Decades of diligent exploration in the mammalian genome has led to the discovery that while only around 2% of this base-pair jungle represents protein-coding sequence, over 90% of our genome gets transcribed into RNA species such as long non-coding RNAs (lncRNAs). However, our knowledge base on many lncRNAs remains in “terra incognita” with scant details on the roles of most of these ~200 nucleotide-long RNAs.
Our lack of lncRNA knowledge also encompasses the telomeric repeat-containing RNA (TERRA) transcripts transcribed from the DNA-protein telomere complexes encountered at the ends of our chromosomes. Many studies have confirmed an expected role for TERRA in telomere maintenance, but a few adventurous studies have hinted that these lncRNAs may stray from their telomeric base camps into the “TERRA” incognita of the rest of the genome!
Now, a TERRA-ific new study from the lab of Jeannie T. Lee (Massachusetts General Hospital/Harvard Medical School, Boston, USA) has employed genomic, proteomic, biochemical, and cytological techniques to demonstrate that while TERRA does play a major role in telomere dynamics, TERRA also binds to sites throughout the genome and can help to regulate gene expression!
Let’s pass our magnifying glass over some of the details gleaned from the logbooks of these intrepid genomic adventurers:
- The exploration of genomic binding locations of TERRA employed a hybrid method named CHIRT
- CHIRT combines elements from the chromatin isolation by RNA purification (CHIRP) and capture hybridization of RNA targets (CHART) techniques
- Analysis of the thousands of binding sites in mouse embryonic stem cells indicates that while the majority of TERRA lncRNAs localize to the telomere, TERRA also binds to additional sites throughout the genome
- The Direct RNA interacting proteins (iDRiP) technique characterized the protein interactome of TERRA lncRNAs
- This analysis identified 134 new protein partners involved in telomere dynamics, chromatin modifications, and transcriptional control
- Of note, TERRA and the chromatin remodeler ATRX interact, and many TERRA binding sites overlap with ATRX binding sites
- RNA-seq combined with TERRA knockdown (using an antisense oligonucleotide) suggested that TERRA transcripts can act as transcriptional regulators, similar to other regulatory lncRNAs, and also that TERRA and ATRX are functionally antagonistic
- While ATRX knockdown promotes the upregulation of nearby genes, TERRA knockdown downregulates the expression of said genes, impairs telomere capping function, and promotes genomic instability
- At the telomere, TERRA competed with telomeric DNA for ATRX binding, suppressed ATRX localization, and ensured telomeric stability
Looking to the future, Chu et al. hope to expand the chromatin and protein interaction networks for TERRA via analysis of the vast amounts of data generated from the CHIRT and iDRiP techniques.
Has this study relocated our lncRNA knowledge from terra incognita to terra firma? See for yourself over at Cell, June 2017.