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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 15, 2015 |
| Title |
RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships (RNA-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Mapping of RNA:DNA hybrids in human cells reveals a number of characteristics of these non-canonical nucleic acid structures. A directional sequencing approach reveals the RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to the stability of these structures. The RNA:DNA hybrids are enriched at loci with decreased DNA methylation and increased DNase hypersensitivity, and within larger domains with characteristics of heterochromatin formation. Studies of chromatin at RNA:DNA hybrids shows the presence of the ILF2 and ILF3 transcription factors, supporting a model of certain transcription factors binding preferentially to the RNA:DNA conformation. Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting a model of RNA generating these structures in trans. The results of the study indicate heterogeneous functions of these genomic elements and new insights into their formation and stability in vivo.
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| Overall design |
Investigation of expression data genome-wide in HEK293T and IMR-90 cells through RNA-seq, including rRNA
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| Contributor(s) |
Nadel JA, Greally JM |
| Citation |
Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, Neil Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey Jeddeloh, Cristina Montagna, Aaron Golden, Cathal Seoighe, John Greally. RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. bioRxiv June 7, 2015; http://dx.doi.org/10.1101/020545
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| Submission date |
May 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Julie Nadel |
| Organization name |
Albert Einstein College of Medicine
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| Department |
Genetics
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| Lab |
Price 314
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| Street address |
1301 Morris Park Avenue
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE68953 |
RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships |
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| Relations |
| BioProject |
PRJNA284147 |
| SRA |
SRP058387 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68938_HEKRNASeqTotal.txt.gz |
765.3 Kb |
(ftp)(http) |
TXT |
| GSE68938_IMR90RNASeqTotal.txt.gz |
764.6 Kb |
(ftp)(http) |
TXT |
| GSE68938_RAW.tar |
1.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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