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Analysis of transcripts in PNA-A(15) oligo treated human HEK-293 cells

ABSTRACT: Mononucleotide A and T repeats are abundant in human genome. Many of A repeats are bound by Argonaute proteins (AGOs). To evaluate the role of AGOs and A repeats in gene regulation, HEK293 cells were treated with 8-amino-3,6-dioxaoctanoic acid added peptide nucleic acid (PNA) AAAAAAAAAAAAAAA oligo (OO-A(15)). Matched two sets of two individual HEK293 cells were transfected with OO-A(15) and scramble OO-PNA oligo, and were analyzed as biological duplicates. Cells were grown in DMEM (Gibco-BRL) according to the manufacturer’s protocol. OO-A(15) and scramble oligo were dilute with dH2O to reach 10μM. Cells were transfected in 6-well plates, seed 6 x 105 cells per well with 50 nM OO-A(15) and scramble oligo using TransIT-siQUEST transfection reagent (Mirus). The transfected cell lines were cultured for 48 h post-transfection and harvested total RNA by Trizol reagent (Invitrogen). All RNA integrity assays were performed and hybridized on beadchip according to the protocol.

ORGANISM(S): Homo sapiens

SUBMITTER: Chatchawit Aporntewan 

PROVIDER: E-GEOD-43185 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.

Aporntewan Chatchawit C   Pin-on Piyapat P   Chaiyaratana Nachol N   Pongpanich Monnat M   Boonyaratanakornkit Viroj V   Mutirangura Apiwat A  

Nucleic acids research 20130808 19

A-repeats are the simplest form of tandem repeats and are found ubiquitously throughout genomes. These mononucleotide repeats have been widely believed to be non-functional 'junk' DNA. However, studies in yeasts suggest that A-repeats play crucial biological functions, and their role in humans remains largely unknown. Here, we showed a non-random pattern of distribution of sense A- and T-repeats within 20 kb around transcription start sites (TSSs) in the human genome. Different distributions of  ...[more]

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