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Characterizing circular and linear non-coding RNA in human aging brains and their association with dementia

ABSTRACT: Total RNA, depleted for ribosomal RNA, is commonly used for RNA sequencing to capture both polyadenylated and non-polyadenylated transcripts, while the poly(A) tail targeting protocols can either enrich (Poly(A)-selection) or deplete (Poly(A)-depletion) the polyadenylated fraction. To ascertain the best library strategy for capturing long non-coding RNAs (lncRNAs, >200nt) and circular RNAs (circRNAs) in aged brains, we applied three protocols (total ribo-depleted, poly(A)-selected, and poly(A)-depleted) to 128 human hippocampus samples. Our results show that both ribo-depleted and poly(A)-depleted perform well for lncRNA and circRNA profiling, with poly(A)-depleted protocol generally having a slightly higher number of non-coding RNAs detected. Additionally, we compared poly(A)-selected and -depleted data for predicting the poly(A) status of hippocampus transcripts. The proportion of non-polyadenylated transcripts was higher than previously found. This study demonstrates how the choice of library construction impacts the outcomes, helping to make informed methodological choices when studying brain non-coding RNAs. In addition, we for the first time examined whether the poly(A) status of protein-coding mRNAs is associated with AD and AD-related dementias.

ORGANISM(S): Homo sapiens

PROVIDER: GSE339279 | GEO | 2026/07/20

REPOSITORIES: GEO

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Project description:The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein coding transcriptome remains unknown. Expression profiling on whole genome tiling microarrays applied to a mixed stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11 %) of the polyadenylated transcription is non-annotated, and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). Almost half (44%) of the detected transcriptional output is non-polyadenylated and probably not protein coding, and of this 70% overlap the boundaries of protein coding genes in a complex manner. Specific analysis of small non-polyadenylated transcripts verified 98% of all annotated small ncRNAs, and suggested that the transcriptome contains about 1,200 small (<500 nt) unannoted non-coding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed. Keywords: RNA fractions RNA was extracted from mixed stage wild-type N2 strain worms cultivated at 20oC according to the Trizol (Invitrogen) protocol. Small RNAs (< 500nt, SNPA sample) were isolated using a Qiagen tip (Qiagen), and the Poly(A) Purist MAG (Ambion) and MicrobExpress kits (Ambion) were adapted to remove remaining mRNAs and rRNAs (Deng et al. 2006). The enriched ncRNA pool was cloned using an adaptor-mediated library construction protocol. RNAs were dephosphorylated with calf intestine alkaline phosphatase (Fermentas), then ligated to the 3M-bM-^@M-^Y-adaptor (3AD) oligonucleotide by T4 RNA ligase (Fermentas) (He et al. 2006). Polyadenylated RNA (PA sample) was isolated from total RNA using the Poly(A) Purist MAG kit (above). Non-polyadenylated RNA (NPA sample) was prepared by removing polyadenylated RNA using the Poly(A) Purist MAG kit and rRNA using the MicrobExpress kit.

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Characterizing circular and linear non-coding RNA in human aging brains and their association with dementia

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