PXD059550-1

PXD059550 is an original dataset announced via ProteomeXchange.

Title	Mapping effective microRNA pairing beyond the seed using abasic modifications
Description	MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base-pairing to complementary sites in mRNAs. The primary element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, the structural determinants of effective pairing outside the seed are not fully understood. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this modification compared to wild-type miR-34a on the cellular transcriptome and proteome using RNA-seq and mass spectrometry. We find that a subset of sites with predicted supplementary pairing are affected by miRNA transfection, with up to two-fold decreases in site repression at the mRNA level, although the effect at the protein level is less pronounced. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_06:48:27.938.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	José Eduardo Araújo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-08 06:20:39	ID requested
⏵ 1	2025-05-07 06:48:28	announced

Kosek DM, Petzold K, Andersson ER, Mapping effective microRNA pairing beyond the seed using abasic modifications. Nucleic Acids Res, 53(8):(2025) [pubmed]

10.1093/nar/gkaf364;

submitter keyword: miRNA, Homo sapiens, miR-34a, HEK293T

Prof Janne Lehtiö
contact affiliation	Karolinska Institute/ScilifeLab
contact email	janne.lehtio@ki.se
lab head
José Eduardo Araújo
contact affiliation	Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet
contact email	jose-eduardo.araujo@scilifelab.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059550
     1. Label: PRIDE project
     2. Name: Mapping effective microRNA pairing beyond the seed using abasic modifications