Posts Tagged ‘embryogenesis’

Junction of the roads for “ovo”: Functional Genomics, Evolution and Decisions

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Stem Cells for Regenerative Medicine, tagged Bioinformatics, Biology, Complementary DNA, Drosoophila, Drosophila, embryogenesis, GenBank, gene, genomics, germline sex determination, oogenesis, Stem cell, Zinc finger on July 20, 2013| Leave a Comment »

Understanding of OVO-like proteins (OVOL), which are members of the zinc finger protein family, serve as transcription factors to regulate gene expression in various differentiation processes and are involved in epithelial development and differentiation in a wide variety of organisms. Thus, comparative genomic analysis among three different OVOL genes (OVOL1-3) in vertebrates may shed a light onto this crucial gene for development of molecular diagnostics and targeted therapies.

The Figure is from:

Genomics. Author manuscript; available in PMC 2010 June 29.

Published in final edited form as: Genomics. 2002 September; 80(3): 319–325.

Analysis of mouse and human OVOL2 gene products. (A) The 5′ end sequences of the mouse Ovol2B cDNA and the deduced OVOL2B protein. The “#” symbol indicates the position of an internal methionine previously mistaken as the initiation codon [14]. (B) Deduced amino acid sequences of OVOL2A proteins in mouse (mOvol2A) and human (hOvol2A). The “*” symbol indicates amino acid identity. The four C2H2 zinc fingers are underlined. The predicted NLS sequences are boxed. Sequences common to mouse OVOL2A and OVOL2B start at the brackets in (A) and (B). Human OVOL2B starts at the internal methionine (bold). Shown in bold and italics are positions where our predicted sequence differs from the previously reported sequence [14]. (C) Phylogenetic analysis of OVO proteins. cOvo, C. elegans OVO (GenBank acc. no. AF134806); dOvo, Drosophila OVO (GenBank acc. no. X59772); mOvol1, mouse OVOL1 (GenBank acc. no. AF134804); hOvol1, human OVOL1 (GenBank acc. no. AF016045); mOvol2, mouse OVOL2 (GenBank acc. no.AY090537); hOvol2, human OVOL2 (GenBank acc. no. AK022284); mOvol3, mouse OVOL3 (GenBank acc. no. BF714064); hOvol3, human OVOL3 (GenBank acc. no. AD001527).

The Ovo gene family encodes evolutionarily conserved proteins contain four DNA-binding C₂H₂ zinc fingers at the C termini and possess transcriptional regulatory activities in diverse array of organisms from Caenorhabditis elegans, Drosophila, Zebrafish, chick, and mammals. Drosophila ovo, the founding member of the family, acts genetically downstream of Wg (fly Wnt homolog) and DER (fly epidermal growth factor receptor homolog) signaling pathways and is required for epidermal denticle formation and oogenesis.

OVOL proteins are characterized by the presence of hypervariable ID regions.

A. Mouse OVOL1 has ID residues in the first 100 amino acids. B. Mouse OVOL2 possesses ID residues in the first 50 amino acids with a glycine-rich and serine rich region as marked in red color. C. Mouse OVOL3 has ID segments within the N-terminal 100 residues. D. Drosophila OVO is intrinsically disordered with large patches of residue biasness as indicated by the red color. We used DISOPRED2 software [47] for the prediction of ID regions. The horizontal line indicates the ordered/disordered threshold for the default false positive rate of 5%. The ‘filter’ curve represents the outputs from DISOPRED2 and the ‘output’ curve represents the outputs from a linear support vector machine (SVM) classifier (DISOPREDsvm). The outputs from DISOPREDsvm are included to indicate shorter as low confidence predictions of disorder.

doi:10.1371/journal.pone.0039399.g001, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

This gene family is identified as mammalian Ovol (Ovo-like) genes, including Ovol1(movo1), Ovol2 (movo2), and Ovol3 (movo3) in mice and OVOL1, OVOL2, andOVOL3 in humans. Ovol1 is the most studied compared to Ovol2 and Ovol3.

Kumar A, Bhandari A, Sinha R, Sardar P, et al. (2012) Molecular Phylogeny of OVOL Genes Illustrates a Conserved C2H2 Zinc Finger Domain Coupled by Hypervariable Unstructured Regions. PLoS ONE 7(6): e39399. doi:10.1371/journal.pone.0039399

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039399

Phylogenetic history of OVOL proteins using the Bayesian method. A. Full-length OVOL proteins. B. Selected region of OVOL proteins.

