PXD023093

PXD023093 is an original dataset announced via ProteomeXchange.

Title	Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences
Description	Here we focus on identifying conserved elements that are required for Chaserr function, a lncRNA that we recently characterized as being essential for mouse viability (https://doi.org/10.1038/s41467-019-13075-8). Chaserr is highly conserved in different species, and is located in close proximity (<2kb) to the transcription start site of CHD2. It acts in concert with the CHD2 protein to maintain proper Chd2 expression levels. Using the LncLOOM framework we identified AUGG enriched conserved elements which are located in the last exon of mouse Chaserr. In order to identify proteins that potentially bind to these conserved regions, we used in vitro transcription to generate the following biotinylated RNAs; along with their antisense controls: 1) The WT sequence, containing the first 322 nt of the last exon of Chaserr (bases 764–1086 of the NR_037601 isoform). An antisense control fragment was also prepared, labelled as AWT 2) The mutant conserved (MC) sequence, that contained AUGG→UACC mutations in four conserved motifs that were found using LncLOOM. An antisense control fragment was also prepared, labelled as AMC 3) The muatant all (MA) sequence in which all seven of the AUGG sites in the last exon were mutated to UACC. An antisense control fragment was also prepared, labelled as AMA 4) We also included a No Probe Control, which did not contain an RNA fragment. The fragments were incubated with N2a cell lysates followed by RNA-pulldown and Mass Spec analysis. The experiment was performed in triplicate. A total of 938 proteins were found to associate with the WT sequence: 74 of these were enriched ≥3-fold compared to the antisense sequence.We identified 9 proteins that had ≥2-fold higher recovery when using the WT sequence compared to both mutants. Included in these proteins was DHX36, which showed the highest enrichment compared to the mutated sequences. We validated the association of DHX36 with Chaserr through RNA immunoprecipitation experiments.
HostingRepository	PRIDE
AnnounceDate	2021-01-18
AnnouncementXML	Submission_2021-01-17_23:19:12.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Caroline Ross
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	biotinylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-13 11:10:03	ID requested
⏵ 1	2021-01-17 23:19:13	announced

Ross CJ, Rom A, Spinrad A, Gelbard-Solodkin D, Degani N, Ulitsky I, Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences. Genome Biol, 22(1):29(2021) [pubmed]

submitter keyword: Chaserr, Dhx36, conserved elements, lncRNAs, LncLOOM

Igor Ulitsky
contact affiliation	Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
contact email	igor.ulitsky@weizmann.ac.il
lab head
Caroline Ross
contact affiliation	The Weizmann Institute of Science
contact email	caroline-jane.ross@weizmann.ac.il
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023093
     1. Label: PRIDE project
     2. Name: Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences