Deng Ke Niu

Summary

Affiliation: Beijing Normal University
Country: China

Publications

  1. ncbi mRNA-mediated intron losses: evidence from extraordinarily large exons
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
    Mol Biol Evol 22:1475-81. 2005
  2. ncbi Low-level illegitimate transcription of genes may be to silence the genes
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
    Biochem Biophys Res Commun 337:413-4. 2005
  3. pmc Protecting exons from deleterious R-loops: a potential advantage of having introns
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biol Direct 2:11. 2007
  4. doi Can ENCODE tell us how much junk DNA we carry in our genome?
    Deng Ke Niu
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 430:1340-3. 2013
  5. doi Nucleosome deposition and DNA methylation may participate in the recognition of premature termination codon in nonsense-mediated mRNA decay
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    FEBS Lett 584:3509-12. 2010
  6. pmc Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss
    Tao Zhu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Xinjiekouwai street 19, Beijing 100875, China
    BMC Biol 11:23. 2013
  7. ncbi Relationship between mRNA stability and intron presence
    Hai fang Wang
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 354:203-8. 2007
  8. pmc Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces
    Tao Zhu
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
    PLoS ONE 8:e61683. 2013
  9. ncbi Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication origin, and termination
    Wen Ru Hou
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 344:1258-62. 2006
  10. ncbi Strand compositional asymmetries in vertebrate large genes
    Hai fang Wang
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
    Mol Biol Rep 35:163-9. 2008

Collaborators

  • Tao Zhu
  • Yi Fei Huang
  • Ning Li
  • Ming Yue Ma
  • Yu Fei Yang
  • Hai fang Wang
  • Liang Feng
  • Xin Ran Lan
  • Wen Ru Hou
  • Lei Ying Zhang
  • Jie Lv
  • Shu Wei Li
  • Heng Yuan Liu
  • Xue Nan Li

Detail Information

Publications21

  1. ncbi mRNA-mediated intron losses: evidence from extraordinarily large exons
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
    Mol Biol Evol 22:1475-81. 2005
    ..We suspected that intron losses from 3' end of genes may be limited in intron-rare eukaryotes. The intron losses from intron-common eukaryotes should have other priming mechanism, like self-primed reverse transcription...
  2. ncbi Low-level illegitimate transcription of genes may be to silence the genes
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
    Biochem Biophys Res Commun 337:413-4. 2005
    ..This hypothetical link gives insight into both analysis of transcription-associated evolutionary events and further interpretation of the mechanism of small RNA-mediated transcriptional repression...
  3. pmc Protecting exons from deleterious R-loops: a potential advantage of having introns
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biol Direct 2:11. 2007
    ..Accumulating evidence indicates that the nascent RNA can invade and pair with one strand of DNA, forming an R-loop structure that threatens the stability of the genome. In addition, the cost and benefit of introns are still in debate...
  4. doi Can ENCODE tell us how much junk DNA we carry in our genome?
    Deng Ke Niu
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 430:1340-3. 2013
    ..Knockout may be the most effective means of distinguishing functional sequences from junk DNA...
  5. doi Nucleosome deposition and DNA methylation may participate in the recognition of premature termination codon in nonsense-mediated mRNA decay
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    FEBS Lett 584:3509-12. 2010
    ..We propose that nucleosomes and DNA methylation just upstream of a normal stop codon are ideal indicators for the position of a normal stop codon and may thus serve as signals in PTC recognition...
  6. pmc Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss
    Tao Zhu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Xinjiekouwai street 19, Beijing 100875, China
    BMC Biol 11:23. 2013
    ..If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss...
  7. ncbi Relationship between mRNA stability and intron presence
    Hai fang Wang
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 354:203-8. 2007
    ..The components of messenger ribonucleoprotein particles recruited during intron splicing may be retained in cytoplasmic mRNPs and act as signals of mRNA stability or simply insulators to avoid mRNA degradation...
  8. pmc Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces
    Tao Zhu
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
    PLoS ONE 8:e61683. 2013
    ..In addition, we found that intron-lost and intron-gained genes had certain similar features, such as similar Gene Ontology categories and expression levels...
  9. ncbi Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication origin, and termination
    Wen Ru Hou
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 344:1258-62. 2006
    ..Furthermore, we found that the most common replicon sizes in vertebrates are 50-100 kb, and show evidence that the replication origin and termination regions of vertebrate genomes range from a discrete site to a broad zone...
  10. ncbi Strand compositional asymmetries in vertebrate large genes
    Hai fang Wang
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
    Mol Biol Rep 35:163-9. 2008
    ..Together with other evidence, we suggest that germline transcription-associated strand asymmetric mutations may be the main cause of the transcription-associated strand compositional asymmetries...
  11. pmc Why eukaryotic cells use introns to enhance gene expression: splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biol Direct 6:24. 2011
    ....
  12. pmc Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution
    Yu Fei Yang
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, China
    Genome Biol Evol 5:723-33. 2013
    ..We argue that the mutational-hazard hypothesis is compatible with these correlations, by suggesting that selection for rapid growth might indirectly increase mutational hazards...
  13. ncbi Relationship between mRNA stability and length: an old question with a new twist
    Liang Feng
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
    Biochem Genet 45:131-7. 2007
    ..This finding suggests the possibility that endonucleolytic attacks by RNA endonuclease and/or mechanical damage may strongly influence mRNA stability in both prokaryotes and eukaryotes...
  14. ncbi Selection for the miniaturization of highly expressed genes
    Shu Wei Li
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
    Biochem Biophys Res Commun 360:586-92. 2007
    ..Selection of the compactness of highly expressed genes for economy is supported...
  15. pmc Imprecise intron losses are less frequent than precise intron losses but are not rare in plants
    Ming Yue Ma
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
    Biol Direct 10:24. 2015
    ..Consistent with previous studies, our results indicate that PILs are a major type of intron loss. However, at least in plants, IILs are unlikely to be as rare as previously reported...
  16. pmc Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase
    Ming Yue Ma
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
    Peerj 4:e2272. 2016
    ..Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals. ..
  17. pmc Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
    Yi Fei Huang
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, P R China
    BMC Evol Biol 8:154. 2008
    ..A popular explanation for this is selection for transcription efficiency, which includes two sub-hypotheses: to minimize the energetic cost or to minimize the time cost...
  18. pmc Exon definition as a potential negative force against intron losses in evolution
    Deng Ke Niu
    Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, PR China
    Biol Direct 3:46. 2008
    ..The most popular model, which suggests that organisms lose introns through a mechanism in which reverse-transcribed cDNA recombines with the genomic DNA, concerns only one mutational force...
  19. doi Evaluation of models of the mechanisms underlying intron loss and gain in Aspergillus fungi
    Lei Ying Zhang
    MOE Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
    J Mol Evol 71:364-73. 2010
    ..Source sequences for most gained introns could not be identified and the possible reasons were discussed. In the four Aspergillus genomes studied, we did not find evidence of frequent parallel intron gains...
  20. doi Association between the availability of environmental resources and the atomic composition of organismal proteomes: evidence from Prochlorococcus strains living at different depths
    Jie Lv
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Xinjiekouwai street 19, Beijing 100875, China
    Biochem Biophys Res Commun 375:241-6. 2008
    ..Our findings indicate that the elemental composition of proteomes is shaped by the availability of resources in the environment...
  21. doi Low contents of carbon and nitrogen in highly abundant proteins: evidence of selection for the economy of atomic composition
    Ning Li
    MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
    J Mol Evol 68:248-55. 2009
    ..By contrast, the amino acid sequences of weakly expressed proteins are more likely to be optimized for their biological functions...