) also established that the loss of the m6A-modified carRNAs by Mettl3 depletion leads to a general upregulation of gene expression and transcription rate
- Genes with m6A-modified upstream carRNAs display higher increases in transcription rate than those with non-m6A-modified upstream carRNAs, indicating that loss of m6A activates the transcription of genes downstream of the carRNAs
- As a mechanism for this observation, the authors found that the loss of m6A on carRNAs enhances chromatin accessibility (by DNase I-TUNEL assays), increases the binding of transcription factors (Ep300 and Yy1 by ChIP-seq), and increases the levels of active histone marks (H3K4me3 and H3K27ac by ChIP-seq) at carRNA loci
Overall, these data support the existence of direct crosstalk between the m6A modification of carRNA and the underlying chromatin state, which supposes an additional layer of transcriptional regulation.
“This has major implications in basic biology,” study leader He said. “It directly affects gene transcriptions, and not just a few of them. It could induce global chromatin change and affects transcription of 6,000 genes in the cell line we studied.” He continues, “I believe this represents a conceptual change. Barriers like these are hard to crack, but once you do, everything flows from there.”
To wheel-y get what we this fascinating new study is driving at, why not take a ride over to Science, January 2020.