|
| Status |
Public on Jan 29, 2014 |
| Title |
Poly(A)-tail profiling reveals an embryonic switch in translational control |
| Organisms |
Arabidopsis thaliana; Schizosaccharomyces pombe; Saccharomyces cerevisiae; Drosophila melanogaster; Danio rerio; Xenopus laevis; Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.
|
| |
|
| Overall design |
64 samples from a variety of species
|
| |
|
| Contributor(s) |
Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP |
| Citation(s) |
24476825 |
| |
| Submission date |
Nov 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Eichhorn |
| E-mail(s) |
eichhorn@wi.mit.edu
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Department |
Biology
|
| Lab |
Bartel
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (13)
|
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
| GPL9319 |
Illumina Genome Analyzer II (Danio rerio) |
| GPL9377 |
Illumina Genome Analyzer II (Saccharomyces cerevisiae) |
| GPL9408 |
Illumina Genome Analyzer II (Xenopus laevis) |
| GPL9453 |
Illumina Genome Analyzer II (Schizosaccharomyces pombe) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL13988 |
Illumina HiSeq 2000 (Schizosaccharomyces pombe) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL17682 |
Illumina HiSeq 2000 (Xenopus laevis) |
|
| Samples (64)
|
|
| Relations |
| BioProject |
PRJNA230112 |
| SRA |
SRP033369 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52809_3T3.txt.gz |
317.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_contact_inhibited_1.txt.gz |
201.2 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_contact_inhibited_2.txt.gz |
216.7 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_0_ribosomes.txt.gz |
187.3 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_11_ribosomes.txt.gz |
224.1 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_1_ribosome.txt.gz |
199.0 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_2_ribosomes.txt.gz |
216.0 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_3_ribosomes.txt.gz |
211.3 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_4_ribosomes.txt.gz |
193.6 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_5.5_ribosomes.txt.gz |
217.0 Kb |
(ftp)(http) |
TXT |
| GSE52809_3T3_polysome_profile_7.5_ribosomes.txt.gz |
219.3 Kb |
(ftp)(http) |
TXT |
| GSE52809_Arabidopsis.txt.gz |
266.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_Cerevisiae.txt.gz |
139.4 Kb |
(ftp)(http) |
TXT |
| GSE52809_Cerevisiae_total.txt.gz |
70.2 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_132_2hpf.txt.gz |
375.3 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_132_4hpf.txt.gz |
338.0 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_132_6hpf.txt.gz |
342.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_155_2hpf.txt.gz |
378.5 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_155_4hpf.txt.gz |
348.0 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_155_6hpf.txt.gz |
339.6 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_mock_2hpf.txt.gz |
334.8 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_mock_4hpf.txt.gz |
335.5 Kb |
(ftp)(http) |
TXT |
| GSE52809_Dre_mock_6hpf.txt.gz |
329.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_Drosophila.txt.gz |
122.5 Kb |
(ftp)(http) |
TXT |
| GSE52809_HEK293T.txt.gz |
340.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_HeLa.txt.gz |
281.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_HeLa_total.txt.gz |
276.1 Kb |
(ftp)(http) |
TXT |
| GSE52809_Liver.txt.gz |
282.3 Kb |
(ftp)(http) |
TXT |
| GSE52809_Pombe.txt.gz |
147.1 Kb |
(ftp)(http) |
TXT |
| GSE52809_RAW.tar |
104.5 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE52809_README.txt |
2.2 Kb |
(ftp)(http) |
TXT |
| GSE52809_Xla_st12_12.5.txt.gz |
286.9 Kb |
(ftp)(http) |
TXT |
| GSE52809_Xla_st3_4.txt.gz |
286.8 Kb |
(ftp)(http) |
TXT |
| GSE52809_Xla_st9.txt.gz |
290.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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