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Series GSE123806 Query DataSets for GSE123806
Status Public on Dec 04, 2020
Title Homotypic clustering of L1 and B1 repeats organizes 3D genome
Organism Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary We postulated that the primary DNA sequences, particularly abundant repetitive elements embedded in the genome, may instruct genome folding. Short and long interspersed nuclear elements (SINEs and LINEs, respectively) are two predominant sub-families of retrotransposons in most mammals. LINE-1 (LINE1 or L1) constitutes the most abundant type of repeat subclasses, making up to 18.8% and 17% (0.9~1.0 million copies) of the genome in mouse and human, respectively. B1 in mouse and its closely related, primate-specific Alu elements in human are the most abundant subclass of SINEs, constituting 2.7%~10% (0.6~1.4 million copies) of mouse and human genomes. Here, we demonstrate that B1/Alu and L1 repeats demarcate the genome into the A/B compartments and serve as the blueprint for the three-dimensional (3D) organization of mammalian genomes. Our finding explains the robustness and evolutionary conservation of nuclear chromatin organization in mammals.

H3K9me3 ChIP-seq upon L1 AMO treatment;
We electrotransfected L1 AMO into mESC to block L1 transcripts for 36 h and a standard control from GenTools was used as control -"SCR". We performed H3K9me3 ChIP-seq in mESCs treated with L1 or SCR AMO for 36 h. We found that L1 AMO did not alter the genome-wide binding of H3K9me3, ruling out the possibility that the loss of organization relates to changes in local heterochromatin marks.
Overall design All HiC were designed to reveal the role of LINE1 RNA in higher-order chromatin structure
Examination of L1 AMO treatment on H3K9me3 modification distribution genome-wide in mESC.
Contributor(s) Lu YJ, Chang L, Li T, Sun Y, Shen X
Citation(s) 33514913
Submission date Dec 13, 2018
Last update date Jun 15, 2021
Contact name jinlong lu
Phone 5853098469
Organization name University of Rochester
Lab Gorbunova & Seluanov Labs
Street address 213 Hutchinson Hall
City Rochester
State/province NY
ZIP/Postal code 14627
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (8)
GSM3511644 Scramble-1
GSM3511645 Scramble-2
GSM3511646 LINE1-AMO-1
BioProject PRJNA509895
SRA SRP173382

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
GSE123806_RAW.tar 344.1 Mb (http)(custom) TAR (of BW, MATRIX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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