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Systematic functional interrogation of human pseudogenes using CRISPRi
- Source :
- Genome Biology, Vol 22, Iss 1, Pp 1-29 (2021), Genome Biology
- Publication Year :
- 2021
- Publisher :
- BMC, 2021.
-
Abstract
- BackgroundThe human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions. However, to what extent human pseudogenes are functionally relevant remains unclear. There has been no large-scale characterization of pseudogene function because of technical challenges, including high sequence similarity between pseudogene and parent genes, and poor annotation of transcription start sites.ResultsTo overcome these technical obstacles, we develop an integrated computational pipeline to design the first genome-wide library of CRISPR interference (CRISPRi) single-guide RNAs (sgRNAs) that target human pseudogene promoter-proximal regions. We perform the first pseudogene-focused CRISPRi screen in luminal A breast cancer cells and reveal approximately 70 pseudogenes that affect breast cancer cell fitness. Among the top hits, we identify a cancer-testis unitary pseudogene, MGAT4EP, that is predominantly localized in the nucleus and interacts with FOXA1, a key regulator in luminal A breast cancer. By enhancing the promoter binding of FOXA1, MGAT4EP upregulates the expression of oncogenic transcription factor FOXM1. Integrative analyses of multi-omic data from the Cancer Genome Atlas (TCGA) reveal many unitary pseudogenes whose expressions are significantly dysregulated and/or associated with overall/relapse-free survival of patients in diverse cancer types.ConclusionsOur study represents the first large-scale study characterizing pseudogene function. Our findings suggest the importance of nuclear function of unitary pseudogenes and underscore their underappreciated roles in human diseases. The functional genomic resources developed here will greatly facilitate the study of human pseudogene function.
- Subjects :
- Hepatocyte Nuclear Factor 3-alpha
Unitary pseudogene
QH301-705.5
Pseudogene
Breast Neoplasms
Computational biology
Biology
QH426-470
Nucleus
Transcriptional regulation
Luminal A breast cancer
medicine
Genetics
Humans
Clustered Regularly Interspaced Short Palindromic Repeats
Biology (General)
Promoter Regions, Genetic
Gene
Transcription factor
CRISPR interference
Cell Proliferation
Cancer
Cell Nucleus
Research
Forkhead Box Protein M1
FOXM1
Computational Biology
Reproducibility of Results
TCGA
medicine.disease
Human genetics
Up-Regulation
Gene Expression Regulation, Neoplastic
MCF-7 Cells
Human genome
GTEx
FOXA1
Pseudogenes
Function (biology)
Protein Binding
RNA, Guide, Kinetoplastida
Subjects
Details
- Language :
- English
- Volume :
- 22
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Genome Biology
- Accession number :
- edsair.doi.dedup.....12e0c0041c977c610c064f95dcb9b909