Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development

Mengyao Sun; Le Chang; Liu He; Li Wang; Zhengyang Jiang; Yanmin Si; Jia Yu; Yanni Ma

doi:10.1016/j.jgg.2024.07.013

Volume 51 Issue 11

Nov. 2024

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2024 > 51(11): 1173-1186

PDF( 9086 KB)

Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development

doi: 10.1016/j.jgg.2024.07.013

a. State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China;
b. Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China;
c. Department of Obstetrics, Haidian District Maternity and Child Health Hospital, Beijing 100080, China;
d. Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China

Funds:

This work was supported by the National Key Research and Development Program of China (2021YFA0805703, 2019YFA0801800, and 2019YFA0802600), the National Natural Science Foundation of China (82330007, 82122005, 92268205 and 81970101), CAMS Innovation Fund for Medical Sciences (2021-I2M-1-019), and Haihe Laboratory of Cell Ecosystem Innovation Fund (22HHXBSS00027).

Received Date: 2024-03-25
Accepted Date: 2024-07-12
Rev Recd Date: 2024-07-12

Available Online: 2025-06-06

Publish Date: 2024-07-20

Abstract

Abstract

More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. Here, we identify pseudogenes that are dynamically expressed during human early embryogenesis, showing different expression patterns from that of adult tissues. We explore the expression correlation between pseudogenes and the parent genes, partly due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1, and FBXW4P1, in maintaining self-renewal of human embryonic stem cells is demonstrated. We further find that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms are significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial roles in the maintenance of normal physiological states.
- Pseudogene,
- Human early embryonic development,
- Non-coding RNA,
- Human embryonic stem cell

FullText(HTML)

References(51)

References

Ai, Z., Niu, B., Yin, Y., Xiang, L., Shi, G., Duan, K., Wang, S., Hu, Y., Zhang, C., Zhang, C., et al., 2023. Dissecting peri-implantation development using cultured human embryos and embryo-like assembloids. Cell Res. 33, 661-678.

Balakirev, E.S., Ayala, F.J., 2003. Pseudogenes: are they "junk" or functional DNA? Annu. Rev. Genet. 37, 123-151.

Charrier, C., Joshi, K., Coutinho-Budd, J., Kim, J.E., Lambert, N., de Marchena, J., Jin, W.L., Vanderhaeghen, P., Ghosh, A., Sassa, T., et al., 2012. Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell 149, 923-935.

Cheetham, S.W., Faulkner, G.J., Dinger, M.E., 2020. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat. Rev. Genet. 21, 191-201.

Chen, J., Hu, L., Chen, J., Wu, F., Hu, D., Xu, G., Zhu, P., Wang, Y., 2016. Low expression lncRNA RPLP0P2 is associated with poor prognosis and decreased cell proliferation and adhesion ability in lung adenocarcinoma. Oncol. Rep. 36, 1665-1671.

Chiang, J.J., Sparrer, K.M.J., van Gent, M., Lassig, C., Huang, T., Osterrieder, N., Hopfner, K.P., Gack, M.U., 2018. Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity. Nat. Immunol. 19, 53-62.

Chiefari, E., Iiritano, S., Paonessa, F., Le Pera, I., Arcidiacono, B., Filocamo, M., Foti, D., Liebhaber, S.A., Brunetti, A., 2010. Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. Nat. Commun. 1, 40.

Dai, X., Xie, Y., Dong, M., Zhao, J., Yu, H., Zhou, B., Xu, Y., Yu, Y., Cao, Y., Zhang, Y., 2019. The long noncoding RNA TPTE2P1 promotes the viability of colorectal cancer cells. J. Cell Biochem. 120, 5268-5276.

Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R., 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21.

Dong, H.X., Wang, R., Jin, X.Y., Zeng, J., Pan, J., 2018. LncRNA DGCR5 promotes lung adenocarcinoma (LUAD) progression via inhibiting hsa-mir-22-3p. J. Cell Physiol. 233, 4126-4136.

Dubois, M.L., Meller, A., Samandi, S., Brunelle, M., Frion, J., Brunet, M.A., Toupin, A., Beaudoin, M.C., Jacques, J.F., Levesque, D., et al., 2020. UBB pseudogene 4 encodes functional ubiquitin variants. Nat. Commun. 11, 1306.

Fiddes, I.T., Lodewijk, G.A., Mooring, M., Bosworth, C.M., Ewing, A.D., Mantalas, G.L., Novak, A.M., van den Bout, A., Bishara, A., Rosenkrantz, J.L., et al., 2018. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell 173, 1356-1369.

