scholarly journals Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Elo Madissoon ◽  
Eeva-Mari Jouhilahti ◽  
Liselotte Vesterlund ◽  
Virpi Töhönen ◽  
Kaarel Krjutškov ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Target Genes ◽  
Genomic Sequence ◽  
Embryonic Stem ◽  
Homeobox Genes ◽  
Preimplantation Embryos ◽  
Human Embryos ◽  
Preimplantation Embryo Development ◽  
Genome Activation

Abstract PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes, ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB, NOBOX, TPRX1 and TPRX2, were expressed in human preimplantation embryos. In the current study we characterized these PRD-like homeobox genes in depth and studied their functions as transcription factors. We cloned multiple transcript variants from human embryos and showed that the expression of these genes is specific to embryos and pluripotent stem cells. Overexpression of the genes in human embryonic stem cells confirmed their roles as transcription factors as either activators (CPHX1, CPHX2, ARGFX) or repressors (DPRX, DUXA, TPRX2) with distinct targets that could be explained by the amino acid sequence in homeodomain. Some PRD-like homeodomain transcription factors had high concordance of target genes and showed enrichment for both developmentally important gene sets and a 36 bp DNA recognition motif implicated in Embryo Genome Activation (EGA). Our data implicate a role for these previously uncharacterized PRD-like homeodomain proteins in the regulation of human embryo genome activation and preimplantation embryo development.

Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region

2020 ◽  
Author(s):  
Hanshuang Li ◽  
Chunshen Long ◽  
Jinzhu Xiang ◽  
Pengfei Liang ◽  
Xueling Li ◽  
...  
Keyword(s):  
Stem Cells ◽  
Signaling Pathways ◽  
Embryonic Stem ◽  
Proximal Promoter ◽  
Human Embryos ◽  
Double Knockout ◽  
Rich Region ◽  
Induced Pluripotent ◽  
Zygote Genome Activation ◽  
Genome Activation

Abstract Developmental pluripotency-associated 2 (Dppa2) and developmental pluripotency-associated 4 (Dppa4) as positive drivers were helpful for transcriptional regulation of zygotic genome activation (ZGA). Here, we systematically assessed the cooperative interplay of Dppa2 and Dppa4 in regulating cell pluripotency and found that simultaneous overexpression of Dppa2/4 can make induced pluripotent stem cells closer to embryonic stem cells (ESCs). Compared with other pluripotency transcription factors, Dppa2/4 can regulate majorities of signaling pathways by binding on CG-rich region of proximal promoter (0–500 bp), of which 85% and 77% signaling pathways were significantly activated by Dppa2 and Dppa4, respectively. Notably, Dppa2/4 also can dramatically trigger the decisive signaling pathways for facilitating ZGA, including Hippo, MAPK and TGF-beta signaling pathways and so on. At last, we found alkaline phosphatase, placental-like 2 (Alppl2) was completely silenced when Dppa2 and 4 single- or double-knockout in ESC, which is consistent with Dux. Moreover, Alppl2 was significantly activated in mouse 2-cell embryos and 4–8 cells stage of human embryos, further predicted that Alppl2 was directly regulated by Dppa2/4 as a ZGA candidate driver to facilitate pre-embryonic development.

scholarly journals Endogenous human stem cell-associated retroviruses

2015 ◽  
Author(s):  
Gennadi Glinsky
Keyword(s):  
Stem Cell ◽  
Malignant Tumors ◽  
Early Stage ◽  
Embryonic Stem ◽  
Preimplantation Embryos ◽  
Human Embryos ◽  
Regulatory Sequences ◽  
Human Stem Cell ◽  
Cancer Phenotypes ◽  
Genome Activation

Recent discoveries of endogenous human stem cell-associated retroviruses (SCARs) revealed consistent activation of specific endogenous retroviral elements in human preimplantation embryos and documented the essential role of the sustained retroviral activities in the maintenance of pluripotency, functional identity and integrity of naïve-state embryonic stem cells, and anti-viral resistance of the early-stage human embryos. SCARs activity have been implicated in seeding thousands’ human-specific regulatory sequences in the hESC genome. Activation of specific SCARs, namely LTR7/HERVH and LTR5_Hs/HERVK, has been demonstrated in patients diagnosed with multiple types of cancer, autoimmune diseases, neurodegenerative disorders and it is likely associated with the emergence of clinically lethal therapy resistant death-from-cancer phenotypes in a sub-set of cancer patients diagnosed with different types of malignant tumors.

scholarly journals Identification and differential expression patterns of porcine OCT4 variants

Reproduction ◽  
2015 ◽  
Vol 149 (1) ◽  
pp. 55-66 ◽  
Author(s):  
Jae Yeon Hwang ◽  
Jong-Nam Oh ◽  
Dong-Kyung Lee ◽  
Kwang-Hwan Choi ◽  
Chi-Hun Park ◽  
...  
Keyword(s):  
Stem Cells ◽  
Crucial Role ◽  
Preimplantation Embryo ◽  
Expression Patterns ◽  
Embryonic Stem ◽  
Blastocyst Stage ◽  
Preimplantation Embryos ◽  
Preimplantation Embryo Development ◽  
Cryptic Exon

