scholarly journals Key gene regulatory sequences with distinctive ontological signatures associate with differentially endonuclease-accessible mouse sperm chromatin

Reproduction ◽  
2011 ◽  
Vol 142 (5) ◽  
pp. 757
Author(s):  
Myriam Saida ◽  
David Iles ◽  
Abdul Elnefati ◽  
Martin Brinkworth ◽  
David Miller
Keyword(s):  
Sperm Chromatin ◽  
Regulatory Sequences ◽  
Mouse Sperm ◽  
Gene Regulatory

scholarly journals Key gene regulatory sequences with distinctive ontological signatures associate with differentially endonuclease-accessible mouse sperm chromatin

Reproduction ◽  
2011 ◽  
Vol 142 (1) ◽  
pp. 73-86 ◽  
Author(s):  
Myriam Saida ◽  
David Iles ◽  
Abdul Elnefati ◽  
Martin Brinkworth ◽  
David Miller
Keyword(s):  
In Silico ◽  
Methylation Status ◽  
Micrococcal Nuclease ◽  
Ctcf Binding ◽  
Sperm Chromatin ◽  
Regulatory Sequences ◽  
Fish Analysis ◽  
Gene Promoters ◽  
Mouse Sperm ◽  
Sperm Nuclei

Using a well-established endonuclease-based chromatin dissection procedure in conjunction with both experimental comparative genome hybridisation (CGH) array profiling andin silicodata mining, we show that mouse spermatozoa contain chromatin that is sensitive and resistant to digestion with micrococcal nuclease (MNase). Sequences represented in the micrococcal nuclease digestion solubilised (MNDS) but not the MND insoluble (MNDI) chromatin are strongly enriched in chromosomal regions of high gene density. Furthermore, by fluorescencein situhybridisation (FISH) analysis, we show that MNDS and MNDI DNAs occupy distinct domains of decondensed mouse sperm nuclei that may also retain abundant histones. More detailedin silicoanalysis of CGH probe location in relation to known promoters and sequences recognised by CCCTC binding factor (CTCF) shows a significant excess of both in MNDS chromatin. A functional analysis of gene promoters reveals strong ontological signatures for ion transport on methylated promoters associated with CTCF binding sequences in MNDS chromatin. Sensory perception is the only strong ontological signature present in MNDI chromatin, driven by promoters that are not associated with CTCF regardless of their methylation status.

scholarly journals Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters

2019 ◽  
Author(s):  
Joanna Mitchelmore ◽  
Nastasiya Grinberg ◽  
Chris Wallace ◽  
Mikhail Spivakov
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Statistical Power ◽  
Target Genes ◽  
Allelic Variation ◽  
Regulatory Function ◽  
Regulatory Sequences ◽  
Distal Enhancer ◽  
Association Testing ◽  
Gene Regulatory

AbstractIdentifying DNA cis-regulatory modules (CRMs) that control the expression of specific genes is crucial for deciphering the logic of transcriptional control. Natural genetic variation can point to the possible gene regulatory function of specific sequences through their allelic associations with gene expression. However, comprehensive identification of causal regulatory sequences in brute-force association testing without incorporating prior knowledge is challenging due to limited statistical power and effects of linkage disequilibrium. Sequence variants affecting transcription factor (TF) binding at CRMs have a strong potential to influence gene regulatory function, which provides a motivation for prioritising such variants in association testing. Here, we generate an atlas of CRMs showing predicted allelic variation in TF binding affinity in human lymphoblastoid cell lines (LCLs) and test their association with the expression of their putative target genes inferred from Promoter Capture Hi-C and immediate linear proximity. We reveal over 1300 CRM TF-binding variants associated with target gene expression, the majority of them undetected with standard association testing. A large proportion of CRMs showing associations with the expression of genes they contact in 3D localise to the promoter regions of other genes, supporting the notion of ‘epromoters’: dual-action CRMs with promoter and distal enhancer activity.

