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Series GSE221756 Query DataSets for GSE221756
Status Public on May 15, 2024
Title Chromatin Accessibility Analysis of LIRIL2R-Deficient and LIRIL2R-Sufficient Induced Regulatory T Cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Factors that determine the epigenetic landscape of regulatory T cells (Tregs), which is critical for their function, remain poorly understood. Long intergenic noncoding RNAs (LincRNA)s are important for shaping and maintaining the epigenetic landscape in different cell types. We identified a novel uncharacterised lincRNA, which we named LincRNA regulator of IL2RA (LIRIL2R), that is upregulated during early differentiation of human Tregs. RNA sequencing (RNA-seq) and data independent (DIA) proteomic analysis of LIRIL2R-deficient Tregs, with genome-wide chromatin occupancy analysis, identified IL2RA as direct LIRIL2R target. This nuclear lincRNA directly binds upstream of IL2RA locus and regulates its transcription by facilitating the accessibility of the locus. LIRIL2R-deficient Tregs had reduced expression of Treg-related genes, including FOXP3, IL2RA, STAT5, CTLA4 and PDCD1, as well as reduced suppressive capacity. Modulating LIRIL2R expression may hold promise for better therapeutic strategies against autoimmunity and cancer.
 
Overall design CD4 T cells were isolated from human umbilical cord blood. Cells were treated with either contrl non targeting (NT) antisense loked nucleic acid oligos (LNAs) or LNAs targeting LIRIL2R. The cells were differentiated under iTreg conditions for 24/72 hours and ATAC-seq was performed.
 
Contributor(s) Khan MM, Andrabi SB, Khan MH, Rasool O, Kalim UU, Junttila S, Elo LL, Lahesmaa R
Citation(s) 38805281
Submission date Dec 26, 2022
Last update date Aug 14, 2024
Contact name Riitta Lahesmaa
E-mail(s) rilahes@utu.fi
Organization name University of Turku
Department Turku Bioscience
Lab Lahesmaa lab
Street address Tykistökatu 6A
City Turku
ZIP/Postal code 20520
Country Finland
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (36)
GSM6895315 1_LNA_NT_24h_rep1_S1_LANE1
GSM6895316 1_LNA_NT_24h_rep1_S1_LANE2
GSM6895317 2_LNA_1_24h_rep1_S2_LANE1
This SubSeries is part of SuperSeries:
GSE221759 Long Noncoding RNA LIRIL2R Modulates FOXP3 Levels and Suppressive Function of Human CD4+ Regulatory T Cells by Regulating IL2RA
Relations
BioProject PRJNA915967

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE221756_bigwig.tar.gz 6.8 Gb (ftp)(http) TAR
GSE221756_narrowPeak.tar.gz 84.3 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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