Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases

Abstract

The transcriptional regulator peroxisome proliferator activated receptor gamma coactivator 1A (PGC-1α), encoded by PPARGC1A, has been linked to neurodegenerative diseases. Recently discovered CNS-specific PPARGC1A transcripts are initiated far upstream of the reference promoter, spliced to exon 2 of the reference gene, and are more abundant than reference gene transcripts in post-mortem human brain samples. The proteins translated from the CNS and reference transcripts differ only at their N-terminal regions. To dissect functional differences between CNS-specific isoforms and reference proteins, we used clustered regularly interspaced short palindromic repeats transcriptional activation (CRISPRa) for selective endogenous activation of the CNS or the reference promoters in SH-SY5Y cells. Expression and/or exon usage of the targets was ascertained by RNA sequencing. Compared to controls, more differentially expressed genes were observed after activation of the CNS than the reference gene promoter, while the magnitude of alternative exon usage was comparable between activation of the two promoters. Promoter-selective associations were observed with canonical signaling pathways, mitochondrial and nervous system functions and neurological diseases. The distinct N-terminal as well as the shared downstream regions of PGC-1α isoforms affect the exon usage of numerous genes. Furthermore, associations of risk genes of amyotrophic lateral sclerosis and Parkinson’s disease were noted with differentially expressed genes resulting from the activation of the CNS and reference gene promoter, respectively. Thus, CNS-specific isoforms markedly amplify the biological functions of PPARGC1A and CNS-specific isoforms and reference proteins have common, complementary and selective functions relevant for neurodegenerative diseases.

Epigenetics of Mitochondria-Associated Genes in Striated Muscle

“…Much of the versatility of this co-regulator in its tissue-specific roles can be ascribed to its multiple tissue-specific mRNA isoforms and corresponding protein isoforms. PGC-1α protein isoforms differ in biochemical properties, protein-protein interactions, stability, and subcellular localization [ 46 , 47 , 48 , 49 ]. Isoform formation depends partly on the choice of one of the following promoters for transcription initiation: the proximal (Prox) promoter (encoding the canonical 797-aa PGC-1α1), the 14-kb upstream alternate (Alt) promoter, the downstream liver-associated promoter, and a ~0.6-Mb upstream brain-associated promoter (distal promoter) ( Figure 7 A and Figure S7 ) [ 43 , 46 ].…”

Covering the Role of PGC-1α in the Nervous System

“…A new promoter of PGC-1α was identified and it is localized far upstream of the reference promoter of the PGC-1α gene [ 26 ] ( Figure 1 ). This promoter initiates CNS-specific transcripts of PGC-1α, which differ from the reference gene transcript in N-terminus sequence and contain novel exons B1-B5 spliced to exon 2 of the reference gene [ 26 , 27 ]. These transcripts encode two full-length and several truncated isoforms of PGC-1α [ 26 ].…”

“…Activation of the CNS-specific PGC-1α promoter by Forkhead Box A2 (FOXA2), a transcription factor vital for differentiation and functioning of dopaminergic midbrain neurons but not the reference gene promoter in SH-SY5Y cells, indicates involvement of CNS-specific transcripts in the generation and maintenance of dopaminergic neurons [ 30 ]. It was shown that activation of CNS-specific PGC-1α promoter affected the expression of ALS and Parkinson’s disease risk genes in SH-SY5Y cells [ 27 ]. Still, the role of these isoforms in the functioning of the CNS or the pathophysiology of neurodegenerative diseases in vivo remains to be elucidated; therefore, it is too early to target them in therapies.…”

“… CNS-specific isoforms of PGC-1α include exons localized upstream to the reference promoter; B1, B4, B5: CNS-specific exons (red, yellow, and green respectively); 7a and 3ext: alternatively spliced transcripts encoding stop codons in exon 7a or in an extension of exon 3 (blue and purple, respectively) (based on [ 26 ] and [ 27 ]). …”

Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population?

“…For example, Cas9 nuclease can be converted into an RNA-guided DNA-binding protein (dCas9) and then fused to transcription activation or repressor domains. These dCas9-activator fusions target the promoter/enhancer regions of endogenous genes to modulate gene expression [ 160 , 161 ].…”