Gene Expression Profiling of Human Oocytes Developed and Matured in Vivo Or in Vitro
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Gene Expression Profiling of Human Oocytes Developed and Matured in Vivo Or in Vitro
Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 879489, 20 pages http://dx.doi.org/10.1155/2013/879489 Review Article Gene Expression Profiling of Human Oocytes Developed and Matured In Vivo or In Vitro Irma Virant-Klun,1 Katja Knez,1 Tomaz Tomazevic,1 and Thomas Skutella2 1 Reproductive Unit, Department of Obstetrics and Gynecology, University Medical Centre Ljubljana, Slajmerjeva 3, 1000 Ljubljana, Slovenia 2 Institute for Anatomy and Cell Biology, Medical Faculty, University of Heidelberg, 69120 Heidelberg, Germany Correspondence should be addressed to Irma Virant-Klun; [email protected] Received 30 September 2012; Revised 7 December 2012; Accepted 8 December 2012 Academic Editor: Xuan Jin Copyright © 2013 Irma Virant-Klun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The quality of the human oocyte determines the success of fertilization and affects the consequent embryo development, pregnancy and birth; it therefore serves as a basis for human reproduction and fertility. The possibility to evaluate oocyte quality in the in vitro fertilization programme is very limited. The only criterion which is commonly used to evaluate oocyte quality is its morphology. There is a mass of oocytes in the in vitro fertilization programme which are not fertilized in spite of normal morphology. In the past, several attempts focused on oocyte gene expression profiling by different approaches. The results elucidated groups of genes related to the human oocyte. It was confirmed that some factors, such as oocyte in vitro maturation, are detectable at the molecular level of human oocytes and their polar bodies in terms of gene expression profile. -
Oocyte Aneuploidy—More Tools to Tackle an Old Problem
COMMENTARY Oocyte aneuploidy—more tools to tackle an old problem COMMENTARY Chris Lodgea and Mary Herberta,1 Meiosis generates a single-copy genome during two centromeric cohesin enables sister centromeres to successive rounds of cell division after a single round biorient on the meiosis II spindle (2, 5). Upon cleavage of DNA replication. Failure to transmit exactly one of centromeric cohesin, dyads are converted to single copy of each chromosome during fertilization gives chromatids, which segregate equationally to opposite rise to aneuploid embryos resulting in infertility and poles of the meiosis II spindle. Protection of a centro- congenital abnormalities such as Down’s syndrome. meric cohesin by Shugoshin proteins (SGOL2 in mam- Aneuploidy attributable to meiotic errors is over- mals) until the onset of anaphase II is essential for whelming due to chromosome segregation errors dur- orderly segregation of chromatids (7, 8). In oocytes, ing female meiosis, and the incidence of these both meiotic divisions are highly asymmetrical, giving increases dramatically as women get older (1, 2). Be- rise to two small nonviable polar bodies (Fig. 1). cause the oocyte is the only viable product of female Consistent with previous studies (9), Tyc et al. (3) meiosis, our understanding of predisposing events in found that only a tiny fraction (<1%) of meiotic errors human oocytes relies largely on inferences from ge- are of paternal origin. Compared with males, the es- netic studies in cases of trisomy and on analysis of tablishment and maintenance of bivalent chromo- oocytes obtained from in vitro fertilization clinics. somes are compromised in female meiosis. In females, Progress toward understanding the underlying mech- there is a greater risk of homologs failing to form cross- anisms has been hampered by a paucity of informa- overs, or of forming them in precarious positions that are tion on the outcome of both meiotic divisions. -
Mutational Inactivation of STAG2 Causes Aneuploidy in Human Cancer
REPORTS mean difference for all rubric score elements was ing becomes a more commonly supported facet 18. C. L. Townsend, E. Heit, Mem. Cognit. 39, 204 (2011). rejected. Univariate statistical tests of the observed of STEM graduate education then students’ in- 19. D. F. Feldon, M. Maher, B. Timmerman, Science 329, 282 (2010). mean differences between the teaching-and- structional training and experiences would alle- 20. B. Timmerman et al., Assess. Eval. High. Educ. 36,509 research and research-only conditions indicated viate persistent concerns that current programs (2011). significant results for the rubric score elements underprepare future STEM faculty to perform 21. No outcome differences were detected as a function of “testability of hypotheses” [mean difference = their teaching responsibilities (28, 29). the type of teaching experience (TA or GK-12) within the P sample population participating in both research and 0.272, = 0.006; CI = (.106, 0.526)] with the null teaching. hypothesis rejected in 99.3% of generated data References and Notes 22. Materials and methods are available as supporting samples (Fig. 1) and “research/experimental de- 1. W. A. Anderson et al., Science 331, 152 (2011). material on Science Online. ” P 2. J. A. Bianchini, D. J. Whitney, T. D. Breton, B. A. Hilton-Brown, 23. R. L. Johnson, J. Penny, B. Gordon, Appl. Meas. Educ. 13, sign [mean difference = 0.317, = 0.002; CI = Sci. Educ. 86, 42 (2001). (.106, 0.522)] with the null hypothesis rejected in 121 (2000). 3. C. E. Brawner, R. M. Felder, R. Allen, R. Brent, 24. R. J. A. Little, J. -
Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment. -
Molecular Dynamics and Evolutionary Aspects of the Transition from the Fully Grown Oocyte to Embryo
Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo Alexei V. Evsikov,1,5 Joel H. Graber,1 J. Michael Brockman,1,2 Aleš Hampl,3 Andrea E. Holbrook,1 Priyam Singh,1,2 John J. Eppig,1 Davor Solter,1,4 and Barbara B. Knowles1 1The Jackson Laboratory, Bar Harbor, Maine 04609, USA; 2 Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA; 3Masaryk University Brno and Institute of Experimental Medicine, 625 00 Brno, Czech Republic; 4Max Planck Institute of Immunobiology, 79108 Freiburg, Germany Fully grown oocytes (FGOs) contain all the necessary transcripts to activate molecular pathways underlying the oocyte-to-embryo transition (OET). To elucidate this critical period of development, an extensive survey of the FGO transcriptome was performed by analyzing 19,000 expressed sequence tags of the Mus musculus FGO cDNA library. Expression of 5400 genes and transposable elements is reported. For a majority of genes expressed in mouse FGOs, homologs transcribed in eggs of Xenopus laevis or Ciona intestinalis were found, pinpointing evolutionary conservation of most regulatory cascades underlying the OET in chordates. A large proportion of identified genes belongs to several gene families with oocyte-restricted expression, a likely result of lineage-specific genomic duplications. Gene loss by mutation and expression in female germline of retrotransposed genes specific to M. musculus is documented. These findings indicate rapid diversification of genes involved in female reproduction. Comparison of the FGO and two-cell embryo transcriptomes demarcated the processes important for oogenesis from those involved in OET and identified novel motifs in maternal mRNAs associated with transcript stability. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
NUFIP1 Sirna (H): Sc-105367
SANTA CRUZ BIOTECHNOLOGY, INC. NUFIP1 siRNA (h): sc-105367 BACKGROUND STORAGE AND RESUSPENSION NUFIP1 (nuclear fragile X mental retardation-interacting protein 1) is a 495 Store lyophilized siRNA duplex at -20° C with desiccant. Stable for at least amino acid protein that localizes to the nucleus and can interact with FMR1 one year from the date of shipment. Once resuspended, store at -20° C, (fragile X mental retardation protein) and BRCA1, a breast and ovarian-specific avoid contact with RNAses and repeated freeze thaw cycles. tumor suppressor. Through its interaction with FMR1, NUFIP1 is thought to Resuspend lyophilized siRNA duplex in 330 µl of the RNAse-free water shuttle specific mRNPs to active neuronal synapses, thereby regulating the provided. Resuspension of the siRNA duplex in 330 µl of RNAse-free water translation of synaptic plasticity-related mRNA. The close interaction of makes a 10 µM solution in a 10 µM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM NUFIP1 with FMR1, a protein that is essential for proper dendritic spine matu- EDTA buffered solution. ration, suggests close involvement in neuronal development. Interaction of NUFIP1 with BRCA1 results in the formation of a complex which binds the APPLICATIONS positive elongation factor P-TEFb, thus stimulating RNA polymerase II (pol II) transcription. When associated with BRAC1, NUFIP1 acts as a transcriptional NUFIP1 siRNA (h) is recommended for the inhibition of NUFIP1 expression in activator contributing to tumor suppressor gene expression. NUFIP1 contains human cells. one C2H2-type zinc finger and is expressed throughout the body. SUPPORT REAGENTS REFERENCES For optimal siRNA transfection efficiency, Santa Cruz Biotechnology’s 1. -
Detection of Aneuploidies by Paralogous Sequence Quantification S Deutsch, U Choudhury, G Merla, C Howald, a Sylvan, S E Antonarakis
