Genome-wide analysis of FLn I-L1 expression profile in developing cerebral cortex of rat
Author(s): LI YunDong, CAI MingDeng, YAO MaoJin, YUAN XiaoBing, ZHANG XiaoYan, School of Life Science and Technology, Tongji University, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Key Laboratory of Brain Functional Genomics, Ministry of Education, School of Life Sciences, East China Normal University, Neurobiology and Anatomy Department, Drexel University College of Medicine, Shanghai Center for Bioinformation Technology
Pages: 3370-3377
Year: 2014 Issue: 34
Journal: Chinese Science Bulletin
Keyword: FLnI-L1; retrotransposon; deep sequencing; cerebral cortex; brain development;
Abstract: The mammalian genome contains a large amount of repeat sequence derived from transposable elements. Whether these repeat sequences play roles in normal developmental and physiological processes remains unclear. As a major component of genomic repeat sequences, long interspersed elements(LINE-1 or L1) have long been regarded as important retrotransposon in mammalian genomes. Although most L1 have lost the retrotransposon activity, active L1 retrotransposons exist in mammalian genomes and L1 may impact the genome in a variety of ways. However, the expression profiles of L1 in normal tissues have not been reported; therefore, whether L1 play retrotransposition-independent functions in normal tissues is unknown. In the present study, global profiling of the L1 m RNA transcriptome of developing rat cerebral cortex was carried out using next-generation sequencing. We observed interesting developmentally-regulated expression of a group of full-length non-intact L1s(FLnI-L1). The relationship between the expression of an L1 and its neighboring genes was also analyzed. A genome-wide analysis of genes whose expressions were correlated closely with FLn I-L1 expression suggested that FLn I-L1 may be involved in pathways related to the regulation of brain development. The dataset described here provides the first comprehensive analysis of a FLn I-L1 expression profile in developing cerebral cortex and will contribute to future understanding of the functions of L1 in brain development.
Pages: 3370-3377
Year: 2014 Issue: 34
Journal: Chinese Science Bulletin
Keyword: FLnI-L1; retrotransposon; deep sequencing; cerebral cortex; brain development;
Abstract: The mammalian genome contains a large amount of repeat sequence derived from transposable elements. Whether these repeat sequences play roles in normal developmental and physiological processes remains unclear. As a major component of genomic repeat sequences, long interspersed elements(LINE-1 or L1) have long been regarded as important retrotransposon in mammalian genomes. Although most L1 have lost the retrotransposon activity, active L1 retrotransposons exist in mammalian genomes and L1 may impact the genome in a variety of ways. However, the expression profiles of L1 in normal tissues have not been reported; therefore, whether L1 play retrotransposition-independent functions in normal tissues is unknown. In the present study, global profiling of the L1 m RNA transcriptome of developing rat cerebral cortex was carried out using next-generation sequencing. We observed interesting developmentally-regulated expression of a group of full-length non-intact L1s(FLnI-L1). The relationship between the expression of an L1 and its neighboring genes was also analyzed. A genome-wide analysis of genes whose expressions were correlated closely with FLn I-L1 expression suggested that FLn I-L1 may be involved in pathways related to the regulation of brain development. The dataset described here provides the first comprehensive analysis of a FLn I-L1 expression profile in developing cerebral cortex and will contribute to future understanding of the functions of L1 in brain development.
Related Articles