OCT4 encoded by POU5F1 has a crucial role of maintaining pluripotency in embryonic stem cells during early embryonic development and several OCT4 variants have been identified in mouse and human studies. The objective of this study was to identify different variants of OCT4 and analyze their expression patterns in preimplantation porcine embryos and various tissues. In this study, we showed that POU5F1 transcribes its three variants, namely OCT4A, OCT4B, and OCT4B1. The OCT4B transcript consists of exons identical to the major form of the OCT4 variant, OCT4A, with a differential N-terminal domain-coding exon. The structure of OCT4B1 mRNA was the same as that of OCT4B mRNA, but harbored a cryptic exon. Based on these findings, the transcription levels were investigated and found that OCT4B and OCT4B1 made up ∼20% among the variants in the embryonic stage and this indicates that OCT4A mRNA is dominantly expressed during preimplantation embryo development. In addition, OCT4B mRNA was detected in all tissues examined, while OCT4A and OCT4B1 were detected only in testis but not in other tissues examined. OCT4B1 showed inversely correlated expression with SOX2 and NANOG expression. OCT4A protein was specifically localized to the nuclei, whereas OCT4B was mainly localized to the cytoplasm of the porcine embryos at the blastocyst stage. The findings of this study reveal that the porcine OCT4 gene can potentially encode three variants (OCT4A, OCT4B, and OCT4B1), and they are differentially expressed and would have roles dissimilar between each other in preimplantation embryos and various adult tissues.

scholarly journals Synthetic and genomic regulatory elements reveal aspects of cis regulatory grammar in Mouse Embryonic Stem Cells

2018 ◽  
Author(s):  
Dana M. King ◽  
Brett B. Maricque ◽  
Barak A. Cohen
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Genomic Sequence ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Site Quality ◽  
Genomic Sequences ◽  
Position Effects

In embryonic stem cells (ESCs), a core network of transcription factors establish and maintain the gene expression program necessary to grow indefinitely in cell culture and generate all three primary germ layers. To understand how interactions between four key pluripotency transcription factors (TFs), SOX2, POU5F1 (OCT4), KLF4, and ESRRB, contribute to cis-regulation in mouse ESCs, we assayed two massively parallel reporter assay (MPRA) libraries composed of different combinations of binding sites for these TFs. One library was an exhaustive set of synthetic cis-regulatory elements and the second was a set of genomic sequences with comparable configurations of binding sites. Comparisons between the libraries allowed us to determine the regulatory grammar requirements for these binding sites in constrained synthetic contexts versus genomic sequence contexts. We found that binding site quality is a common attribute for active elements in both the synthetic and genomic contexts. For synthetic regulatory elements, the level of expression is mostly determined by the number of binding sites but is tuned by a grammar that includes position effects. Surprisingly, this grammar appears to only play a small role in setting the output levels of genomic sequences. The relative activity of genomic sequences is best explained by the predicted affinity of binding sites, regardless of identity, and optimized spacing between sites. Our findings highlight the need for detailed examinations of complex sequence space when trying to understand cis-regulatory grammar in the genome.

scholarly journals Regulation of sarcomagenesis by the empty spiracles homeobox genes EMX1 and EMX2

2021 ◽  
Vol 12 (6) ◽  
Author(s):  
Manuel Pedro Jimenez-García ◽  
Antonio Lucena-Cacace ◽  
Daniel Otero-Albiol ◽  
Amancio Carnero
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Transcription Factors ◽  
Neural Crest ◽  
Tumor Suppressors ◽  
Homeobox Genes ◽  
Neuronal Cell ◽  
Cell Gene Expression

AbstractThe EMX (Empty Spiracles Homeobox) genes EMX1 and EMX2 are two homeodomain gene members of the EMX family of transcription factors involved in the regulation of various biological processes, such as cell proliferation, migration, and differentiation, during brain development and neural crest migration. They play a role in the specification of positional identity, the proliferation of neural stem cells, and the differentiation of certain neuronal cell phenotypes. In general, they act as transcription factors in early embryogenesis and neuroembryogenesis from metazoans to higher vertebrates. The EMX1 and EMX2’s potential as tumor suppressor genes has been suggested in some cancers. Our work showed that EMX1/EMX2 act as tumor suppressors in sarcomas by repressing the activity of stem cell regulatory genes (OCT4, SOX2, KLF4, MYC, NANOG, NES, and PROM1). EMX protein downregulation, therefore, induced the malignance and stemness of cells both in vitro and in vivo. In murine knockout (KO) models lacking Emx genes, 3MC-induced sarcomas were more aggressive and infiltrative, had a greater capacity for tumor self-renewal, and had higher stem cell gene expression and nestin expression than those in wild-type models. These results showing that EMX genes acted as stemness regulators were reproduced in different subtypes of sarcoma. Therefore, it is possible that the EMX genes could have a generalized behavior regulating proliferation of neural crest-derived progenitors. Together, these results indicate that the EMX1 and EMX2 genes negatively regulate these tumor-altering populations or cancer stem cells, acting as tumor suppressors in sarcoma.

