Relation of chromosome structure and gene expression

1987 ◽  
Vol 317 (1187) ◽  
pp. 563-574 ◽  
Keyword(s):  
Gene Expression ◽  
Topoisomerase Ii ◽  
Regulatory Region ◽  
Extraction Procedure ◽  
Early Embryo ◽  
Sequence Motifs ◽  
Gene Encoding ◽  
Binding Domains ◽  
Glue Proteins ◽  
High Level

We have been able to map specific DNA fragments at the bases of chromatin loops with the help of a novel extraction procedure by using lithium -3',5'-diiodosalicylate. One such scaffold-attached region (SAR) is found in the non-transcribed spacer in each repeat of the histone gene cluster, on a 657 base pair (b.p.) restriction fragment. Exonuclease III digestion has localized two protein-binding domains on the sar of the histone cluster. Each covers approxim ately 200 b.p. and they are separated by a nuclease-accessible region of about 100 b.p. These domains are rich in sequences closely related to the topoisomerase II cleavage consensus. We have studied the scaffold association of three developmentally regulated genes of Drosophila melanogaster : alcohol dehydrogenase ( Adh ), the homoeotic gene fushi tarazu ( ftz ) and Sgs-4 , a gene encoding one of the glue proteins secreted by third-instar larvae. We find regions attached to the nuclear scaffold (SARS) both 5' and 3' of all three genes, defining small domains ranging from 4.5 to 13 kilobases. In the case of Adh , a gene with two promoters, we find two upstream and two downstream sars. Those 5' of the gene co-map with regulatory regions for the adult and the larval transcripts, respectively. For Sgs -4, the 5' SAR covers 866 b.p. immediately upstream of the transcript, and encompasses the 200 b.p. regulatory region defined by two deletion mutants that produce little or no Sgs-4 protein. In ftz the 5' SAR is found 4.8 kilobases upstream of the start of transcription within a 2.5 kilobase element required for a high level of ftz expression in the early embryo. Sequence analysis of five upstream SARS reveals clusters of sequences closely related to the cleavage consensus of topoisomerase II. In addition, they contain multiple copies of two sequence motifs: a specific 10 b.p. A-rich sequence, and another 10 b.p. T-rich stretch. In conclusion, the intimate association of the SAR with the upstream/enhancer elements, the presence of clustered sequences highly homologous to the topoisomerase II cleavage consensus, and the localization of topoisomerase II in the scaffold, suggest a structure-function relation between chromosome organization and gene expression.

scholarly journals Brg1 Enables Rapid Growth of the Early Embryo by Suppressing Genes That Regulate Apoptosis and Cell Growth Arrest

2016 ◽  
Vol 36 (15) ◽  
pp. 1990-2010 ◽  
Author(s):  
Ajeet P. Singh ◽  
Julie F. Foley ◽  
Mark Rubino ◽  
Michael C. Boyle ◽  
Arpit Tandon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Growth ◽  
Cell Cycle Progression ◽  
Regulatory Region ◽  
Global Gene Expression ◽  
Early Embryo ◽  
Open Chromatin ◽  
Cycle Progression ◽  
Cell Growth Arrest ◽  
Global Gene Expression Analysis

SWI/SNF (switching/sucrose nonfermenting)-dependent chromatin remodeling establishes coordinated gene expression programs during development, yet important functional details remain to be elucidated. We show that the Brg1 (Brahma-related gene 1; Smarca4) ATPase is globally expressed at high levels during postimplantation development and its conditional ablation, beginning at gastrulation, results in increased apoptosis, growth retardation, and, ultimately, embryonic death. Global gene expression analysis revealed that genes upregulated inRosa26CreERT2;Brg1flox/floxembryos (here referred to asBrg1d/dembryos to describe embryos with deletion of theBrg1flox/floxalleles) negatively regulate cell cycle progression and cell growth. In addition, the p53 (Trp53) protein, which is virtually undetectable in early wild-type embryos, accumulated in theBrg1d/dembryos and activated the p53-dependent pathways. Using P19 cells, we show that Brg1 and CHD4 (chromodomain helicase DNA binding protein 4) coordinate to control target gene expression. Both proteins physically interact and show a substantial overlap of binding sites at chromatin-accessible regions adjacent to genes differentially expressed in theBrg1d/dembryos. Specifically, Brg1 deficiency results in reduced levels of the repressive histone H3 lysine K27 trimethylation (H3K27me3) histone mark and an increase in the amount of open chromatin at the regulatory region of thep53andp21(Cdkn1a) genes. These results provide insights into the mechanisms by which Brg1 functions, which is in part via the p53 program, to constrain gene expression and facilitate rapid embryonic growth.

