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Series GSE134761 Query DataSets for GSE134761
Status Public on Aug 04, 2019
Title Dynamic 3D chromosomal landscapes in acute leukemia [Hi-C]
Organism Homo sapiens
Experiment type Other
Summary Background: Disruptions of 3D chromatin architecture can alter the activity of topologically associated domains (TADs), rewire enhancer-promoter interactions and thus significantly impact gene regulatory programs. Recently, such disruptions have been implicated in tumorigenesis, highlighting the need for a deeper understanding of their detailed role.
Methods: T-ALL primary samples and prototypical cell lines as well as healthy T cell counterparts were profiled by in-situ Hi-C, RNA-Seq and CTCF ChIP-Seq. Data was subsequently integrated.
Results: Our studies showed that the genome of leukemia cells does not display global changes in TAD structures but presents local changes in selected TAD boundaries as well as alterations of intra-TAD activity which are associated with changes in gene expression of key oncogenes and tumor suppressors, strong correlation with CTCF-mediated insulation and enhancer activity. Finally, we showed that 3D interactions on selected loci can be partially corrected pharmacologically, potentially accounting for the anti-leukemogenic effects of these drugs.
Conclusions: Our studies underscore the need for further investigation of factors that rewire long range interactions especially during tumorigenesis, as they could be targets for pharmacological targeting.
Overall design Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) as well as healthy T cell counterparts from three different donors were collected.
Contributor(s) Kloetgen A, Thandapani P, Ntziachristos P, Aifantis I, Tsirigos A
Citation(s) 32203470
Andreas Kloetgen, Palaniraja Thandapani, Panagiotis Ntziachristos, et al. Dynamic 3D chromosomal landscapes in acute leukemia. bioRxiv 2019. doi:10.1101/724427
Submission date Jul 24, 2019
Last update date Mar 25, 2020
Contact name Andreas Kloetgen
Organization name Helmholtz Centre for Infection Research
Department Department for Computational Biology of Infection Research
Street address Inhoffenstr 7
City Braunschweig
State/province NI
ZIP/Postal code 38124
Country Germany
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (20)
GSM3967114 Tcell1 (Hi-C)
GSM3967115 Tcell2 (Hi-C)
GSM3967116 Tcell3 (Hi-C)
This SubSeries is part of SuperSeries:
GSE115896 Dynamic 3D chromosomal landscapes in acute leukemia
BioProject PRJNA556356
SRA SRP216194

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
GSE134761_CUTLL1_DMSO_Arima_TADs_hicratio-500kb-activity.bed.gz 17.7 Kb (ftp)(http) BED
GSE134761_CUTLL1_DMSO_HindIII_TADs_hicratio-500kb-activity.bed.gz 18.1 Kb (ftp)(http) BED
GSE134761_CUTLL1_THZ1_Arima_TADs_hicratio-500kb-activity.bed.gz 17.6 Kb (ftp)(http) BED
GSE134761_CUTLL1_gSI_TADs_hicratio-500kb-activity.bed.gz 18.2 Kb (ftp)(http) BED
GSE134761_RAW.tar 230.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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