908 J Med Genet: first published as 10.1136/jmg.2004.023184 on 9 December 2004. Downloaded from ORIGINAL ARTICLE Detection of aneuploidies by paralogous sequence quantification S Deutsch, U Choudhury, G Merla, C Howald, A Sylvan, S E Antonarakis ............................................................................................................................... J Med Genet 2004;41:908–915. doi: 10.1136/jmg.2004.023184 Background: Chromosomal aneuploidies are a common cause of congenital disorders associated with cognitive impairment and multiple dysmorphic features. Pre-natal diagnosis of aneuploidies is most See end of article for commonly performed by the karyotyping of fetal cells obtained by amniocentesis or chorionic villus authors’ affiliations sampling, but this method is labour intensive and requires about 14 days to complete. ....................... Methods: We have developed a PCR based method for the detection of targeted chromosome number Correspondence to: abnormalities termed paralogous sequence quantification (PSQ), based on the use of paralogous genes. Professor Stylianos E Paralogous sequences have a high degree of sequence identity, but accumulate nucleotide substitutions in Antonarakis, Department a locus specific manner. These sequence differences, which we term paralogous sequence mismatches of Genetic Medicine and Development, University of (PSMs), can be quantified using pyrosequencing technology, to estimate the relative dosage between Geneva Medical School, different chromosomes. We designed 10 assays for the detection of trisomies of chromosomes 13, 18, and GE 1211, Geneva, 21 and sex chromosome aneuploidies. Switzerland; Stylianos. antonarakis@medecine. Results: We evaluated the performance of this method on 175 DNAs, highly enriched for abnormal unige.ch samples. A correct and unambiguous diagnosis was given for 119 out of 120 aneuploid samples as well as for all the controls. -
Tricarboxylic Acid Cycle Metabolites As Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos
Supplementary Materials Tricarboxylic Acid Cycle Metabolites as Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos Figure S1. (A) Total number of cells in fast (FBL) and slow (SBL) blastocysts; (B) Fluorescence intensity for 5-methylcytosine and 5-hydroxymethylcytosine of fast and slow blastocysts of cells from Trophoectoderm (TE) or inner cell mass (ICM). Fluorescence intensity for 5-methylcytosine of cells from the ICM or TE in blastocysts cultured with (C) dimethyl-succinate or (D) dimethyl-α- ketoglutarate. Statistical significance is identified by different letters. Figure S2. Experimental design. Table S1. Selected genes related to metabolism and epigenetic mechanisms from RNA-Seq analysis of bovine blastocysts (slow vs. fast). Genes in blue represent upregulation in slow blastocysts, genes in red represent upregulation in fast blastocysts. log2FoldCh Gene p-value p-Adj ange PDHB −1.425 0.000 0.000 MDH1 −1.206 0.000 0.000 APEX1 −1.193 0.000 0.000 OGDHL −3.417 0.000 0.002 PGK1 −0.942 0.000 0.002 GLS2 1.493 0.000 0.002 AICDA 1.171 0.001 0.005 ACO2 0.693 0.002 0.011 CS −0.660 0.002 0.011 SLC25A1 1.181 0.007 0.032 IDH3A −0.728 0.008 0.035 GSS 1.039 0.013 0.053 TET3 0.662 0.026 0.093 GLUD1 −0.450 0.032 0.108 SDHD −0.619 0.049 0.143 FH −0.547 0.054 0.149 OGDH 0.316 0.133 0.287 ACO1 −0.364 0.141 0.297 SDHC −0.335 0.149 0.311 LIG3 0.338 0.165 0.334 SUCLG −0.332 0.174 0.349 SDHA 0.297 0.210 0.396 SUCLA2 −0.324 0.248 0.439 DNMT1 0.266 0.279 0.486 IDH3B1 −0.269 0.296 0.503 SDHB −0.213 0.339 0.544 DNMT3B 0.181 0.386 0.598 APOBEC1 0.629 0.386 0.598 TDG 0.427 0.398 0.611 IDH3G 0.237 0.468 0.675 NEIL2 0.509 0.572 0.720 IDH2 0.298 0.571 0.720 DNMT3L 1.306 0.590 0.722 GLS 0.120 0.706 0.821 XRCC1 0.108 0.793 0.887 TET1 −0.028 0.879 0.919 DNMT3A 0.029 0.893 0.920 MBD4 −0.056 0.885 0.920 PDHX 0.033 0.890 0.920 SMUG1 0.053 0.936 0.954 TET2 −0.002 0.991 0.991 Table S2. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Comparative Mrna and Mirna Expression in European
Heredity (2019) 122:172–186 https://doi.org/10.1038/s41437-018-0090-1 ARTICLE Comparative mRNA and miRNA expression in European mouflon (Ovis musimon) and sheep (Ovis aries) provides novel insights into the genetic mechanisms for female reproductive success 1 1,2 1,2 3 1,2 1,2 1,2 Ji Yang ● Xin Li ● Yin-Hong Cao ● Kisun Pokharel ● Xiao-Ju Hu ● Ze-Hui Chen ● Song-Song Xu ● 3 3 3 1 Jaana Peippo ● Mervi Honkatukia ● Juha Kantanen ● Meng-Hua Li Received: 12 January 2018 / Revised: 20 March 2018 / Accepted: 18 April 2018 / Published online: 21 May 2018 © The Author(s) 2018. This article is published with open access Abstract Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis 1234567890();,: 1234567890();,: musimon) and performed an mRNA–miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep. We identified several novel genes with differentially expressed mRNAs (e.g., EREG, INHBA, SPP1, AMH, TDRD5, and ZP2) between the wild and domestic sheep, which are functionally involved in oocyte and follicle development and fertilization, and are significantly (adjusted P-value < 0.05) enriched in the Gene Ontology (GO) terms of various reproductive process, including the regulation of fertilization, oogenesis, ovarian follicle development, and sperm–egg recognition. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.