scholarly journals Methylation of 23S rRNA Nucleotide G748 by RlmAIIMethyltransferase Renders Streptococcus pneumoniae Telithromycin Susceptible

2013 ◽  
Vol 57 (8) ◽  
pp. 3789-3796 ◽  
Author(s):  
Akiko Takaya ◽  
Yoshiharu Sato ◽  
Tatsuma Shoji ◽  
Tomoko Yamamoto
Keyword(s):  
Streptococcus Pneumoniae ◽  
Stop Codon ◽  
Regulatory Region ◽  
Dimethyl Sulfate ◽  
23S Rrna ◽  
Gene Encoding ◽  
Content Type ◽  
Resistant Mutants ◽  
High Level ◽  
Domain V

ABSTRACTSeveral posttranscriptional modifications of bacterial rRNAs are important in determining antibiotic resistance or sensitivity. In all Gram-positive bacteria, dimethylation of nucleotide A2058, located in domain V of 23S rRNA, by the dimethyltransferase Erm(B) results in low susceptibility and resistance to telithromycin (TEL). However, this is insufficient to produce high-level resistance to TEL inStreptococcus pneumoniae. Inactivation of the methyltransferase RlmAII, which methylates the N-1 position of nucleotide G748, located in hairpin 35 of domain II of 23S rRNA, results in increased resistance to TEL inerm(B)-carryingS. pneumoniae. Sixteen TEL-resistant mutants (MICs, 16 to 32 μg/ml) were obtained from a clinically isolatedS. pneumoniaestrain showing low TEL susceptibility (MIC, 2 μg/ml), with mutation resulting in constitutive dimethylation of A2058 because of nucleotide differences in the regulatory region oferm(B) mRNA. Primer extension analysis showed that the degree of methylation at G748 in all TEL-resistant mutants was significantly reduced by a mutation in the gene encoding RlmAIIto create a stop codon or change an amino acid residue. Furthermore, RNA footprinting with dimethyl sulfate and a molecular modeling study suggested that methylation of G748 may contribute to the stable interaction of TEL with domain II of 23S rRNA, even after dimethylation of A2058 by Erm(B). This novel finding shows that methylation of G748 by RlmAIIrendersS. pneumoniaeTEL susceptible.

scholarly journals Gene regulatory factors of the sea urchin embryo. II. Two dissimilar proteins, P3A1 and P3A2, bind to the same target sites that are required for early territorial gene expression

Development ◽  
1991 ◽  
Vol 112 (1) ◽  
pp. 351-364 ◽  
Author(s):  
C. Hoog ◽  
F.J. Calzone ◽  
A.E. Cutting ◽  
R.J. Britten ◽  
E.H. Davidson
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Sea Urchin ◽  
Specific Gene ◽  
Target Sequence ◽  
Sequence Motifs ◽  
Binding Domains ◽  
Protein Factor ◽  
Sea Urchin Embryo ◽  
Target Sites

