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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 16, 2024 |
| Title |
Synthetic reversed sequences reveal default genomic states [mESC_ATACseq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Understanding default genome states would help interpret whether pervasive transcriptional activity has biological meaning. The genomes of extant organism have undergone billions of years of evolution, making it unclear whether observed genomic activities represent the effects of selection or “noise”. We addressed this question by introducing a novel 101-kb locus into the genomes of S. cerevisiae and M. musculus, and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including substantial flank-ing regions, retaining basic sequence features but ablating evolved coding or regulatory infor-mation. We observed widespread activity of both reversed and native HPRT1 loci in yeast, de-spite the lack of evolved yeast promoters. In contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, instead showing repressive chromatin signatures. The re-pressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless this variant too was transcriptionally inactive. These results show that novel genomic sequences lacking coding information are active in yeast, but inactive in mouse embryonic stem cells, con-sistent with a major difference in “default genomic states” between these two divergent eukary-otic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information, and new gene birth.
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| Overall design |
Exploratory ATAC-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are accessible in mouse embryonic stem cells, and to compare to the rest of the respective genome.
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| Contributor(s) |
Camellato BR, Brosh R, Ashe HJ, Maurano MT, Boeke JD |
| Citation(s) |
38448583 |
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| Submission date |
Jan 03, 2024 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Brendan R. Camellato |
| E-mail(s) |
brendan.camellato@nyulangone.org
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| Organization name |
NYU Langone Health
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| Department |
Institute for Systems Genetics
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| Lab |
Boeke Lab
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| Street address |
435 E 30th St
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (20)
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| GSM8001812 |
mESC, synHPRT1 integrated on chrX, clone 1, rep 1 |
| GSM8001813 |
mESC, synHPRT1 integrated on chrX, clone 1, rep 2 |
| GSM8001814 |
mESC, synHPRT1 integrated on chrX, clone 2, rep 1 |
| GSM8001815 |
mESC, synHPRT1 integrated on chrX, clone 2, rep 2 |
| GSM8001816 |
mESC, synHPRT1R integrated on chrX, clone 1, rep 1 |
| GSM8001817 |
mESC, synHPRT1R integrated on chrX, clone 1, rep 2 |
| GSM8001818 |
mESC, synHPRT1R integrated on chrX, clone 2, rep 1 |
| GSM8001819 |
mESC, synHPRT1R integrated on chrX, clone 2, rep 2 |
| GSM8001820 |
mESC, synHPRT1R integrated on chr3, clone 1, rep 1 |
| GSM8001821 |
mESC, synHPRT1R integrated on chr3, clone 1, rep 2 |
| GSM8001822 |
mESC, synHPRT1R integrated on chr3, clone 2, rep 1 |
| GSM8001823 |
mESC, synHPRT1R integrated on chr3, clone 2, rep 2 |
| GSM8001824 |
mESC, synHPRT1RnoCpG integrated on chrX, clone 1, rep 1 |
| GSM8001825 |
mESC, synHPRT1RnoCpG integrated on chrX, clone 1, rep 2 |
| GSM8001826 |
mESC, synHPRT1RnoCpG integrated on chrX, clone 2, rep 1 |
| GSM8001827 |
mESC, synHPRT1RnoCpG integrated on chrX, clone 2, rep 2 |
| GSM8001828 |
mESC, synHPRT1RnoCpG integrated on chr3, clone 1, rep 1 |
| GSM8001829 |
mESC, synHPRT1RnoCpG integrated on chr3, clone 1, rep 2 |
| GSM8001830 |
mESC, synHPRT1RnoCpG integrated on chr3, clone 2, rep 1 |
| GSM8001831 |
mESC, synHPRT1RnoCpG integrated on chr3, clone 2, rep 2 |
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| This SubSeries is part of SuperSeries: |
| GSE252482 |
Synthetic reversed sequences reveal default genomic states |
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| Relations |
| BioProject |
PRJNA1060708 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE252476_RAW.tar |
24.6 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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