Transcriptional-Readthrough RNAs Reflect the Phenomenon of “A Gene Contains Gene(s)” or “Gene(s) within a Gene” in the Human Genome, and Thus Are Not Chimeric RNAs

Yan He; Chengfu Yuan; Lichan Chen; Mingjuan Lei; Lucas Zellmer; Hai Huang; Dezhong Liao

doi:10.3390/genes9010040

Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?

Science ◽

10.1126/science.1061036 ◽

2001 ◽

Vol 292 (5523) ◽

pp. 1903-1906 ◽

Cited By ~ 187

Author(s):

S. L. Salzberg

Keyword(s):

Human Genome ◽

Gene Loss ◽

Lateral Transfer ◽

Microbial Genes ◽

Or Gene

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COMPARING SYNONYMOUS CODON USAGE OF ALTERNATIVELY SPLICED GENES WITH NON-ALTERNATIVELY SPLICED GENES IN HUMAN GENOME

Journal of Biological System ◽

10.1142/s021833900400104x ◽

2004 ◽

Vol 12 (01) ◽

pp. 91-103

Author(s):

FEI MA ◽

YONGLONG ZHUANG ◽

LIMING CHEN ◽

LUPING LIN ◽

YANDA LI ◽

...

Keyword(s):

Alternative Splicing ◽

Codon Usage ◽

Human Genome ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Dna Mutation ◽

Usage Patterns ◽

Alternatively Spliced ◽

Or Gene

It is becoming clear that alternative splicing plays an important role in expanding protein diversity. However, the previous studies on codons usage did not distinguish alternative splicing from non-alternative splicing. Do codon usage patterns hold distinctions between them? Thus, we attempted to systematically compare the differences of synonymous codon usage patterns between alternatively and non-alternatively spliced genes by analyzing the large datasets from human genome. The results indicated:(1) There are highly significant differences in the average Nc values between non-alternatively spliced genes and the longer isoform genes as well as the shorter isoform genes, and the level of codon usage bias of non-alternatively spliced genes is to some extent higher than that in alternatively spliced genes.(2) Very extensive heterogeneity of G+C content in silent third codon position (GC3s) was evident among these genes, and it could be also shown there are highly significant differences in the average GC3s values between non-alternatively spliced genes and the longer isoform genes as well as the shorter isoform genes.(3) The Nc-plots and correspondence analysis reveal that codon usage bias are mainly dominated by mutation bias, and no correlation between gene expression level and synonymous codon biased usage is found in human genes.(4) Overall codon usage data analysis indicated that the C-ending codons usage has a highly significant differences between the longer isoform genes and non-alternatively spliced genes as well as the shorter isoform genes, it further found out that there is no significant differences of C-ending codons usage between the shorter isoform genes and non-alternatively spliced genes.Finally, our results seem to imply that alternative splicing gene may originate from non-alternative splicing gene, and may be created by DNA mutation or gene fusion, and be retained through nature selection and adaptive evolution.

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Effects of activation of the LINE-1 antisense promoter on the growth of cultured cells

Scientific Reports ◽

10.1038/s41598-020-79197-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Tomoyuki Honda ◽

Yuki Nishikawa ◽

Kensuke Nishimura ◽

Da Teng ◽

Keiko Takemoto ◽

...

Keyword(s):

Cell Growth ◽

Human Genome ◽

Cultured Cells ◽

Biological Significance ◽

Bidirectional Promoter ◽

Chimeric Rnas ◽

Biological Impacts ◽

Exogenous Expression ◽

Potential Strategy

AbstractLong interspersed element 1 (LINE-1, or L1) is a retrotransposon that constitutes ~ 17% of the human genome. Although ~ 6000 full-length L1s spread throughout the human genome, their biological significance remains undetermined. The L1 5′ untranslated region has bidirectional promoter activity with a sense promoter driving L1 mRNA production and an antisense promoter (ASP) driving the production of L1-gene chimeric RNAs. Here, we stimulated L1 ASP activity using CRISPR-Cas9 technology to evaluate its biological impacts. Activation of the L1 ASP upregulated the expression of L1 ASP-driven ORF0 and enhanced cell growth. Furthermore, the exogenous expression of ORF0 also enhanced cell growth. These results indicate that activation of L1 ASP activity fuels cell growth at least through ORF0 expression. To our knowledge, this is the first report demonstrating the role of the L1 ASP in a biological context. Considering that L1 sequences are desilenced in various tumor cells, our results indicate that activation of the L1 ASP may be a cause of tumor growth; therefore, interfering with L1 ASP activity may be a potential strategy to suppress the growth.

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DNA methylation in satellite repeats disorders

Essays in Biochemistry ◽

10.1042/ebc20190028 ◽

2019 ◽

Vol 63 (6) ◽

pp. 757-771 ◽

Cited By ~ 4

Author(s):

Claire Francastel ◽

Frédérique Magdinier

Keyword(s):

Dna Methylation ◽

Human Genome ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Repeats ◽

Tremendous Progress ◽

Genes Encoding ◽

Dna Elements ◽

Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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