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| Status |
Public on Jul 29, 2024 |
| Title |
Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro |
| Organisms |
Pan troglodytes; Homo sapiens; Mus musculus; synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA-binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.
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| Overall design |
Natural sequence RNA bind-n-seq (nsRBNS) and 100vertebrate RNA bind-n-seq (100vertRBNS) for unkempt (UNK) zinc fingers 1-6
Please note that all organism/species included in the *100vertRBNS samples are listed in the Series supplementary 'organisms.txt' file.
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| Contributor(s) |
Harris SE, Alexis MS, Giri G, Cavazos FF Jr, Murn J, Aleman MM, Burge CB, Dominguez D, Hu Y |
| Citation(s) |
39333159 |
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| Submission date |
Mar 27, 2024 |
| Last update date |
Oct 15, 2024 |
| Contact name |
Daniel Dominguez |
| Organization name |
UNC Chapel Hill
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| Department |
Pharmacology
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| Lab |
Dominguez Lab
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| Street address |
120 Mason farm
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platforms (3) |
| GPL16512 |
Illumina HiSeq 2000 (Homo sapiens; Mus musculus) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
| GPL34340 |
Illumina NextSeq 500 (Homo sapiens; Pan troglodytes) |
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| Samples (18)
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| GSM8171700 |
UNK nsRBNS, 50nM, rep2 |
| GSM8171701 |
UNK nsRBNS, 500nM, rep1 |
| GSM8171702 |
UNK nsRBNS, 500nM, rep2 |
| GSM8171703 |
nsRBNS input |
| GSM8171704 |
UNK 100vertRBNS, 100nM, rep1 |
| GSM8171705 |
UNK 100vertRBNS, 100nM, rep2 |
| GSM8171706 |
UNK 100vertRBNS, 100nM, rep3 |
| GSM8171707 |
100vertRBNS input |
| GSM8303617 |
UNK ZnF1-3 RBNS, 250nM |
| GSM8303618 |
UNK ZnF1-3 RBNS, 500nM |
| GSM8303619 |
UNK ZnF1-3 RBNS, 1000nM |
| GSM8303620 |
UNK ZnF4-6 RBNS, 250 nM |
| GSM8303621 |
UNK ZnF4-6 RBNS, 500nM |
| GSM8303622 |
UNK ZnF4-6 RBNS, 1000nM |
| GSM8303623 |
20mer_RNA_input |
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| Relations |
| BioProject |
PRJNA1092528 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE262560_100vertRBNS_custom_genome.fa.gz |
218.4 Kb |
(ftp)(http) |
FA |
| GSE262560_RAW.tar |
5.1 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE262560_nsRBNS_custom_genome.fa.gz |
1022.8 Kb |
(ftp)(http) |
FA |
| GSE262560_organisms.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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