Posterior probabilities scores are depicted by various color balls. The placozoan OVOL protein (e_gw1.4.509.1) was used as the outgroup in this phylogenetic tree. Red x indicates sequence position, which did not accord with species phylogeny. BFL: B. floridae (lancelet), SPU: S. purpuratus (sea urchin), NVE: N. vectensis (sea anemone), HRO: H. robusta (annelids), LGI: L. gigantean (molluscs) and TAD: T. adhaerens(placozoan). Trees in figures 7A and 7B are generated using the MrBayes 3.2 [53] from alignments supplied in supplementary Files S1 and S2, respectively. (Figure 7 of doi:10.1371/journal.pone.0039399.g007, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

“Fine scale analysis of gene expression in Drosophila melanogaster gonads reveals Programmed cell death 4 promotes the differentiation of female germline stem cells” Amy C Cash and Justen Andrews* BMC Developmental Biology 2012, 12:4 doi:10.1186/1471-213X-12-4

”Regulatory and functional interactions between ovarian tumor and ovo during Drosophila oogenesis. “ Shannon Hinson, Janette Pettus, Rod N Nagoshi Mechanisms of Development Volume 88, Issue 1, 1 October 1999, Pages 3–14 http://www.sciencedirect.com/science/article/pii/S0925477399001677

“Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions.” Kumar A, Bhandari A, Sinha R, Sardar P, Sushma M, Goyal P, Goswami C, Grapputo A. PLoS One. 2012;7(6):e39399. doi: 10.1371/journal.pone.0039399. Epub 2012 Jun 21.

“Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.

Nucleic Acids Res. 1997 Sep 1; 25(17):3389-402.

Ovol1:

Chromosomal localization of OVOL1 gene from selected vertebrates, flanked by a set of conserved marker genes. SIPA1: signal-induced proliferation-associated 1; RELA: v-rel reticuloendotheliosis viral oncogene homolog A (avian); KAT5: K (lysine) acetyltransferase; SNX32: sorting nexin 32; MUS81: MUS81 endonuclease homolog (S. cerevisiae); BANF1: barrier to autointegration factor 1; EXOC6B: exocyst complex component 6B; DYSF: dysferlin, limb girdle muscular dystrophy 2B; COL4A5: collagen, type IV, alpha 5; DAK: dihydroxyacetone kinase 2 S. cerevisiae homolog. doi:10.1371/journal.pone.0039399.g003, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

Drosophila ovo/svb (dovo) is required for epidermal cuticle/denticle differentiation and is genetically downstream of the wg signaling pathway, so does a mouse homolog of dovo, movo1. Also, Li group showed that movo1 promoter is activated by the lymphoid enhancer factor 1 (LEF1)/β-catenin complex, a transducer of wnt signaling. Simply these data showed movo1 is a developmental target of wnt signaling during hair morphogenesis in mice, and there is a conserved regulatory pathway at wg/wnt-ovolink in epidermal appendage. human OVOL1 has been identified as a gene that is responsive to TGF-β1/BMP7 treatment via a Smad4-dependent pathway (Kowanetz et al., 2004).

Ovo1 li“Characterization of a human homolog (OVOL1) of the Drosophila ovo gene, which maps to chromosome 11q13.” Chidambaram A, Allikmets R, Chandrasekarappa S, Guru SC, Modi W, Gerrard B, Dean M. Mamm Genome. 1997 Dec;8(12):950-1.nks Wnt signaling with N-cadherin localization during neural crest migrationDevelopment 2010 137 (12) 1981-1990.

“Id2 and Id3 define the potency of cell proliferation and differentiation responses to transforming growth factor beta and bone morphogenetic protein.” Marcin Kowanetz,

Ulrich Valcourt, Rosita Bergström ‡,Carl-Henrik Heldin and Aristidis Moustakas *

. Mol. Cell. Biol., 24 (2004), pp. 4241–4254 http://mcb.asm.org/content/24/10/4241

“The LEF1/β-catenin complex activates movo1, a mouse homolog of Drosophila ovo required for epidermal appendage differentiation” Baoan Li, Douglas R. Mackay, Qian Dai, Tony W. H. Li, Mahalakshmi Nair, Magid Fallahi, Christopher P. Schonbaum, Judith Fantes, Anthony P. Mahowald, Marian L. Waterman,Elaine Fuchs, and Xing DaiPNAS vol. 99 no. 9 Baoan Li, 6064–6069. http://www.pnas.org/content/99/9/6064.abstract?ijkey=a7d2985635ef09ca63982ae4397ef325aa46252b&keytype2=tf_ipsecsha

“Expression of murine novel zinc finger proteins highly homologous to Drosophila ovo gene product in testis.” Masu Y, Ikeda S, Okuda-Ashitaka E, Sato E, Ito S. FEBS Lett. 1998 Jan 16;421(3):224-8.

