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Differential L1 Regulation in Pluripotent Stem Cells of Humans and Apes

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Differential L1 Regulation in Pluripotent Stem Cells of Humans and Apes LETTER doi:10.1038/nature12686 Differential L1 regulation in pluripotent stem cells of humans and apes Maria C. N. Marchetto1*, In˜igo Narvaiza1*, Ahmet M. Denli1, Christopher Benner1, Thomas A. Lazzarini1, Jason L. Nathanson2, Apua˜ C. M. Paquola1, Keval N. Desai3, Roberto H. Herai4, Matthew D. Weitzman5, Gene W. Yeo2, Alysson R. Muotri4,6 & Fred H. Gage1,6 Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understand- ing of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative a studies between humans, chimpanzees (Pan troglodytes) and bono- Karyotype: bos (Pan paniscus)1,2. However, these tissue samples do not fairly 2n = 48 ytes represent the distinctive traits of live cell behaviour and are not zee Fibroblast iPS XY lod pan amenable to genetic manipulation. We propose that induced plur- rog Chim ipotent stem (iPS) cells could be a unique biological resource to P. t determine relevant phenotypical differences between human and Merge Tra-1-81 Nanog DAPI NHPs, and that those differences could have potential adaptation and speciation value. Here we describe the generation and initial 2n = 48 XY characterization of iPS cells from chimpanzees and bonobos as new iscus Fibroblast iPS pan Bonobo tools to explore factors that may have contributed to great ape evolu- . tion. Comparative gene expression analysis of human and NHP P iPS cells revealed differences in the regulation of long interspersed Merge Tra-1-81 Nanog DAPI element-1 (L1, also known as LINE-1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution3–5. Decreased levels 2n = 46 XY of L1-restricting factors APOBEC3B (also known as A3B)6 and Fibroblast iPS Human PIWIL2 (ref. 7) in NHP iPS cells correlated with increased L1 mobi- H. sapiens lity and endogenous L1 messenger RNA levels. Moreover, results from the manipulation of A3B and PIWIL2 levels in iPS cells sup- Merge Tra-1-81 Nanog DAPI ported a causal inverse relationship between levels of these proteins b c Ecto and L1 retrotransposition. Finally, we found increased copy numbers Meso iPS EBs of species-specific L1 elements in the genome of chimpanzees com- O Endo 2 Chimpanzee pared to humans, supporting the idea that increased L1 mobility in H HCBHCB Nanog Meso NHPs is not limited to iPS cells in culture and may have also occurred bo Ecto in the germ line or embryonic cells developmentally upstream to Musashi Endo germline specification during primate evolution. We propose that Brachyury Bono Meso differences in L1 mobility may have differentially shaped the gen- AFP Ecto omes of humans and NHPs and could have continuing adaptive Actin Human significance. Endo Humans, chimpanzees and bonobos are genetically very similar, sharing nearly 98% of their alignable genomic sequence1–3. However, Figure 1 | Characterization of iPS cells derived from the three primate cellular and molecular phenotypes, especially at identical stages of species. a, Morphology of fibroblasts and iPS cells. No karyotypic development, are difficult to establish, mainly owing to limited access abnormalities were observed in iPS cells clones. Immunofluorescence for the to embryonic material from humans and NHPs8. We reprogrammed pluripotency markers Tra-1-81 and Nanog in iPS cells is shown. DAPI, 49,6- fibroblasts from two bonobos and two chimpanzees into iPS cells as diamidino-2-phenylindole. b, Reverse transcription PCR (RT–PCR) for previously described9,10 (Extended Data Fig. 1a). After culture in undifferentiation (Nanog) and for the three germ cell layers (musashi, brachyury and a-fetoprotein (AFP)) markers in human (H), chimpanzee (C) human embryonic stem (ES) cell-supporting conditions, NHP iPS cell and bonobo (B) iPS cells, and in differentiated embryoid bodies (EBs). colonies could be distinguished by the high nucleus-to-cytoplasm c, Haematoxylin and eosin staining of teratoma sections showing ratio morphology. iPS cell clones from both species continuously differentiation into three germ layers: goblet cells in gastrointestinal tract expressed pluripotency markers, retained an undifferentiated morpho- (endo), neuroretinal epithelium (ecto), and muscle and cartilage/bone (meso). logy in culture, and maintained a normal karyotype (Fig. 1a). After Scale bars, 100 mm(a) and 150 mm(c). 1Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA. 2University of California San Diego, Department of Cellular and Molecular Medicine, Stem Cell Program, Institute for Genomic Medicine, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, California 92037, USA. 3University of California San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, USA. 4University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children’s Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, Sanford Consortium, MC 0695, 2880 Torrey Pines Scenic Drive, La Jolla, California 92093, USA. 5Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine and Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4318, USA. 6Center for Academic Research and Training in Anthropogeny (CARTA), 9500 Gilman Drive, La Jolla, California 92093, USA. *These authors contributed equally to this work. 00 MONTH 2013 | VOL 000 | NATURE | 1 ©2013 Macmillan Publishers Limited. All rights reserved RESEARCH LETTER embryoid-body-mediated differentiation in vitro, clones contained genes with increased expression in NHP iPS cells, whereas no signifi- tissue derivatives from the three embryonic germ layers and down- cant differences were observed in 11,585 protein-coding genes. Next, regulated expression of pluripotency markers (Fig. 1b). iPS-cell-selected we focused on genes differentially expressed between human and NHP clones were also able to differentiate into the three embryonic germ iPS cells (Fig. 2c–e and Extended Data Fig. 1c, d), and found, among the layers in vivo, as shown by analysis of teratomas in nude mice (Fig. 1c). top 50 genes with increased expression in human compared to NHP Together, these data demonstrate that NHP iPS cell clones re-established iPS cells, two genes involved in the restriction of L1 retrotransposition, pluripotency at the molecular and cellular levels. namely A3B and PIWIL2 (Fig. 2d). To gain insight into differences in gene expression between human Active, full-length L1 elements have the ability to move from one and NHP iPS cells, we performed high-throughput RNA sequencing location in the genome to another by a copy–paste mechanism known (RNA-seq) analyses on four human, two chimpanzee and two bonobo as retrotransposition11. Active L1 elements have been detected in both iPS cell lines (Extended Data Fig. 1b). The expression profiles of iPS germline and somatic tissues, and can affect genome integrity12,13.As cells from the three species clustered together with human ES cells uncontrolled retrotransposition activity can be deleterious to the host14, (HUES6 and H1), and were distinguishable from ES-cell-derived neural organisms have evolved mechanisms to control L1 mobility11. A3B is progenitor cells (Fig. 2a); chimpanzee and bonobo iPS cells clustered a member of the APOBEC3 family of cytidine deaminases that can closer to each other than to human iPS cells (Fig. 2a). We then per- inhibit L1 mobility in different cell types, including human ES and iPS formed pairwise comparisons of protein-coding gene expression levels cells, via a still unclear mechanism6,15,16. PIWIL2 is an effector of the (Fig. 2b). Venn diagrams in Fig. 2b represent expressed genes with Piwi-interacting RNA (piRNA) pathway involved in L1 silencing non-significant differences between species (purple), and upregulated mainly in the germ line7. genes with estimated false discovery rates (FDR) of less than 5% and a To confirm differences in A3B and PIWIL2 in human versus NHP fold change greater than twofold (pale orange and blue). Comparison iPS cells, we first cloned their complementary DNAs from the three between humans and NHPs (Fig. 2b, bottom right) revealed 1,376 species, and found a high degree of conservation between humans and genes with increased expression in human iPS cells, and 1,042 common NHPs (Extended Data Fig. 2). Quantification of A3B mRNA levels by a b Figure 2 | RNA-seq profiling of human and NHP iPS cells. a, High- Human Chimp Human Bonobo throughput sequencing of 14 RNA samples corresponding to four 1,446 11,391 1,124 1,369 11,586 975 human, two chimp and two bonobo iPS cell lines. Expression profiles of human ES cells (H1 and HUES6, arrowheads) and ES-cell-derived neural progenitor cells (NPCs) are Chimp Bonobo Human NHP shown. Heat-map representation of mapped reads corresponds to protein-coding genes. b, Venn 279 13,267 88 1,376 11,585 1,042 diagrams showing pairwise comparison of protein-coding genes. Pale orange and blue denote significantly upregulated genes Expression , . relative to d e (FDR 0.05 and fold change 2); #Name Log FC FDR #Name Log FCFDR the mean 1 RPL12 5.45 8.54 × 10–155 1 MEIG1 6.88 2.86 × 10–55 purple denotes expressed genes with 2 NLRP2 6.82 2.20 × 10–142 2 PLA2G7 3.44 2.05 × 10–53 no significant differences in mRNA 8× 3 MMP24 5.94 1.55 × 10–110 3 TDRD6 4.27 1.76 × 10–41 4× 4 PGAM1 3.41 6.52 × 10–94 4 JMJD7 2.70 1.05 × 10–38 levels between compared species. 2× 5 IDO1 6.50 2.26 × 10–90 5 SLC7A6 1.71 6.43 × 10–35 6 EIF3F 2.88 8.94 × 10–83 6 C16orf95 3.28 1.89 × 10–32 c, Heat-map representation of 1× 7 PRODH 5.41 2.50 × 10–82 7 PLA2G4B 3.36 4.43 × 10–31 0.50× 8 PIWIL2 6.91 4.40 × 10–64 8 SDSL 4.47 1.86 × 10–30 differentially expressed protein- –61 –30 0.25× 9 COL6A2 3.88 1.79 × 10 9 AKR7A3 4.96 2.86 × 10 10 COL14A1 3.35 6.05 × 10–58 10 SHMT1 1.59 4.46 × 10–29 coding genes with FDR , 0.05 and 0.125× 11 CBS 2.30 3.21 × 10–57 11 MX1 2.89 3.45 × 10–28 12 VSNL1 4.91 3.53 × 10–55 12 SLC2A5 6.07 6.85 × 10–27 fold change .
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