Co-expression of insulin and somatostatin genes in pancreatic endocrine cells selected for their high level of insulin gene transcription

1992 ◽  
Vol 101 (4) ◽  
pp. 795-799
Author(s):  
C. Saulnier-Michel ◽  
M. Fromont-Racine ◽  
R. Pictet
Keyword(s):  
Endocrine Cells ◽  
Selective Pressure ◽  
Cell Types ◽  
Insulin Gene ◽  
Regulatory Sequences ◽  
Endogenous Insulin ◽  
Pancreatic Endocrine Cells ◽  
Gene Regulatory ◽  
High Level ◽  
Two Populations

RW cells are pancreatic endocrine RIN cells that have been stably transfected with a chimeric gene that places the expression of the dominant selection gpt gene under the control of the insulin gene regulatory sequences. These RW cells were examined for hormone content using immunocytochemistry. This analysis shows that: first, there are cells that are negative for insulin although they were cultured under selective pressure. Second, there is a higher proportion of somatostatin-producing cells than in the parental RIN cells; these somatostatin cells form two populations: one of cells containing only somatostatin and, surprisingly, one made of cells containing both insulin and somatostatin. Thus: (1) expression of the transfected and endogenous insulin regulatory sequences is not regulated in a coordinate fashion; (2) the presence of both hormones in the same cell suggests that the regulation of the expression of insulin and somatostatin genes and the differentiation pathway of the two respective cell types may be closely related.

Lead-induced changes in the stabilization of the mouse sperm chromatin

Toxicology ◽  
1988 ◽  
Vol 51 (1) ◽  
pp. 11-24 ◽  
Author(s):  
Lars Johansson ◽  
Carlo E. Pellicciari
Keyword(s):  
Sperm Chromatin ◽  
Mouse Sperm ◽  
Induced Changes

Interactions between gametes leading to fertilization: the sperm's eye view

1995 ◽  
Vol 7 (4) ◽  
pp. 927 ◽  
Author(s):  
BT Storey
Keyword(s):  
Plasma Membrane ◽  
Acrosome Reaction ◽  
Mammalian Species ◽  
Sperm Chromatin ◽  
Peptide Backbone ◽  
Mouse Sperm ◽  
Gamete Interactions ◽  
Sperm Plasma Membrane ◽  
Sperm Penetration ◽  
Strong Candidate

Sexual reproduction requires that the gamete carrying the male-derived haploid chromatin join with the gamete carrying the female-derived haploid chromatin during fertilization to produce the diploid zygote. To accomplish this feat, the sperm must not only meet the egg, it must recognize the egg and be recognized in turn by the egg, and in the end must enter and be engulfed by the egg. In this selective overview of gamete interactions that lead to fertilization, encounters of three kinds, followed by the finale of gamete fusion, are considered from the sperm's viewpoint, with particular emphasis on the mammalian species with the mouse as the principal model. The first encounter is with the zona pellucida of the egg, to whose surface the sperm must bind. Mouse sperm appear to have four binding sites for zona ligands. Three interact with sugar moieties of the oligosaccharide chains of the mouse zona glycoprotein ZP3; the fourth binds a peptide backbone arginine. Capacitation is not required for this encounter, but is obligate for the second encounter--induction of the acrosome reaction in the bound sperm. The acrosome reaction is an exocytotic process that makes available the enzymatic machinery needed for sperm penetration the zona which is the end point of a sequence of reactions directed by intracellular signalling systems. In mouse sperm, these systems are presumed to be activated by ligands on ZP3 binding to ligand-specific sperm receptors with consequent aggregation of receptors. No receptor has been identified with certainty, nor have candidates for putative ZP3 ligands been identified. Completion of the acrosome reaction allows the sperm to penetrate the zona and, bind to the egg plasma membrane, thereby completing the third encounter. In the mouse, a 94-kDa protein appears essential for this binding. In the guinea-pig, a sperm plasma membrane protein (formerly PH-30, now fertilin), is a strong candidate for the mediator of the fusion process by which the egg engulfs the sperm. Decondensation of the sperm chromatin reverses the remarkable packing of DNA organized by sperm protamines. Mitochondrial DNA is also engulfed by the egg; the question of whether this DNA makes a small finite, or null, contribution to cytosolic inheritance is still in debate. The puzzles attending these encounters are presented as reminders of the intricacy and fascination, as well as of the vital necessity, of gamete interaction.

