Genome-wide Study of Gene Copy Numbers, Transcripts, and Protein Levels in Pairs of Non-invasive and Invasive Human Transitional Cell Carcinomas

Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.

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257 Genome wide estimation of gene copy numbers in cervical carcinomas: Relationship to gene expression

Radiotherapy and Oncology ◽

10.1016/s0167-8140(06)80734-6 ◽

2006 ◽

Vol 78 ◽

pp. S91-S92

Author(s):

S.R. Brovig ◽

O.T. Brustugun ◽

D.H. Svendsrud ◽

E. Galteland ◽

P. De Angelis ◽

...

Keyword(s):

Gene Expression ◽

Gene Copy ◽

Cervical Carcinomas ◽

Copy Numbers ◽

Genome Wide ◽

Gene Copy Numbers

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Faculty Opinions recommendation of Fewer genes than organelles: extremely low and variable gene copy numbers in mitochondria of somatic plant cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.7497956.7792054 ◽

2011 ◽

Author(s):

Wataru Sakamoto

Keyword(s):

Plant Cells ◽

Gene Copy ◽

Copy Numbers ◽

Variable Gene ◽

Gene Copy Numbers

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Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)

Canadian Journal of Microbiology ◽

10.1139/cjm-2013-0083 ◽

2013 ◽

Vol 59 (7) ◽

pp. 456-464 ◽

Cited By ~ 20

Author(s):

Jie Hou ◽

Xiuyun Cao ◽

Chunlei Song ◽

Yiyong Zhou

Keyword(s):

Amoa Gene ◽

Eutrophic Lake ◽

Gene Copy ◽

Nirs Gene ◽

Bacterial Amoa Gene ◽

Archaeal Amoa Gene ◽

Copy Numbers ◽

Significant Difference ◽

Nirk Gene ◽

Gene Copy Numbers

The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.

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Evolution of dosage compensation does not depend on genomic background

10.1101/2020.08.14.251801 ◽

2020 ◽

Author(s):

Michail Rovatsos ◽

Lukáš Kratochvíl

Keyword(s):

Dosage Compensation ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Genomic Region ◽

Gene Copy ◽

Gene Dose ◽

Copy Numbers ◽

Compensation Mechanisms ◽

Gene Copy Numbers ◽

Softshell Turtles

AbstractOrganisms evolved various mechanisms to cope with the differences in the gene copy numbers between sexes caused by degeneration of Y and W sex chromosomes. Complete dosage compensation or at least expression balance between sexes was reported predominantly in XX/XY, but rarely in ZZ/ZW systems. However, this often-reported pattern is based on comparisons of lineages where sex chromosomes evolved from non-homologous genomic regions, potentially differing in sensitivity to differences in gene copy numbers. Here we document that two reptilian lineages (XX/XY iguanas and ZZ/ZW softshell turtles), which independently co-opted the same ancestral genomic region for the function of sex chromosomes, evolved different gene dose regulatory mechanisms. The independent co-option of the same genomic region for the role of sex chromosome as in the iguanas and the softshell turtles offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and for gene identity. We showed that the parallel loss of functional genes from the Y chromosome of the green anole and the W chromosome of the Florida softshell turtle led to different dosage compensation mechanisms. Our approach controlling for genetic background thus does not support that the variability in the regulation of the gene dose differences is a consequence of ancestral autosomal gene content.

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Expanding an expanded genome: long-read sequencing ofTrypanosoma cruzi

10.1101/279174 ◽

2018 ◽

Cited By ~ 3

Author(s):

Luisa Berná ◽

Matías Rodríguez ◽

María Laura Chiribao ◽

Adriana Parodi-Talice ◽

Sebastián Pita ◽

...

Keyword(s):

Repetitive Sequences ◽

Gc Content ◽

Gene Copy ◽

Accurate Estimation ◽

Sequencing Technologies ◽

Copy Numbers ◽

Long Reads ◽

Long Read ◽

Large Clusters ◽

Gene Copy Numbers

Although the genome ofTrypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degree of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated withT. cruzi´sgenome since they permit directly determining the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, allows not only accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of twoT. cruziclones: the hybrid TCC (DTU TcVI) and the non-hybrid Dm28c (DTU TcI), determined by PacBio SMRT technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome ofT. cruziis composed of a "core compartment" and a "disruptive compartment" which exhibit opposite gene and GC content composition. New tandem and disperse repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families MUC and trans-sialidases allows now a better overview of these complex groups of genes.

