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Jian Lu


Jian Lu

 

Email: lujian0311(at)gmail(dot)com;

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Research Area:

A central task in evolutionary biology is to understand how genotypes affect phenotypes and whether/how natural selection operates during this process. We are interested in a wide range of topics related to this question. Our current research focuses on gene regulation mediated by small RNAs (microRNAs, endogenous siRNAs and piRNAs) and long intergenic non-coding RNAs (lincRNAs) from perspectives of evolutionary biology.

The whole genome sequencing projects in flies (~ 500 strains of Drosophila melanogaster and > 20 Drosophila species) and in humans (1000 Genomes Project) provide us a golden opportunity to study the evolutionary patterns and functional impacts of non-coding RNAs on transcriptomes and phenotypes at the intra- and inter-species levels. We are currently combining approaches of next-generation sequencing, computational, comparative and functional genomics with evolutionary theory and population genetics modeling. The goal of our research is to understand how non-coding RNA regulation confers robustness to biological processes and how genetic variations related to non-coding RNA regulation contribute to phenotypic changes and diseases at the systems level.

Specifically, we are conducting the following research projects:

1) Origin and evolution of non-coding RNAs and the forces driving the evolution of the newly-emerged non-coding RNA genes.

2) Identification of target genes of non-coding RNAs with techniques of RNA-Seq, ribosome profiling, gene knockout and evolutionary genomics.

3) The impacts of non-coding RNA regulation on natural variation in gene expression and pathogenesis of diseases.
4) Hybrid dysgenesis caused by the interactions between piRNAs and transposable elements.

 

Selected Publications:

1. Lu J, Shen Y,Wu QF, Kumar S, He B, Carthew RW, Wang SM, Wu CI (2008) The birth and death of microRNA genes in Drosophila. Nature Genetics 40: 351-355; author reply in 42: 9-10.

2. Lu J, Li WH, Wu CI (2003) Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes". Science 302: 988.
3. Lu J, Clark AG (2012) Impact of microRNA regulation on variation in human gene expression. Genome Research 22 :1243–1254

4. Lu J, Clark AG (2010)Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Research 20: 212-227.

5. Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew RW, Wu CI (2008) Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Molecular Biology and Evolution 25: 929-938.
6. Lu J, Tang T, Tang H, Huang JZ, Shi SH, Wu CI (2006) The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends in Genetics 22: 126-131 (Lu J and Tang T equally contribute to the paper).

7. Tang T, Lu J, Huang J, He J, McCouch SR, Purugganan MD, Shi SH, Wu CI (2006) Genomic variation in rice - Genesis of highly polymorphic linkage blocks during domestication. PLoS Genetics 2(11):e199 (Tang T and Lu J equally contribute to the paper).

8. Lu J, Wu CI (2005) Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proceedings of the National Academy of Sciences 102: 4063-4067.

9. Zhou RC, Ling SP, Zhao WM, Osada N, Chen SF, Zhang M, He ZW, Bao H, Zhong CR, Zhang B, Lu XM, Turissini D, Duke NC, Lu J, Shi SH, Wu CI (2011) Population genetics in non-model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms. Molecular Biology and Evolution doi: 10.1093 (Lu J is a co-corresponding author).

10. Tang T, Kumar S, Shen Y, Lu J, Wu ML, Shi S, Li WH, Wu CI (2010)Adverse interactions between micro-RNAs and target genes from different species. Proceedings of the National Academy of Sciences 107: 12935-12940.

11. Wang HY, Fu Y, McPeek MS, Lu X, Nuzhdin S, Xu A, Lu J, Wu ML, Wu CI (2008) Complex genetic interactions underlying expression differences between Drosophila races: analysis of chromosome substitutions. Proceedings of the National Academy of Sciences 105: 6362-6367.

12. Wu QF, Kim YC, Lu J, Xuan ZY, Chen J, Zheng YL, Zhou T, Zhang MQ, Wu CI, Wang SM (2008) Poly A- Transcripts Expressed in HeLa Cells. PLoS ONE 3(7): e2803.

13. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA et al (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218 (Lu J is a coauthor of this paper).

14. Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA, Fang S, Wang HY, Hudson RR, Nielsen R, Chen Z, Wu CI (2007) Adaptive Genic Evolution in the Drosophila Genomes. Proceedings of the National Academy of Sciences 104: 2271-2276.
15. Tang H, Wyckoff GJ, Lu J, Wu CI (2004) A universal evolutionary index for amino acid changes. Molecular Biology and Evolution 21: 1548-1556.

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