scholarly journals Embryoid research calls for reassessment of legal regulations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Markus Hengstschläger ◽  
Margit Rosner
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Legal Status ◽  
Embryonic Stem ◽  
Basic Research ◽  
Human Embryos ◽  
Human Being ◽  
Legal Regulations ◽  
Definition Of

AbstractIt is known that in countries, in which basic research on human embryos is in fact prohibited by law, working with imported human embryonic stem cells (hESCs) can still be permitted. As long as hESCs are not capable of development into a complete human being, it might be the case that they do not fulfill all criteria of the local definition of an embryo. Recent research demonstrates that hESCs can be developed into entities, called embryoids, which increasingly could come closer to actual human embryos in future. By discussing the Austrian situation, we want to highlight that current embryoid research could affect the prevailing opinion on the legal status of work with hESCs and therefore calls for reassessment of the regulations in all countries with comparable definitions of the embryo.

scholarly journals Identification of New Transcription Factors that Can Promote Pluripotent Reprogramming

2021 ◽  
Author(s):  
Ping Huang ◽  
Jieying Zhu ◽  
Yu Liu ◽  
Guihuan Liu ◽  
Ran Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Rna Sequencing ◽  
Human Urine ◽  
Embryonic Stem ◽  
Rna Seq ◽  
Reprogramming Efficiency ◽  
Yamanaka Factors ◽  
Urine Cells

Abstract Background Four transcription factors, Oct4, Sox2, Klf4, and c-Myc (the Yamanka factors), can reprogram somatic cells to induced pluripotent stem cells (iPSCs). Many studies have provided a number of alternative combinations to the non-Yamanaka factors. However, it is clear that many additional transcription factors that can generate iPSCs remain to be discovered. Methods The chromatin accessibility and transcriptional level of human embryonic stem cells and human urine cells were compared by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to identify potential reprogramming factors. Selected transcription factors were employed to reprogram urine cells, and the reprogramming efficiency was measured. Urine-derived iPSCs were detected for pluripotency by Immunofluorescence, quantitative polymerase chain reaction, RNA sequencing and teratoma formation test. Finally, we assessed the differentiation potential of the new iPSCs to cardiomyocytes in vitro. Results ATAC-seq and RNA-seq datasets predicted TEAD2, TEAD4 and ZIC3 as potential factors involved in urine cell reprogramming. Transfection of TEAD2, TEAD4 and ZIC3 (in the presence of Yamanaka factors) significantly improved the reprogramming efficiency of urine cells. We confirmed that the newly generated iPSCs possessed pluripotency characteristics similar to normal H1 embryonic stem cells. We also confirmed that the new iPSCs could differentiate to functional cardiomyocytes. Conclusions In conclusion, TEAD2, TEAD4 and ZIC3 can increase the efficiency of reprogramming human urine cells into iPSCs, and provides a new stem cell sources for the clinical application and modeling of cardiovascular disease. Graphical abstract

Regenerative Medicine: Applications and Development in Urology

2007 ◽  
Vol 74 (4) ◽  
pp. 197-205
Author(s):  
F. Pinto ◽  
A. Calarco ◽  
A. Brescia ◽  
E. Sacco ◽  
A. D'addessi ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Regenerative Medicine ◽  
Cell Transplantation ◽  
Materials Science ◽  
Experimental Studies ◽  
Embryonic Stem ◽  
Human Embryos ◽  
Engineering Applications

Purpose Congenital abnormalities and acquired disorders can lead to organ damage and loss. Nowadays, transplantation represents the only effective treatment option. However, there is a marked decrease in the number of organ donors, which is even yearly worsening due to the population aging. The regenerative medicine represents a realistic option that allows to restore and maintain the normal functions of tissues and organs. This article reviews the principles of regenerative medicine and the recent advances with regard to its application to the genitourinary tract. Recent findings The field of regenerative medicine involves different areas of technology, such as tissue engineering, stem cells and cloning. Tissue engineering involves the field of cell transplantation, materials science and engineering in order to create functional replacement tissues. Stem cells and cloning permit the extraction of pluripotent, embryonic stem cells offering a potentially limitless source of cells for tissue engineering applications. Most current strategies for tissue engineering depend upon a sample of autologous cells from the patient's diseased organ. Biopsies from patients with extensive end-stage organ failure, however, may not yield enough normal cells. In these situations, stem cells are envisaged as being an alternative source. Stem cells can be derived from discarded human embryos (human embryonic stem cells), from fetal tissue or from adult sources (bone marrow, fat, skin). Therapeutic cloning offers a potentially limitless source of cells for tissue engineering applications. Regenerative medicine and tissue engineering scientists have increasingly applied the principles of cell transplantation, materials science and bioengineering to construct biological substitutes that will restore and maintain normal function in urological diseased and injured tissues such as kidney, ureter, bladder, urethra and penis. Conclusions Regenerative medicine offers several applications in acquired and congenital genitourinary diseases. Tissue engineering, stem cells and, mostly, cloning have been applied in experimental studies with excellent results. Few preliminary human applications have been developed with promising results.

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