title: Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development.
abstract: Transcriptional program that drives human preimplantation development is largely unknown. Here, by using single-cell RNA sequencing of 348 oocytes, zygotes and single blastomeres from 2- to 3-day-old embryos, we provide a detailed analysis of the human preimplantation transcriptome. By quantifying transcript far 5'-ends (TFEs), we include in our analysis transcripts that derive from alternative promoters. We show that 32 and 129 genes are transcribed during the transition from oocyte to four-cell stage and from four- to eight-cell stage, respectively. A number of identified transcripts originates from previously unannotated genes that include the PRD-like homeobox genes ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB and LEUTX. Employing de novo promoter motif extraction on sequences surrounding TFEs, we identify significantly enriched gene regulatory motifs that often overlap with Alu elements. Our high-resolution analysis of the human transcriptome during preimplantation development may have important implications on future studies of human pluripotent stem cells and cell reprograming.
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.|Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden.
authors.forename: Virpi
authors.initials: V
authors.lastname: Töhönen
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.|Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden.|Science for Life Laboratory, Tomtebodavägen 23 A, Solna 171 21, Sweden.
authors.forename: Shintaro
authors.initials: S
authors.lastname: Katayama
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.|Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden.
authors.forename: Liselotte
authors.initials: L
authors.lastname: Vesterlund
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.|Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden.
authors.forename: Eeva-Mari
authors.initials: EM
authors.lastname: Jouhilahti
authors.affiliation: Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden.
authors.forename: Mona
authors.initials: M
authors.lastname: Sheikhi
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.|Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden.
authors.forename: Elo
authors.initials: E
authors.lastname: Madissoon
authors.affiliation: ProCreaLab SA, Lugano CH-6900, Switzerland.
authors.forename: Giuditta
authors.initials: G
authors.lastname: Filippini-Cattaneo
authors.affiliation: Department of Pathology and Immunology, Faculty of Medicine, Geneva University, 1 rue Michel-Servet, Geneva 4, 1211, Switzerland.
authors.forename: Marisa
authors.initials: M
authors.lastname: Jaconi
authors.affiliation: Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Johnsson
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Bürglin
authors.affiliation: Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden.
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
authors.affiliation: Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden.
authors.forename: Outi
authors.initials: O
authors.lastname: Hovatta
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.|Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden.|Science for Life Laboratory, Tomtebodavägen 23 A, Solna 171 21, Sweden.|Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Biomedicum 1, Haartmaninkatu 8, Helsinki 00290, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Kere
mesh_terms: D020121:5' Untranslated Regions; D001755:Blastocyst / Q000378:metabolism*; D001757:Blastomeres / Q000378:metabolism*; D047108:Embryonic Development / Q000235:genetics*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D057809:HEK293 Cells; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D009865:Oocytes / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D018626:Retroelements / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D015053:Zygote / Q000378:metabolism*
chemical_list: D020121:5' Untranslated Regions; D018398:Homeodomain Proteins; D012333:RNA, Messenger; D018626:Retroelements; D014157:Transcription Factors