Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development

Nature Communications

Volumn 6, Issue , 2015, Pages

  Töhönen, Virpi ^a   Katayama, Shintaro ^a,b   Vesterlund, Liselotte ^a   Jouhilahti, Eeva Mari ^a   Sheikhi, Mona ^c   Madissoon, Elo ^a   Filippini Cattaneo, Giuditta ^d   Jaconi, Marisa ^e   Johnsson, Anna ^a   Bürglin, Thomas R ^a,g   Linnarsson, Sten ^a   Hovatta, Outi ^c   Kere, Juha ^a,b,f  

^a KAROLINSKA INSTITUTE   (Sweden)

^b SCIENCE FOR LIFE LABORATORY   (Sweden)

^c KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^d ProCreaLab SA   (Switzerland)

^e UNIVERSITY OF GENEVA   (Switzerland)

^f FOLKHÄLSAN INSTITUTE OF GENETICS   (Finland)

^g UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARGFX PROTEIN; CPHX1 PROTEIN; CPHX2 PROTEIN; DNA BINDING PROTEIN; DPRX PROTEIN; DUXA PROTEIN; DUXB PROTEIN; LEUTX PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG; 5' UNTRANSLATED REGION; HOMEODOMAIN PROTEIN; MESSENGER RNA; RETROPOSON;

APOPTOSIS; EMBRYO; GENE EXPRESSION; GENETIC ANALYSIS; RNA;

5' UNTRANSLATED REGION; ALU SEQUENCE; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BLASTOMA; CELL DIVISION; CELL SIZE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DNA BINDING; DOWN REGULATION; EMBRYO; EMBRYO DEVELOPMENT; EXTRACTION; FEMALE; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENE NUMBER; GENETIC CONSERVATION; HOMEOBOX; HUMAN; HUMAN CELL; HUMAN DEVELOPMENT; INTRON; OOCYTE; PROMOTER REGION; RETROPOSON; RNA ANALYSIS; RNA DEGRADATION; RNA SEQUENCE; TRANSCRIPTION INITIATION SITE; UPREGULATION; ZYGOTE; BLASTOCYST; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HEK293 CELL LINE; METABOLISM; SEQUENCE ANALYSIS;

5' UNTRANSLATED REGIONS; BLASTOCYST; BLASTOMERES; EMBRYONIC DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HEK293 CELLS; HOMEODOMAIN PROTEINS; HUMANS; OOCYTES; RETROELEMENTS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; ZYGOTE;

EID: 84941347016     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms9207     Document Type: Article

References (34)

1. Assou, S. et al. Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. Hum. Reprod. Update 17, 272-290 (2011).
2. Galan, A. et al. Functional genomics of 5-to 8-cell stage human embryos by blastomere single-cell cDNA analysis. PloS One 5, e13615 (2010).
3. Zhang, P. et al. Transcriptome profiling of human pre-implantation development. PloS ONE 4, e7844 (2009).
4. Wong, C. C. et al. Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage. Nat. Biotechnol. 28, 1115-1121 (2010).
5. Yan, L. et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131-1139 (2013).
6. Xue, Z. et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500, 593-597 (2013).
7. Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
8. Katayama, S., Tohonen, V., Linnarsson, S. & Kere, J. SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. Bioinformatics 29, 2943-2945 (2013).
9. Dobson, A. T. et al. The unique transcriptome through day 3 of human preimplantation development. Hum. Mol. Genet. 13, 1461-1470 (2004).
10. Tang, F. et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc. 5, 516-535 (2010).
11. Dey, S. S., Kester, L., Spanjaard, B., Bienko, M. & van Oudenaarden, A. Integrated genome and transcriptome sequencing of the same cell. Nat. Biotechnol. 33, 285-289 (2015).
12. Hnida, C., Engenheiro, E. & Ziebe, S. Computer-controlled, multilevel, morphometric analysis of blastomere size as biomarker of fragmentation and multinuclearity in human embryos. Hum. Reprod. 19, 288-293 (2004).
13. Piko, L. & Clegg, K. B. Quantitative changes in total RNA, total poly(A), and ribosomes in early mouse embryos. Dev. Biol. 89, 362-378 (1982).
14. Braun, J. E. et al. A direct interaction between DCP1 and XRN1 couples mRNA decapping to 50 exonucleolytic degradation. Nat. Struct. Mol. Biol. 19, 1324-1331 (2012).
15. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676 (2006).
16. Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872 (2007).
17. Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013).
18. Su, M., Han, D., Boyd-Kirkup, J., Yu, X. & Han, J. D. Evolution of Alu elements toward enhancers. Cell Rep. 7, 376-385 (2014).
19. Korenberg, J. R. & Rykowski, M. C. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 53, 391-400 (1988).
20. Polak, P. & Domany, E. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7, 133 (2006).
21. Burglin, T. R. Homeodomain subtypes and functional diversity. Subcell. Biochem. 52, 95-122 (2011).
22. Hirata, T. et al. Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells. Sci. Rep. 2, 208 (2012).
23. Zhong, Y. F. & Holland, P. W. The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages. BMC Evol. Biol. 11, 169 (2011).
24. Kigami, D., Minami, N., Takayama, H. & Imai, H. MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol. Reprod. 68, 651-654 (2003).
25. Cridland, J. M., Thornton, K. R. & Long, A. D. Gene Expression Variation in Drosophila melanogaster Due to Rare Transposable Element Insertion Alleles of Large Effect. Genetics 199, 85-93 (2014).
26. Islam, S. et al. Highly multiplexed and strand-specific single-cell RNA 50 end sequencing. Nat. Protoc. 7, 813-828 (2012).
27. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
28. Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540-1542 (2006).
29. Li, J. & Tibshirani, R. Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat. Methods Med. Res. 22, 519-536 (2013).
30. Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
31. Bailey, T. L. & Gribskov, M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54 (1998).
32. Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L. & Noble, W. S. Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).
33. Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012).
34. Du, J., Zeng, J., Zhao, Y., Boulaire, J. & Wang, S. The combined use of viral transcriptional and post-transcriptional regulatory elements to improve baculovirus-mediated transient gene expression in human embryonic stem cells. J. Biosci. Bioeng. 109, 1-8 (2010).