As modern technology develops, we grow increasingly connected with one another while also striving to maintain our individual identities. Although some may blame social media for our desire to be unique snowflakes just like everyone else, exciting new research demonstrates a molecular mechanism for individual neuronal identity in the brain that may just be the inspiration behind such cognitive desires.
At the center of such a complex mechanism are the clustered protocadherins, and boy are they one complex cluster. This single locus contains three main clusters known as α, β, and γ, where α and γ contain variable and constant exons, and each variable exon has its own promoter. These clusters generate transcriptional diversity that parallels the immune system; however, unlike the immune system, this diversity isn’t achieved through genetic recombination but instead by some incredibly complex chromosome conformations sculpted by CTCF and cohesin. Given the role of CTCF, it should come as no surprise that the DNA methylation is a key player. Stochastic promoter methylation determines which promoter will be brought into the proximity of an enhancer element by DNA looping and thus which alternate gene from the α cluster will be expressed. Then, to top off all this complexity, each allele has its own profile. Ultimately, this mechanism plays a large role in how neurons of same type know to form connections with their neighbors and not themselves.
Now, the protocadherin pioneers from the lab of Tom Maniatis (Columbia University, USA) have uncovered a new player behind the stochastic promoter choice of the protocadherin α cluster.
During their protocadherin pilgrimage, the talented team threw the force of the New York Genome Center at the locus. They examined a human neuronal cell line (SK-N-SH) and mouse olfactory neurons, where they utilized RNA-seq, capture RNA-seq, Start-Seq, s4UDRB-seq, ChIP-seq and ChIP-qPCR for CTCF, H3K4me3, and H3K27ac, In situ Chromatin Capture Conformation (Hi-C), methylated DNA immunoprecipitation sequencing (MeDIP-seq), bisuflite sanger sequencing, CRISPR/Cas9 genome editing, and CRISPR-activation.
While all the details are a bit too complex for our concise summary, here’s the exciting mechanism they uncovered:
- In their ground developmental state, all the alternate α protocadherin gene promoters are methylated
- Each alternate exon has its own antisense promoter nearby, and antisense expression runs into the sense promoter of the related alternate α protocadherin
- The antisense lncRNA recruits TET3 to demethylate both its own antisense promoter and the related sense alternate gene promoter
- CTCF then binds the demethylated alternate gene promoter, where it forms a DNA loop and brings it into proximity of the enhancer element to drive its expression
Overall, these findings bring an exciting mechanism to light, where antisense lncRNA transcription recruits TET3 to demethylate a promoter, which allows it to be recruited to an enhancer by CTCF. Furthermore, these results have exciting implications for not only our understanding of neurodevelopment, but also for psychiatric disorders and environmental exposures.
Go learn how to make the right type of connections in your brain over in Cell, April 2019