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Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1718854115 ◽

2018 ◽

Vol 115 (23) ◽

pp. 6022-6027 ◽

Cited By ~ 60

Author(s):

Tiantian Yu ◽

Weichao Wu ◽

Wenyue Liang ◽

Mark Alexander Lever ◽

Kai-Uwe Hinrichs ◽

...

Keyword(s):

Energy Source ◽

Estuarine Sediments ◽

Gene Copy ◽

Organic Substrates ◽

Metabolic Functions ◽

Copy Numbers ◽

Tetraether Lipids ◽

Archaeal Lipids ◽

Gene Copy Numbers ◽

Direct Confirmation

Members of the archaeal phylumBathyarchaeotaare among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth ofBathyarchaeotain the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth ofBathyarchaeotasubgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth ofBathyarchaeota. Meanwhile, putative bathyarchaeotal tetraether lipids incorporated13C from13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth’s most abundant biopolymers in anoxic marine sediment.

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Coordinate expression of amplified metallothionein I and II genes in cadmium-resistant Chinese hamster cells

Molecular and Cellular Biology ◽

10.1128/mcb.5.12.3525-3531.1985 ◽

1985 ◽

Vol 5 (12) ◽

pp. 3525-3531

Author(s):

J K Griffith

Keyword(s):

Cell Line ◽

Cell Lines ◽

Recombinant Dna ◽

Chinese Hamster ◽

Single Copy ◽

Ovary Cell ◽

Gene Copy ◽

Mrna Levels ◽

Protein Levels ◽

Copy Numbers

Recombinant DNA probes complementary to Chinese hamster metallothionein (MT)-1 and MT-2 mRNAs were used to compare MT gene copy numbers, zinc-induced MT mRNA levels, and uninduced MT mRNA levels in cadmium-resistant (Cdr) Chinese hamster ovary cell lines. Quantitative hybridization analyses determined that the MT-1 and MT-2 genes are each present at approximately single-copy levels in the genome of cell line Cdr2C10 and are coordinately amplified approximately 7, 3, and 12 times over the Cdr2C10 value in the genomes of cell lines Cdr20F4, Cdr30F9, and Cdr200T1, respectively. The maximum zinc-induced MT-1 mRNA concentrations in cell lines Cdr20F4, Cdr30F9, and Cdr200T1 were equal to 1, 3, and 15 times that measured in Cdr2C10, respectively. Similarly, the maximum zinc-induced MT-2 mRNA concentrations were equal to 1, 3, and 14 times that measured in Cdr2C10, respectively, and in each instance they were 90 to 150 times greater than their respective concentrations in uninduced cells. Thus, relative MT gene numbers are closely correlated with both zinc-induced and uninduced MT mRNA levels in Cdr2C10, Cdr30F9, and Cdr200T1, but not in Cdr20F4. Each of the latter two lines possesses structurally altered chromosomes whose breakpoints are near the MT locus. Nonetheless, the ratio of the levels of MT-1 to MT-2 mRNAs was constant in each of the four cell lines, including Cdr20F4. These results demonstrate that MT-1 and MT-2 mRNAs are induced coordinately in each Cdr cell line. Therefore, the coordination of the induction of MT-1 and MT-2 mRNA is independent of MT gene amplification, MT gene rearrangement, and the relative inducibilities of amplified MT genes. However, MT mRNA and protein levels each indicate that MT-1 and MT-2 expression is non-coordinate in uninduced cells. Thus, regulation of MT expression may involve two different mechanisms which are differentially operative in induced and uninduced cells.

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Gene Copy Numbers

10.1007/springerreference_96955 ◽

2012 ◽

Keyword(s):

Gene Copy ◽

Copy Numbers ◽

Gene Copy Numbers

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