Effects of L1-ORF2 fragments on green fluorescent protein gene expression

Wang, Xiufang; Jin, Xia; Wang, Xiaoyan; Liu, Jing; Feng, Jun; Yang, QinQing; Mu, Wenli; Shi, Xiaojuan; Lu, Zhanjun

doi:10.1590/s1415-47572009005000068

Cited by 10 publications

(6 citation statements)

References 35 publications

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“…However, when retrotransposons integrate, they may also impact transcriptional regulation [17] , [19] , [20] and/or chromatin structure [21] , [22] . For example, Wang et al showed that different fragments of the L1-ORF2 modulated transcription termination of upstream GFP expression [23] , demonstrating functional impact of the L1 sequence on gene transcription without a direct disruption of coding sequence. The functional consequences of RT retrotransposition are not always deleterious, however, and in some instances they have led to the evolution of mammalian-specific [24] and human-specific traits [25] .…”

Section: Introductionmentioning

confidence: 99%

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity

Linker

Hedges

2013

PLoS ONE

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Retrotransposons comprise approximately half of the human genome and contribute to chromatin structure, regulatory motifs, and protein-coding sequences. Since retrotransposon insertions can disrupt functional genetic elements as well as introduce new sequence motifs to a region, they have the potential to affect the function of genes that harbour insertions as well as those nearby. Partly as a result of these effects, the distribution of retrotransposons across the genome is non-uniform and there are observed imbalances in the orientation of insertions with respect to the transcriptional direction of the containing gene. Although some of the factors underlying the observed distributions are understood, much of the variability remains unexplained. Detailed characterization of retrotransposon density in genes could help inform predictions of the functional consequence of de novo as well as polymorphic insertions. In order to characterize the relationship between genes and inserted elements, we have examined the distribution of retrotransposons and their internal motifs within tissue-specific and housekeeping genes. We have identified that the previously established retrotransposon antisense bias decays at a linear rate across genes, resulting in an equal density of sense and antisense retrotransposons near the 3′-UTR. In addition, the decay of antisense bias across genes is less pronounced among tissue-specific genes. Our results provide support for the scenario in which this linear decay in antisense bias is established by natural selection shortly after retrotransposon integration, and that total antisense bias observed is above and beyond any bias introduced by the integration process itself. Finally, we provide an example of a retrotransposon acting as an eQTL on a coincident gene, highlighting one of several possible avenues through which insertions may modulate gene function.

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Section: Introductionmentioning

confidence: 99%

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity

Linker

Hedges

2013

PLoS ONE

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“…Since XCI is a mechanism of gene dosage compensation by regulating gene expression [31][32][33][34] and our previous studies proved that L1s and Alus played a role in regulating gene expression [35][36], we speculated that these two repetitive sequences (L1 and Alu) may be involved in the process of XCI by regulating gene expression.…”

Section: Introductionmentioning

confidence: 90%

Low RNA Binding Strength of Human X Chromosome May Explain X Chromosome Inactivation

