|
| Status |
Public on Dec 11, 2009 |
| Title |
Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We developed a novel approach to isolate and characterize, at nucleotide-level resolution, the RNAs derived from RNA polymerase II (Pol II) in early elongation complexes. We find that high numbers of these short RNAs are not correlated with gene expression but instead are indicative of promoter-proximally stalled polymerase. High amounts of these short RNAs are generated from more than one third of all genes, indicating that Pol II stalls in the promoter-proximal region on global scale. We also find that the nucleotide composition of the initially transcribed sequence plays an important role in promoting transcriptional stalling and that early elongation complexes are highly susceptible to backtracking and arrest.
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| |
|
| Overall design |
Global analysis of RNAs produced by promoter-proximal Pol II.
|
| |
|
| Contributor(s) |
Nechaev S, Fargo DC, DosSantos G, Liu L, Gao Y, Adelman K |
| Citation(s) |
20007866 |
| |
| Submission date |
Oct 20, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Sergei Nechaev |
| E-mail(s) |
nechaevs@niehs.nih.gov
|
| Phone |
(919) 541-3525
|
| Organization name |
NIEHS/NIH
|
| Department |
Laboratory of Molecular Carcinogenesis
|
| Street address |
111 Alexander Dr
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27560 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
|
| Samples (9)
|
| GSM463297 |
S2_Rpb3_S2_Pol_II_ChIPSeq_rep1+rep2 |
| GSM463298 |
S2_Cap_shortRNA_5'_RNAseq_untreated_rep1+rep2 |
| GSM463299 |
S2_Cap_shortRNA_3'_RNAseq_untreated_rep1+rep2 |
| GSM463300 |
S2_Cap_shortRNA_3'_RNAseq_IISdepleted_rep1+rep2 |
| GSM463301 |
S2_Cap_shortRNA_3'_RNAseq_LacZdepleted_rep1+rep2 |
| GSM463302 |
S2_Cap_longtRNA_5'_RNAseq_untreated_rep1 |
| GSM463303 |
S2_Cap_longtRNA_5'_RNAseq_untreated_rep2 |
| GSM463304 |
Embryo_Cap_shortRNA_5'_RNAseq_untreated |
| GSM463305 |
Embryo_Cap_shortRNA_3'_RNAseq_untreated |
|
| Relations |
| SRA |
SRP001584 |
| BioProject |
PRJNA121575 |
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