“The ovo gene required for cuticle formation and oogenesis in flies is involved in hair formation and spermatogenesis in mice” Xing Dai, Christopher Schonbaum, Linda Degenstein, Wenyu Bai,Anthony Mahowald, and Elaine Fuchs. (1998) Genes Dev. 12, 3452–3463 http://www.ncbi.nlm.nih.gov/pubmed/9808631

OvoL2 at the Junction of Decisions:

Brain development is fascinating and complex since cranial neurulation is an integral component of brain morphogenesis and there are factors present outside of the neuroepithelium can also affect the morphogenesis of the cranial neural tube. Previous studies revealed Ovol2 expression in brain, testis, and epithelial tissues such as skin and intestine of adult mice (Li et al., 2002a).

OVOL2 orthologs identified in vertebrates by comparing chromosomal localization.

RRBP1: ribosome binding protein 1 homolog; BANF2: barrier to autointegration factor 2; SNX5: sorting nexin 5; CSRP2BP: CSRP2 binding protein; SEC23B: protein transport protein Sec23B; POLR3F: polymerase (RNA) III (DNA directed) polypeptide F; RBBP9: Retinoblastoma-binding protein 9; DTD1: D-tyrosyl-tRNA deacylase 1. doi:10.1371/journal.pone.0039399.g004, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

Neural/non-neural cell fate decisions is carried by bone morphogenetic protein (BMP) signaling, which inhibits precocious neural differentiation and allows for proper differentiation of mesoderm, endoderm, and epidermis, during early embryonic development. There are many unknown in this mechanism yet the expression of Ovol2, which encodes an evolutionarily conserved zinc finger transcription factor, is down-regulated during neural differentiation of mouse embryonic stem cells since null Ovol2 in embryonic stem cells facilitates neural conversion and inhibits mesendodermal differentiation, whereas Ovol2 overexpression gives rise to the opposite phenotype. Furthermore, the studies also prove BMP4 and ovo2 interacted to rescue these changes. If BMP4 is provided, Ovol2 knockdown partially rescues the neural inhibition. Mechanism studies show the regulation pattern between these BMP and Ovol2. BMP4 directly regulates Ovol2 expression through the binding of Smad1/5/8 to the second intron of the Ovol2 gene. Thus, Ovol2 acts downstream of BMP pathway. In addition, in vivo chick studies presented that when Ovol2 is ectopically expressed the prospective neural plate represses the expression of the definitive neural plate marker cSox2In the chick embryo. Also, lack of Ovol2 prevented increase BMP4 expression. During early germ layer development there is an important comment between neuroectoderm and mesendoderm provided by Ovol2.

In addition, Ovol2 acts in downstream of key developmental signaling pathways including Wg/Wnt and BMP/TGF-β. Based on findings from chromatin immunoprecipitation, luciferase reporter, and functional rescue assays, Wells group demonstrated that Ovol2 directly represses two critical downstream targets, c-Mycand Notch1. Hence, this action suppresses keratinocyte transient proliferation and terminal differentiation. Like a twilight zone to choose when to proliferate and when to resist differentiation.

“Ovol

“Ovol2, a Mammalian Homolog of Drosophila ovo: Gene Structure, Chromosomal Mapping, and Aberrant Expression in Blind-Sterile Mice.” Baoan Li, Qian Dai, Ling Li, Mahalakshmi Nair, Douglas R. Mackay, Xing DaiGenomics Volume 80, Issue 3, September 2002, Pages 319–325.

Ovol2 directly represses two critical downstream targets, c-Myc and Notch1, thereby suppressing keratinocyte transient proliferation and terminal differentiation, respectively

Wells J, Lee B, Cai AQ, Karapetyan A, Lee WJ, Rugg E, Sinha S, Nie Q, Dai X.

J Biol Chem. 2009 Oct 16;284(42):29125-35. doi: 10.1074/jbc.M109.008847. Epub 2009 Aug 21.

