GSE181136
GSE GEOGlobal Identification of the miR-130a targetome in human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]
Relations
Summary
Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells have firmly established the existence of shared core stemness properties. However, the discordance between mRNA and protein signatures underscores an important role for post-transcriptional regulation by miRNAs in governing this critical nexus. Here, we identify miR-130a as a regulator of hematopoietic stem cell (HSC) self-renewal and lineage differentiation. Integration of mass spectrometry and chimeric AGO2 eCLIP-seq identify TBL1XR1 as a primary miR-130a target. TBL1XR1 loss of function impairs lymphoid differentiation and expands long-term (LT)-HSC. This post-transcriptional regulation by miR-130a is usurped in t(8,21) acute myeloid leukemia (AML). Reduction of miR-130a levels in t(8,21) AML cells results in altered chromatin binding and composition of the AML1-ETO complex, demonstrating that miR-130a is critical for maintaining the oncogenic molecular program mediated by AML1-ETO. Our study establishes that comprehensive identification of the miRNA targetome within primary tissue enables the discovery of novel genes and molecular networks underpinning stemness properties of normal and leukemic cells.
Overall Design
Examination of binding occupancy of AML1-ETO following miR-130a knock-down in Kasumi-1 cell line. >>>Submitter states: Raw data is being submitted separately to the EGA as we require controlled access for some data.<<<
Analysis (15 steps)
View Data Processing- Library strategy: CUT&RUN
- CUT&RUN paired-end data was trimmed using fastp v.
- 0.19.5 to remove adapters and low quality base pairs with base pair quality score <30 and read length <35 bp.
- Trimmed reads were aligned to the hg38 human reference genome using bowtie2 v.
- 2.3.5.
- Reads were also aligned to the S. cerevisiae yeast genome (sacCer3) yeast genome to evaluate the yeast spike-in control for the normalization.
- Peaks were called from the pooled replicates against the IgG using MACS2 v.
- 2.2.5 with normalizing the samples based on the spike-in reads qunatification.