Previous work demonstrated that a negative regulatory interaction mediated by factor(s) termed ‘P3A’ is required for correct territory-specific gene expression in the sea urchin embryo. A probe derived from a P3A target site in the skeletogenic SM50 gene of Strongylocentrotus purpuratus was used to isolate a cDNA clone coding for a factor that binds specifically to this site. This factor, called P3A1, contains two sequence elements that belong to the Zn finger class of DNA-binding motifs, and in these regions is most closely similar to the Drosophila hunchback factor. The P3A1 factor also binds to a similar target sequence in a second gene, CyIIIa, expressed in embryonic aboral ectoderm. Another sea urchin embryo protein factor, P3A2, has been isolated by affinity chromatography and cloned, as described in Calzone et al. Development 112, 335–350 (1991). P3A2 footprints the same target sites in the SM50 and CyIIIa genes as does P3A1, but lacks the Zn finger sequence motifs and in amino acid sequence is almost entirely dissimilar to P3A1. A deletion analysis of P3A2 delimited the DNA-binding region, revealing that five specific amino acids in the first P3A1 finger region and four in the second P3A1 finger region are also present in equivalent positions in P3A2. The P3A1 and P3A2 factors could function as regulatory antagonists, having evolved similar target specificities from dissimilar DNA-binding domains.

scholarly journals EVOLUTION AND VARIATION OF RENIN GENES IN MICE

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 651-667
Author(s):  
Douglas P Dickinson ◽  
Kenneth W Gross ◽  
Nina Piccini ◽  
Carol M Wilson
Keyword(s):  
Gene Expression ◽  
Submandibular Gland ◽  
Regulation Of Gene Expression ◽  
Inbred Strains ◽  
Duplication Event ◽  
Comparative Sequence Analysis ◽  
Chromosome 1 ◽  
Gene Encoding ◽  
Prior Estimate ◽  
Low Levels

ABSTRACT Inbred strains of mice carry Ren-1, a gene encoding the thermostable Renin-1 isozyme. Ren-1 is expressed at relatively low levels in mouse submandibular gland and kidney. Some strains also carry Ren-2, a gene encoding the thermolabile Renin-2 isozyme. Ren-2 is expressed at high levels in the mouse submandibular gland and at very low levels, if at all, in the kidney. Ren-1 and Ren-2 are closely linked on mouse chromosome 1, show extensive homology in coding and noncoding regions and provide a model for studying the regulation of gene expression. An investigation of renin genes and enzymatic activity in wild-derived mice identified several restriction site polymorphisms as well as putative variants in renin gene expression and protein structure. The number of renin genes carried by different subpopulations of wild-derived mice is consistent with the occurrence of a gene duplication event prior to the divergence of M. spretus (2.75-5.5 million yr ago). This conclusion is in agreement with a prior estimate based upon comparative sequence analysis of Ren-1 and Ren-2 from inbred laboratory mice.

scholarly journals Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ami Shah ◽  
Madison Ratkowski ◽  
Alessandro Rosa ◽  
Paul Feinstein ◽  
Thomas Bozza
Keyword(s):  
Gene Expression ◽  
Large Family ◽  
Sequence Motifs ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Trace Amine ◽  
Sequence Elements ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

scholarly journals Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ting-Ying Wu ◽  
Marlen Müller ◽  
Wilhelm Gruissem ◽  
Navreet K. Bhullar
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Expression Patterns ◽  
Grain Filling ◽  
Aleurone Layer ◽  
Rice Grain ◽  
Sequence Motifs ◽  
Grain Development ◽  
Spatio Temporal ◽  
Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main Text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

scholarly journals The CD11b promoter directs high-level expression of reporter genes in macrophages in transgenic mice [published erratum appears in Blood 1995 Apr 1;85(7):1983]

Blood ◽  
1995 ◽  
Vol 85 (2) ◽  
pp. 319-329 ◽  
Author(s):  
S Dziennis ◽  
RA Van Etten ◽  
HL Pahl ◽  
DL Morris ◽  
TL Rothstein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgenic Mice ◽  
Transgene Expression ◽  
Heterologous Gene Expression ◽  
Myeloid Cells ◽  
Reporter Genes ◽  
Regulatory Elements ◽  
Specific Expression ◽  
High Level

Abstract CD11b is the alpha chain of the Mac-1 integrin and is preferentially expressed in myeloid cells (neutrophils, monocytes, and macrophages). We have previously shown that the CD11b promoter directs cell-type- specific expression in myeloid lines using transient transfection assays. To confirm that these promoter sequences contain the proper regulatory elements for correct myeloid expression of CD11b in vivo, we have used the -1.7-kb human CD11b promoter to direct reporter gene expression in transgenic mice. Stable founder lines were generated with two different reporter genes, a Thy 1.1 surface marker and the Escherichia coli lacZ (beta-galactosidase) gene. Analysis of founders generated with each reporter demonstrated that the CD11b promoter was capable of driving high levels of transgene expression in murine macrophages for the lifetime of the animals. Similar to the endogenous gene, transgene expression was preferentially found in mature monocytes, macrophages, and neutrophils and not in myeloid precursors. These experiments indicate that the -1.7 CD11b promoter contains the regulatory elements sufficient for high-level macrophage expression. This promoter should be useful for targeting heterologous gene expression to mature myeloid cells.