“The zinc finger transcription factor Ovol2 acts downstream of the bone morphogenetic protein pathway to regulate the cell fate decision between neuroectoderm and mesendoderm.” Zhang T, Zhu Q, Xie Z, Chen Y, Qiao Y, Li L, Jing N. J Biol Chem. 2013 Mar 1;288(9):6166-77. doi: 10.1074/jbc.M112.418376. Epub 2013 Jan 14.

“The mouse Ovol2 gene is required for cranial neural tube development” Douglas R. Mackay ^a, Ming Hu ^a, Baoan Li ^a, Catherine Rhéaume ^a, Xing Dai^.lDevelopmental Biology Volume 291, Issue 1, 1 March 2006, Pages 38–52.

Ovol3

While tracing the OVOL genes, we identified a third OVOL gene, OVOL3, in a wide array of mammals including humans (chromosome 19), chimpanzees (chromosome 19), mice (chromosome 7), rats (chromosome 1), cows (chromosome 18), pigs (chromosome 6), and opossums (chromosome 4) with a conserved synteny. The conserved synteny comprises an octet of genes, LIN37-PRODH2-KIRREL2-APLP11-NKF3ID-LPFN3-SDHAF1-CLIF3,on one side and POLR2L-CAPSN1-COX7A1 on the other side of OVOL3 in a region of about 400 kb (Figure 5 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399).

Synteny analysis of OVOL3 genes illustrates the loss of OVOL3a after duplication event and maintenance of paralogous OVOL3b in fishes.

LIN37: lin-37 homolog (C. elegans); PRODH2: proline dehydrogenase (oxidase) 2; KIRREL2: kin of IRRE like 2 (Drosophila); APLP1: amyloid beta (A4) precursor-like protein 1; NFKBID: nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta; LRFN3: leucine rich repeat and fibronectin type III domain containing 3; SDHAF1: succinate dehydrogenase complex assembly factor 1; CLIP3: CAP-GLY domain containing linker protein 3; POLR2I: polymerase (RNA) II (DNA directed) polypeptide I, 14.5 kDa; CAPNS1: calpain, small subunit 1; COX7A1: cytochrome c oxidase subunit VIIa polypeptide 1 (muscle); DMPK: dystrophia myotonica-protein kinase; HLCS: holocarboxylase synthetase; AMOT: angiomotin; REXO2: REX2 RNA exonuclease 2 homolog (S. cerevisiae). (Reference from doi:10.1371/journal.pone.0039399.g005 , http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

There are not many studies on Ovol 3but my interest in this region lies on Chromosome 19 since “it has the highest gene density of all human chromosomes and the large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance.”

“The DNA sequence and biology of human chromosome 19.” Grimwood J, et al. Nature. 2004 Apr 1;428(6982):529-35.

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How Genes Function

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Cell Biology, Signaling & Cell Circuits, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Industry Competitive Intelligence, tagged Biology, DNA, embryogenesis, gene, gene expression, Non-coding RNA, RNA, Wistar Institute on March 4, 2013| 6 Comments »

New Insight into How Genes Function

Reporter: Larry H Bernstein, MD, FCAP

New Insight into How Genes Function

GENNewsHighlights Feb 17, 2013

Long segments of noncoding RNA are key to

physically manipulating DNA in order to activate certain genes.
These noncoding RNA-activators (ncRNA-a) have a crucial role in

http://www.genengnews.com/…news…/new-insight-into-how-genes-function/

An illustration of the central dogma of molecu...

Diagram of a eukaryotic gene (Photo credit: Wikipedia)

This image shows the coding region in a segment of eukaryotic DNA. (Photo credit: Wikipedia)

English: Sporulation involved ncRNA (Photo credit: Wikipedia)

English: Genes required for ectodermal specification during early embryogenesis (Photo credit: Wikipedia)

‘Activating’ RNA takes DNA on a loop through time and space (phys.org)
Gene Sequencing – to the bedside (pharmaceuticalintelligence.com)
Deafness Gene Breakthrough (amplifon.co.uk)
Reliv Launches Most Potent Form of Lunasin Ever Produced (prweb.com)
Paired genes in stem cells shed new light on gene organization and regulation (esciencenews.com)

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Endothelial Differentiation and Morphogenesis of Cardiac Precursors

Posted in Cardiovascular Pharmacogenomics, tagged congenital heart defects, development, embryo, embryogenesis, Endothelium, gene expression, heart development, transcription factors, vasculogenesis on July 17, 2012| 3 Comments »

Reporter: Sudipta Saha, Ph.D.

