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Series GSE96033 Query DataSets for GSE96033
Status Public on Aug 30, 2018
Title Genome-wide Mapping of Lamin B1 Reveals the Existence of Dynamic and Functional Euchromatin Lamin B1 Domains (eLADs) at the onset of the Epithelial to Mesenchymal Transition
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Lamins (A/C and B) are type V intermediate filaments and constitute the major cytoskeleton component of nuclei. They are assembled forming a filamentous meshwork that is mainly located between the inner nuclear membrane and the peripheral chromatin in where they form structural and conserved elements called lamin-associated domains (LADs) that cover around 40% of the mammalian genome. However, a small fraction of lamins are also located in the nucleoplasm although is still unclear if represents a fraction that is in transit towards the nuclear membrane, a reservoir for protein turnover or they have specific functions in nuclear organization6. Here we mapped genome-wide the localization of lamin B1 from an enriched euchromatin fraction. Our analysis show for the first time that lamin B1 can be also associated with active euchromatin forming domains of about half a megabase on average in size. These euchromatin lamin B1 domains (eLADs) are constituted by active and accessible euchromatin showed by RNAseq and ATACseq. Importantly, we have analyzed its behavior at the onset of the epithelial to mesenchymal transition (EMT), a cellular transformation process essential during development and reactivated in cancer cells. Our results suggest that eLADs are dynamic and functional during EMT. Finally, Hi-C data during this cellular transformation showed changes in the frequency of chromatin contacts around the TSS in genes enriched in lamin B1 before the generation of new regulatory elements in the mesenchymal state. Taken together, these results demonstrate that not only heterochromatin but euchromatin is organized into lamin domains as well. Moreover, these eLADs are dynamic, functional and essential for chromatin organization and gene regulation during the EMT.
Overall design List of ChIPseq samples (LaminB1 at 0h/8h/24h), ATACseq samples (at 0h/8h/24h), RNAseq samples (control at 0h/8h/24h and control/LaminB1 knock-down at 0h/8h/24h) and HiC samples (EMT transformation at 0h/8h/24h).
Contributor(s) Pascual-Reguant L, Blanco E, Marti-Renom M, DiCroce L, Peiro S
Citation(s) 30143639
Submission date Mar 09, 2017
Last update date May 15, 2019
Contact name Enrique Blanco
Phone +34 93 316 01 00
Organization name Center for Genomic Regulation (CRG)
Department Gene Regulation, Stem Cells and Cancer
Lab Epigenetic Events in Cancer (L. Di Croce's lab)
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (27)
GSM2527708 ChIP_LB1_0h
GSM2527709 ChIP_LB1_8h
GSM2527710 ChIP_LB1_24h
BioProject PRJNA378636
SRA SRP101630

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
GSE96033_FPKM_0h-8h-24h.txt.gz 455.5 Kb (ftp)(http) TXT
GSE96033_FPKMs_0CT1_0CT2_0shLB1_0shLB2-8CT1_8CT2_8shLB1_8shLB2-24CT1_24CT2_24shLB1_24shLB2.txt.gz 842.1 Kb (ftp)(http) TXT
GSE96033_RAW.tar 427.4 Mb (http)(custom) TAR (of BED, BEDGRAPH, TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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