N¹,

Lv²,

Song³

et al. 2018

Preprint

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Two X chromosomes of female mammals randomly inactivate one of paternal or maternal X chromosome in early embryonic development and all the daughter cells produced from these cells retain the same feature of X chromosome inactivation, which is called X chromosome inactivation (XCI). Studying the mechanisms of XCI is important for understanding epigenetic that plays an important role in age-associated diseases. The previous studies have demonstrated that binding of RNAs and DNAs may play a role in activating gene expression. In this paper, our study aims to explore whether the mechanisms of XCI involve the RNA binding strength to X chromosome DNAs. The bioinformatics analyses based on big data were used to analyze the simulated binding strength of RNAs (RNA binding strength) to 23 chromosomes (including X chromosome and 22 human autosomes) and the characteristics of repetitive sequences in the X-inactivation centre. The results revealed that RNA binding strength of the long arm of the X chromosome that is almost entirely inactivated in XCI was significantly lower than that of all autosomes and the short arm of X chromosome, meanwhile the RNA binding strengths of inactivation regions in X chromosome were significantly lower than that of regions escaping from XCI. Different repetitive sequence clusters within the center of XCI presented a cross distribution characteristic. To further prove whether the repetitive sequences in human X chromosome involve in XCI, we cloned long interspersed element (LINE-1, L1) and short interspersed element (Alu) from human Xq13, the center of XCI, and constructed expression vectors carrying sense-antisense combination repetitive sequences (L1s or Alus). Effects of combined L1 or combined Alu sequences on expression of EGFP reporter gene were examined in stably transfected HeLa cells, which simulates the effects of repetitive sequences located on chromosomes. The results of experiments revealed transcribed L1 repetitive sequences activated EGFP reporter gene expression, so did the Alus. The experiment results suggested repetitive sequences activated genes by interaction of transcribed RNAs and DNAs. Since the binding of RNAs and DNAs can activate gene, so the low RNA binding strength of human X chromosome may be one of reasons of XCI. The cross distribution characteristics of different repetitive sequence clusters leading to a cascade of gene activation or gene inactivation may be the reason of transcriptional silencing one of the X chromosomes in female mammals.

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“…The pAlu14 and pORF2 expression vectors were constructed as described elsewhere ( Wang et al , 2009a , b ) by inserting 14 head-to-tail tandem Alu (283 bp) elements or an ORF2 (3825 bp) downstream of the GFP gene in the pEGFP-C1 vector.…”

Section: Methodsmentioning

confidence: 99%

“…Alu elements were initially considered to have no role in gene stability and expression, but recent work has shown that these elements can extensively influence gene expression. In previous work, we have shown that Alu tandem repeats and Line-1 - ORF2 ( ORF2 ) inhibited green fluorescent protein (GFP) gene expression when inserted downstream of this gene in the pEGFP-C1 vector ( Wang et al , 2009a , b ). Downstream noncoding gene sequences are highly structured and contain important regulatory elements such as 3′ UTRs, transcription termination signals ( Andreassi and Riccio, 2009 ) and enhancers ( Mao et al , 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of two critical sequences in SV40PolyA that activate the green fluorescent protein reporter gene

Wang

Sun

et al. 2011

Genet. Mol. Biol.

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Alu repeats or Line-1-ORF2 (ORF2) inhibit expression of the green fluorescent protein (GFP) gene when inserted downstream of this gene in the vector pEGFP-C1. In this work, we studied cis-acting elements that eliminated the repression of GFP gene expression induced by Alu and ORF2 and sequence characteristics of these elements. We found that sense and antisense PolyA of simian virus 40 (SV40PolyA, 240 bp) eliminated the repression of GFP gene expression when inserted between the GFP gene and the Alu (283 bp) repeats or ORF2 (3825 bp) in pAlu14 (14 tandem Alu repeats were inserted downstream of the GFP gene in the vector pEGFP-C1) or pORF2. Antisense SV40PolyA (PolyAas) induced stronger gene expression than its sense orientation (PolyA). Of four 60-bp segments of PolyAas (1F1R, 2F2R, 3F3R and 4F4R) inserted independently into pAlu14, only two (2F2R and 3F3R) eliminated the inhibition of GFP gene expression induced by Alu repeats. Deletion analysis revealed that a 17 nucleotide AT repeat (17ntAT; 5′-AAAAAAATGCTTTATTT-3′) in 2F2R and the fragment 3F38d9 (5′-ATAAACAAGTTAACAACA ACAATTGCATT-3′) in 3F3R were critical sequences for activating the GFP gene. Sequence and structural analyses showed that 17ntAT and 3F38d9 included imperfect palindromes and may form a variety of unstable stem-loops. We suggest that the presence of imperfect palindromes and unstable stem-loops in DNA enhancer elements plays an important role in GFP gene activation.

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Effects of L1-ORF2 fragments on green fluorescent protein gene expression

Cited by 10 publications

References 35 publications

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity

Low RNA Binding Strength of Human X Chromosome May Explain X Chromosome Inactivation

Identification and characterization of two critical sequences in SV40PolyA that activate the green fluorescent protein reporter gene

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