Bulk RNA-seq, small RNA-seq, and miRNA pulldown profiling of H19 RNA editing and miR-675-3p retargeting in mouse hematopoietic cells

Adenosine-to-inosine RNA editing can alter RNA structure, processing, and target recognition, but its physiological functions during hematopoietic stem cell development remain incompletely understood. This study investigates how developmental editing of the imprinted long noncoding RNA H19 regulates hematopoietic stem cell quiescence through the biogenesis and target specificity of miR-675-3p. The deposited datasets comprise conventional bulk RNA sequencing, small RNA sequencing, and biotinylated miRNA pulldown RNA sequencing from mouse hematopoietic stem and progenitor cells and related cell-line models. Bulk RNA-seq was performed in 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A; primary mouse c-Kit-positive cells expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T allele; poly(I)-treated Ki67-eGFP-negative LT-HSCs carrying H19-A, H19-G, or H19-T alleles; and steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs. Small RNA-seq was used to quantify miRNA production in 32D-LV-H19 and primary c-Kit-positive cells under the corresponding ADAR1- and H19-dependent experimental conditions. In parallel, biotinylated miRNA pulldown RNA-seq was performed in 32D cells transfected with scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics. Input and pulldown fractions were sequenced to identify transcripts preferentially associated with each miRNA species. Together, these datasets enable integrated analysis of H19 editing-dependent transcriptional changes, miR-675-3p biogenesis, and editing-induced miRNA target retargeting in hematopoietic cells.