PXD046452

PXD046452 is an original dataset announced via ProteomeXchange.

Title	Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human
Description	Functional studies of long noncoding RNAs (lncRNAs) have long been hindered by a lack of methods to assess their evolution. Here, we present lncHOME (lncRNA Homology Explorer), a computational pipeline that identifies a unique coPARSE-lncRNA class with conserved genomic locations and patterns of RNA binding protein (RBP) binding sites. Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects that were rescued by predicted zebrafish homologs. Knocking down the coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Moreover, we verified that human, mouse, and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved fuctions relying on specific RBP binding sites. Overall, our study demonstrates a comprehensive approach for studying functional conservation of lncRNAs and implicates numerous lncRNAs in regulating cellular physiology.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:27:49.487.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenze Huang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-27 06:02:17	ID requested
1	2024-01-26 14:07:24	announced
⏵ 2	2024-10-22 06:27:55	announced	2024-10-22: Updated project metadata.

10.1038/s41588-023-01620-7;

Huang W, Xiong T, Zhao Y, Heng J, Han G, Wang P, Zhao Z, Shi M, Li J, Wang J, Wu Y, Liu F, Xi JJ, Wang Y, Zhang QC, Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human. Nat Genet, 56(1):124-135(2024) [pubmed]

submitter keyword: mouse,human, zebrafish, RBP, LC-MS/MS

Qiangfeng Cliff Zhang
contact affiliation	MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
contact email	qczhang@tsinghua.edu.cn
lab head
Wenze Huang
contact affiliation	Tsinghua University
contact email	hwz16@tsinghua.org.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/01/PXD046452

PRIDE project URI

• PRIDE
  1. PXD046452
     1. Label: PRIDE project
     2. Name: Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human