Secretion of foreign proteins mediated by chicken lysozyme gene regulatory sequences

2002 ◽  
Vol 80 (6) ◽  
pp. 777-788 ◽  
Author(s):  
Gregory R Lampard ◽  
Ann M. Verrinder Gibbins
Keyword(s):  
Fluorescent Protein ◽  
Regulatory Sequences ◽  
Heterologous Proteins ◽  
Transgenic Chicken ◽  
Reporter Protein ◽  
Lysozyme Gene ◽  
Foreign Proteins ◽  
Gene Regulatory ◽  
Chicken Lysozyme

Exploitation of the insulating properties of the complete chicken lysozyme gene domain may facilitate the production of transgenic chicken bioreactors with the capacity to deposit valuable proteins in the egg white. Chimeric genes consisting of the chicken lysozyme gene regulatory sequences and sequences encoding foreign proteins could be inserted randomly into the chicken genome and retain appropriate expression levels. The research reported here established that chicken lysozyme gene regulatory sequences can be used to direct the production and secretion of green fluorescent protein (used as a reporter protein) in transiently transfected chicken blastodermal cells. Attempts to verify these findings in transgenic hens are currently in progress. To provide a rapid means of generating constructs encoding other foreign proteins under the control of lysozyme gene regulatory sequences that can facilitate the secretion of heterologous proteins in vivo, a generic lysozyme gene regulatory scaffold was created using a poxvirus-mediated gene targeting system.Key words: chicken lysozyme gene, secretion, homologous recombination.

scholarly journals A plant mitochondrial sequence transcribed in transgenic tobacco chloroplasts is not edited.

1995 ◽  
Vol 15 (3) ◽  
pp. 1377-1381 ◽  
Author(s):  
C A Sutton ◽  
O V Zoubenko ◽  
M R Hanson ◽  
P Maliga
Keyword(s):  
Transgenic Tobacco ◽  
Rna Editing ◽  
Ribosomal Protein Gene ◽  
Regulatory Sequences ◽  
Mitochondrial Rna ◽  
Higher Plant ◽  
Rna Sequences ◽  
Exon 2 ◽  
Chimeric Genes ◽  
Gene Regulatory

RNA editing occurs in two higher-plant organelles, chloroplasts and mitochondria. Because chloroplasts and mitochondria exhibit some similarity in editing site selection, we investigated whether mitochondrial RNA sequences could be edited in chloroplasts. We produced transgenic tobacco plants that contained chimeric genes in which the second exon of a Petunia hybrida mitochondrial coxII gene was under the control of chloroplast gene regulatory sequences. coxII transcripts accumulated to low or high levels in transgenic chloroplasts containing chimeric genes with the plastid ribosomal protein gene rps16 or the rRNA operon promoter, respectively. Exon 2 of coxII was chosen because it carries seven editing sites and is edited in petunia mitochondria even when located in an abnormal context in an aberrant recombined gene. When editing of the coxII transcripts in transgenic chloroplasts was examined, no RNA editing at any of the usual sites was detected, nor was there any novel editing at any other sites. These results indicate that the RNA editing mechanisms of chloroplasts and mitochondria are not identical but must have at least some organelle-specific components.

scholarly journals Hypermethylation of calcitonin gene regulatory sequences in human breast cancer as revealed by genomic sequencing

1996 ◽  
Vol 69 (6) ◽  
pp. 471-474 ◽  
Author(s):  
Mika Hakkarainen ◽  
Jarmo Wahlfors ◽  
Sanna Myöhänen ◽  
Mikko O. Hiltunen ◽  
Matti Eskelinen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Human Breast Cancer ◽  
Genomic Sequencing ◽  
Regulatory Sequences ◽  
Human Breast ◽  
Calcitonin Gene ◽  
Gene Regulatory
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