Beyond characterization of the fundamental anatomy of vascular development, the first investigators in this field participated in one of the classic debates in all of developmental biology: where and when do endothelial cells (and hence blood vessels) arise in the developing embryo? Because blood vessels are first observed in the yolk sac in avian and mammalian embryos. It was initially assumed that all blood vessels arise from extra-embryonic tissues. However, careful histological analysis subsequently indicated that isolated foci of endothelial cells can also be observed in the embryo proper, which suggested that blood vessels arise from an intraembryonic source (specifically, the mesoderm) rather than via colonization. The formation of new blood vessels in the adult organism not only contributed to the progression of diseases such as cancer and diabetic retinopathy but also can be promoted in therapeutic approaches to various ischemic pathologies. Because many of the signals important to blood vessel development during embryogenesis are recapitulated during adult blood vessel formation, much work has been performed to better-understand the molecular control of endothelial differentiation in the developing embryo. Activators and inhibitors of developmental pathways have been tested for their ability to modulate angiogenesis in early phase clinical trials, and in the case of anti-Flk1 antibodies clinical utility has been demonstrated for anti-tumor strategies. Analyses of circulating endothelial progenitor cells, which have angiogenic potential, do indeed suggest that there are similarities in the biology of these cells compared with developmental endothelial precursors. Stem cell therapeutics therefore represents another potential arena for translation of insights from vascular development to clinical practice. Even though our understanding of endothelial development is much richer than it was even a few years ago and despite the potential applications of this knowledge in clinical medicine, there are still a number of key issues on this topic that remain to be resolved. Precisely how early are endothelial precursors specified during development, and what is the nature of this progenitor cell pool? What are the relationships among signaling pathways that specify endothelial fates in a coordinated fashion? Is there a transcriptional hierarchy that regulates vascular development? The answers to these and other questions about endothelial development are likely to be forthcoming in the near future as experimental methods continue to evolve (http://atvb.ahajournals.org/content/25/11/2246.full).

The development of the vertebrate heart can be considered an additive process, in which additional layers of complexity have been added throughout the evolution of a simple structure (linear heart tube) in the form of modular elements (atria, ventricles, septa, and valves). Each modular element confers an added capacity to the vertebrate heart and can be identified as individual structures patterned in a precise manner. An understanding of the individual modular steps in cardiac morphogenesis is particularly relevant to congenital heart disease, which usually involves defects in specific structural components of the developing heart. Organ formation requires the precise integration of cell type-specific gene expression and morphological development; both are intertwined in their regulation by transcription factors. Although many transcription factors have been described as regulators of cardiac-specific gene expression, the transcriptional regulation of cardiac morphogenesis is still not well explored. For a transcription factor to be considered directly involved in heart development, it must be expressed in developing heart tissues and exert an influence on processes that impact the morphogenesis of the developing heart. Transcription factors can regulate the expression of other genes in a tissue-specific and quantitative manner and are thus major regulators of embryonic developmental processes. A number of complex transcriptional networks and interactions are involved in the morphogenesis of the developing vertebrate heart. The identities of crucial regulators involved in defined events in cardiogenesis are being uncovered at a rapid rate, but a number of critical questions remain. First and foremost, it is still not known which transcription factors are involved in the earliest differentiation of cardiac cells from the mesoderm. Second, the downstream pathways regulated by transcription factors responsible for key morphogenetic events are still largely unknown. Third, the concept of maintained function or redeployment of functions throughout various stages of development remains to be addressed in detail. The challenge for the future lies in defining pathways downstream from cardiac transcription factors and understanding the intersection of these pathways as the heart develops from a simple patterned structure into a complex multifunctional organ (http://circres.ahajournals.org/content/90/5/509.full).

Tissue development and regeneration involve tightly coordinated and integrated processes: selective proliferation of resident stem and precursor cells, differentiation into target somatic cell type, and spatial morphological organization. The role of the mechanical environment in the coordination of these processes is poorly understood. It has been reported that multipotent cells derived from native cardiac tissue continually monitored cell substratum rigidity and showed enhanced proliferation, endothelial differentiation, and morphogenesis when the cell substratum rigidity closely matched that of myocardium. Mechanoregulation of these diverse processes required p190RhoGAP, a guanosine triphosphatase-activating protein for RhoA, acting through RhoA-dependent and -independent mechanisms. Natural or induced decreases in the abundance of p190RhoGAP triggered a series of developmental events by coupling cell-cell and cell-substratum interactions to genetic circuits controlling differentiation (http://www.ncbi.nlm.nih.gov/pubmed/22669846).