SPLASH: in vivo mapping of eukaryotic RNA interactomes
This is the home of SPLASH (Sequencing of Psoralen crosslinked,
Ligated, and Selected Hybrids).
Method and results are described
in Aw et al. (2016;
Molecular Cell).
Press Releases:
Abstract
The extent of functional biological interactions between RNAs in
living cells is largely unknown. Identifying pairwise RNA-RNA
interactions is key to understanding how RNAs fold and how they
interact with other RNA partners in the cell. We present a novel
high-throughput approach, SPLASH, that maps pairwise RNA interaction
partners with high sensitivity and low false discovery rate (<4%)
in a non-selective, genome-wide manner in-vivo. Applying SPLASH to the
human and yeast transcriptomes revealed the diversity and dynamics of
thousands of long-range intramolecular and intermolecular RNA-RNA
interactions. Analysis of this large collection of interactions
highlighted key differences in structural organization of RNA classes,
including the modular organization of mRNAs and its impact on their
translation and decay, as well as the enrichment of long-range
interactions in non-coding RNAs. Additionally, intermolecular mRNA
interactions were found to be organized into network clusters of
co-regulated genes with similar functions, which underwent significant
reorganization during cellular differentiation. SPLASH analysis
identified hundreds of known and new snoRNA-rRNA binding sites that
serve to refine and expand our understanding of rRNA biogenesis. These
results highlight the under-explored complexity of RNA interactomes
and their role in gene regulation, and paves the way for deepening our
understanding of how RNA organization impacts biology.
Read Data for Human Samples
Sequencing data for the human samples can be accessed under BioProject
ID PRJNA318958
and SRA accession
ID SRP073550
(release date: 30th April 2016).
Our human transcriptome reference can
be downloaded
here.
The originally overlapping, paired-end reads were preprocessed
with SeqPrep and
successfully merged reads were uploaded. See table for a list of accessible samples:
| Accession | Sample Name |
|---|
| SAMN04870484 | Lymphoblastoid Cells Total RNA Replicate 1 |
| SAMN04870485 | Lymphoblastoid Cells Total RNA Replicate 2 |
| SAMN04870486 | Lymphoblastoid Cells Total RNA Replicate 3 |
| SAMN04870487 | Lymphoblastoid Cells Total RNA Replicate 4 |
| SAMN04870488 | Lymphoblastoid snoRNA IP |
| SAMN04870489 | Lymphoblastoid Cells PolyA Replicate 1 |
| SAMN04870490 | Lymphoblastoid Cells PolyA Replicate 2 |
| SAMN04870491 | Lymphoblastoid Cells PolyA Replicate 3 |
| SAMN04870492 | Lymphoblastoid Cells PolyA Replicate 4 |
| SAMN04870493 | Human ES PolyA Replicate 1 |
| SAMN04870494 | Human ES PolyA Replicate 2 |
| SAMN04870495 | Human RA PolyA Replicate 1 |
| SAMN04870496 | Human RA PolyA Replicate 2 |
| SAMN04870497 | Biotinylated psoralen libraries replicate 1 |
| SAMN04870498 | Biotinylated psoralen libraries replicate 2 |
| SAMN04870499 | Psoralen libraries replicate 1 |
| SAMN04870500 | Psoralen libraries replicate 2 |
| SAMN04870501 | DMSO libraries replicate 1 |
| SAMN04870502 | DMSO libraries replicate 2 |
List of derived RNA-RNA Interactions for Human cells
The following CSV files list interacting RNAs and regions that were
detected by SPLASH in the four cell-line types. The "bin" field is the
approximate crosslink i.e. interaction position in the
respective RNAs (truncated window of 100 basepairs; see section
"Binning and filtering of interacting RNA pairs" in the paper). The
"covfilter" field lists interaction counts
Yeast
Source Code
Please see the SPLASH github repository for source code.