Fogarty, N.M.E., McCarthy, A., Snijders, K.E., Powell, B.E., Kubikova, N., Blakeley, P., Lea, R., Elder, K., Wamaitha, S.E., Kim, D., et al., 2017. Genome editing reveals a role for OCT4 in human embryogenesis. Nature 550, 67-73.

Gonzales, K.A., Ng, H.H., 2011. FoxO: a new addition to the ESC cartel. Cell Stem Cell 9, 181-183.

Hu, X., Yang, L., Mo, Y.Y., 2018. Role of Pseudogenes in Tumorigenesis. Cancers (Basel) 10, 256.

Huang, H., Yang, X., Chen, J., Fu, J., Chen, C., Wen, J., Mo, Q., 2019. lncRNA DGCR5 inhibits the proliferation of colorectal cancer cells by downregulating miR-21. Oncol. Lett. 18, 3331-3336.

Johnson, R., 2012. Long non-coding RNAs in Huntington's disease neurodegeneration. Neurobiol. Dis. 46, 245-254.

Jukam, D., Shariati, S.A.M., Skotheim, J.M., 2017. Zygotic Genome Activation in Vertebrates. Dev. Cell 42, 316-332.

Kalyana-Sundaram, S., Kumar-Sinha, C., Shankar, S., Robinson, D.R., Wu, Y.M., Cao, X., Asangani, I.A., Kothari, V., Prensner, J.R., Lonigro, R.J., et al., 2012. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell 149, 1622-1634.

Karreth, F.A., Reschke, M., Ruocco, A., Ng, C., Chapuy, B., Leopold, V., Sjoberg, M., Keane, T.M., Verma, A., Ala, U., Tay, Y., et al., 2015. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 161, 319-332.

Ke, L., Yang, D.C., Wang, Y., Ding, Y., Gao, G., 2020. AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse. Nucleic Acids Res. 48, W230-W238.

Korneev, S.A., Park, J.H., O'Shea, M., 1999. Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J. Neurosci. 19, 7711-7720.

Kwon, J., Liu, Y.V., Gao, C., Bassal, M.A., Jones, A.I., Yang, J., Chen, Z., Li, Y., Yang, H., Chen, L., et al., 2021. Pseudogene-mediated DNA demethylation leads to oncogene activation. Sci. Adv. 7, eabg1695.

Li, B., Dewey, C.N., 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.

Li, J.H., Liu, S., Zhou, H., Qu, L.H., Yang, J.H., 2014. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92-97.

Liu, N., Dou, L., Zhang, X., 2020. LncRNA PTTG3P Sponge Absorbs microRNA-155-5P to Promote Metastasis of Colorectal Cancer. Onco Targets Ther. 13, 5283-5291.

Lu, X., Yu, Y., Liao, F., Tan, S., 2019. Homo Sapiens Circular RNA 0079993 (hsa_circ_0079993) of the POLR2J4 Gene Acts as an Oncogene in Colorectal Cancer Through the microRNA-203a-3p.1 and CREB1 Axis. Med. Sci. Monit. 25, 6872-6883.

Ma, Y., Liu, S., Gao, J., Chen, C., Zhang, X., Yuan, H., Chen, Z., Yin, X., Sun, C., Mao, Y., et al., 2021. Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in beta-thalassemia. Dev. Cell 56, 478-493.

Meistermann, D., Bruneau, A., Loubersac, S., Reignier, A., Firmin, J., Francois-Campion, V., Kilens, S., Lelievre, Y., Lammers, J., Feyeux, M., et al., 2021. Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification. Cell Stem Cell 28, 1625-1640.

Mole, M.A., Weberling, A., Zernicka-Goetz, M., 2020. Comparative analysis of human and mouse development: From zygote to pre-gastrulation. Curr. Top Dev. Biol. 136, 113-138.

Pei, B., Sisu, C., Frankish, A., Howald, C., Habegger, L., Mu, X.J., Harte, R., Balasubramanian, S., Tanzer, A., Diekhans, M., et al., 2012. The GENCODE pseudogene resource. Genome Biol. 13, R51.

Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W.J., Pandolfi, P.P., 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033-1038.

Rapicavoli, N.A., Qu, K., Zhang, J., Mikhail, M., Laberge, R.M., Chang, H.Y., 2013. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife 2, e00762.