Metallothionein gene expression and secretion in white adipose tissue

2000 ◽  
Vol 279 (6) ◽  
pp. R2329-R2335 ◽  
Author(s):  
Paul Trayhurn ◽  
Jacqueline S. Duncan ◽  
Anne M. Wood ◽  
John H. Beattie
Keyword(s):  
Gene Expression ◽  
Molecular Weight ◽  
Adipose Tissue ◽  
White Adipose Tissue ◽  
Stromal Vascular Fraction ◽  
Low Molecular Weight ◽  
Secretory Product ◽  
Mrna Levels ◽  
Gene Encoding ◽  
Adrenoceptor Agonist

White adipose tissue (WAT) has been examined to determine whether the gene encoding metallothionein (MT), a low-molecular-weight stress response protein, is expressed in the tissue and whether MT may be a secretory product of adipocytes. The MT-1 gene was expressed in epididymal WAT, with MT-1 mRNA levels being similar in lean and obese ( ob/ ob) mice. MT-1 mRNA was found in each of the main adipose tissue sites (epididymal, perirenal, omental, subcutaneous), and there was no major difference between depots. Separation of adipocytes from the stromal-vascular fraction of WAT indicated that the MT gene (MT-1 and MT-2) was expressed in adipocytes themselves. Treatment of mice with zinc had no effect on MT-1 mRNA levels in WAT, despite strong induction of MT-1 expression in the liver. MT-1 gene expression in WAT was also unaltered by fasting or norepinephrine. However, administration of a β3-adrenoceptor agonist, BRL-35153A, led to a significant increase in MT-1 mRNA. On differentiation of fibroblastic preadipocytes to adipocytes in primary culture, MT was detected in the medium, suggesting that the protein may be secreted from WAT. It is concluded that WAT may be a significant site of MT production; within adipocytes, MT could play an antioxidant role in protecting fatty acids from damage.

Fertility in Cheviot ewes. 2. The effect of level of pre-mating nutrition on ovulation rate and early embryo mortality in North and South Country Cheviot ewes in moderately-good condition at mating

1979 ◽  
Vol 29 (1) ◽  
pp. 17-23 ◽  
Author(s):  
R. G. Gunn ◽  
J. M. Doney ◽  
W. F. Smith
Keyword(s):  
Food Intake ◽  
Good Condition ◽  
Early Embryo ◽  
Ovulation Rate ◽  
Corpora Lutea ◽  
Restricted Feeding ◽  
Embryo Mortality ◽  
The North ◽  
Breed Difference ◽  
High Level

ABSTRACTIn two experiments over 2 years, 57 North Country Cheviot and 82 South Country Cheviot hill ewes were differentially group-fed indoors over a 2-month period to achieve either good or moderate body con- dition. Over 5 weeks prior to mating, ewes in good condition were brought down in condition by restricted feeding and ewes in mod- erate condition were raised in condition by a high level of feeding. The ewes were thus in moderately-good condition at mating. After mating, ewes were maintained in this condition until killed either on return to service or at 29 ± 8 days for counts of corpora lutea and viable embryos.Ovulation rate in each breed was positively related to the level of pre-mating food intake at the condition level studied. Embryo mortality, as ova loss, was not influenced overall by the level of pre-mating food intake but loss of multiple-shed ova was greater than that of single-shed ova in ewes which had been on restricted feeding before mating. Although a greater proportion of ewes in the North Country Cheviot breed were not pregnant at slaughter, this could not be identified as a breed difference since the breeds were studied in different years.

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