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| Status |
Public on Nov 01, 2017 |
| Title |
Lamins organize the three dimensional genome from nuclear periphery in ES cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Lamins are the major structural components of the nuclear lamina (NL) beneath the inner nuclear membrane. Although lamins are believed to regulate genome organization and transcription, how they perform these functions remains poorly understood. Combining Hi-C with fluorescence in situ hybridization (FISH) and Histone and Lamina landscape (HiLands) analyses of chromatin domains, we show that lamins differentially regulate the NL-associated HiLands-P and -B domains in mouse ES cells (mESCs). Lamin loss leads to HiLands-P expansion at the NL, detachment of HiLands-B from the NL, and genome-wide changes of 3D chromatin interactions in NL-associated and interior HiLands in mESCs. Further epigenome and transcriptome analyses show that lamins can function from the NL to maintain the boundaries of active and repressive chromatin domains, thereby influencing gene expression throughout the genome. These findings should provide the basis to further understand how changes in the NL-associated chromatin influence transcription in development and NL-associated diseases.
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| Overall design |
Comparison of transcriptome (RNA-seq, 2 replicates), histone modifications(H3K4me3, H3K27me3, H3K9me3, H3K4me1, H3K27Ac, each 3-4 replicates), and 3D genome organization (Hi-C, 2 replicates) in WT and lamin-B1/B2/A triple knockout mESCs.
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| Contributor(s) |
Zheng X, Hu J, Kim Y, Zheng Y |
| Citation missing |
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| |
| Submission date |
Nov 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yixian Zheng |
| E-mail(s) |
[email protected]
|
| Organization name |
Carnegie Institution for Science
|
| Department |
Embryology
|
| Lab |
Yixian Zheng
|
| Street address |
3520 San Martin Drive
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA352471 |
| SRA |
SRP092589 |
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