Rossant, J., Tam, P.P.L., 2017. New Insights into Early Human Development: Lessons for Stem Cell Derivation and Differentiation. Cell Stem Cell 20, 18-28.

Rossant, J., Tam, P.P.L., 2022. Early human embryonic development: Blastocyst formation to gastrulation. Dev. Cell 57, 152-165.

Schulz, K.N., Harrison, M.M., 2019. Mechanisms regulating zygotic genome activation. Nat. Rev. Genet. 20, 221-234.

Shi, D., Liang, L., Zheng, H., Cai, G., Li, X., Xu, Y., Cai, S., 2017. Silencing of long non-coding RNA SBDSP1 suppresses tumor growth and invasion in colorectal cancer. Biomed. Pharmacother. 85, 355-361.

Shih, J.H., Chen, H.Y., Lin, S.C., Yeh, Y.C., Shen, R., Lang, Y.D., Wu, D.C., Chen, C.Y., Chen, R.H., Chou, T.Y., et al., 2020. Integrative analyses of noncoding RNAs reveal the potential mechanisms augmenting tumor malignancy in lung adenocarcinoma. Nucleic Acids Res. 48, 1175-1191.

Straniero, L., Rimoldi, V., Samarani, M., Goldwurm, S., Di Fonzo, A., Kruger, R., Deleidi, M., Aureli, M., Solda, G., Duga, S., et al., 2017. The GBAP1 pseudogene acts as a ceRNA for the glucocerebrosidase gene GBA by sponging miR-22-3p. Sci. Rep. 7, 12702.

Suzuki, I.K., Gacquer, D., Van Heurck, R., Kumar, D., Wojno, M., Bilheu, A., Herpoel, A., Lambert, N., Cheron, J., Polleux, F., et al., 2018. Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation. Cell 173, 1370-1384.

Tay, Y., Rinn, J., Pandolfi, P.P., 2014. The multilayered complexity of ceRNA crosstalk and competition. Nature 505, 344-352.

Thomson, D.W., Dinger, M.E., 2016. Endogenous microRNA sponges: evidence and controversy. Nat. Rev. Genet. 17, 272-283.

Wei, Y., Chang, Z., Wu, C., Zhu, Y., Li, K., Xu, Y., 2017. Identification of potential cancer-related pseudogenes in lung adenocarcinoma based on ceRNA hypothesis. Oncotarget 8, 59036-59047.

Wu, Z.H., Huang, K.H., Liu, K., Wang, G.T., Sun, Q., 2018. DGCR5 induces osteogenic differentiation by up-regulating Runx2 through miR-30d-5p. Biochem. Biophys. Res. Commun. 505, 426-431.

Yan, L., Yang, M., Guo, H., Yang, L., Wu, J., Li, R., Liu, P., Lian, Y., Zheng, X., Yan, J., et al., 2013. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131-1139.

Zhang, J., Ratanasirintrawoot, S., Chandrasekaran, S., Wu, Z., Ficarro, S.B., Yu, C., Ross, C.A., Cacchiarelli, D., Xia, Q., Seligson, M., et al., 2016. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell 19, 66-80.

Zhang, X., Yalcin, S., Lee, D.F., Yeh, T.Y., Lee, S.M., Su, J., Mungamuri, S.K., Rimmele, P., Kennedy, M., Sellers, R., et al., 2011. FOXO1 is an essential regulator of pluripotency in human embryonic stem cells. Nat. Cell Biol. 13, 1092-1099.

Zhao, J., Cheng, W., He, X., Liu, Y., Li, J., Sun, J., Li, J., Wang, F., Gao, Y., 2018. Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. Onco Targets Ther. 11, 3129-3140.

Zheng, C., Li, X., Ren, Y., Yin, Z., Zhou, B., 2019. Long Noncoding RNA RAET1K Enhances CCNE1 Expression and Cell Cycle Arrest of Lung Adenocarcinoma Cell by Sponging miRNA-135a-5p. Front. Genet. 10, 1348.

Zhong, M.E., Chen, Y., Zhang, G., Xu, L., Ge, W., Wu, B., 2019. LncRNA H19 regulates PI3K-Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network. Cancer Cell Int. 19, 148.

Zou, Z., Zhang, C., Wang, Q., Hou, Z., Xiong, Z., Kong, F., Wang, Q., Song, J., Liu, B., Liu, B., et al., 2022. Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation. Science 378, abo7923.

Relative Articles

Supplements(0)

Cited By

Proportional views