Doctoral Student , The Pennsylvania State University
Use a novel Functional Data Analysis (FDA) tool to characterize human transposable element activity
Transposable Elements (TEs), first known as "Jumping Genes", were discovered by Barbara McClintock in the 1950s and later on led to a Nobel Prize in 1983. Over the years, it has been widely recognized that TEs from different families constitute a considerable portion of most eukaryotic genomes, including over 50% in ours.
The Long Interspersed Element-1 (L1) is one of the most active human TEs and composes over 17% of the human genome. L1 transposition follows a ‘copy-and-paste’ mode, given that the “original copy” of L1 is kept in the genome after the event. The process includes the transcription of genomic L1 sequence, a reverse transcription of the RNA intermediate followed by the insertion of L1 cDNA into genomic locations with specific target sequences. Also the reverse transcriptase encoded by L1 can be hijacked by other TEs such as short interspersed elements (SINEs), while altogether different TE families are critical in shaping the modern human genome. Moreover, the regulatory impacts of TE activities have also been revealed in multiple cases such as transcription, RNA processing, and DNA methylation. Therefore, characterizing the transpositional activity of L1s and their interactions with the genomic landscape is critical for understanding genome evolution and function.
However, to date, the dynamics of L1 integration and fixation has not been studied comprehensively. And here for the first time, we investigate L1 transposition on the genome-wide scale and in the evolutionary framework, while considering interactions with an extensive range of genomic features. We also applied Interval-Wise Testing (IWT), a novel Functional Data Analysis tool, to contrast the genomic landscapes at multiple scales and identify signatures of L1 integration and fixation. This study sheds light on the dynamics of TE landscape and will advance our understanding of the structure, evolution and function of the human genome.
Abstract: A major unanswered question in neuroscience is whether there exists genomic variability between individual neurons of the brain, contributing to functional diversity or to an unexplained burden of neurological disease. To address this question, we developed a method to amplify genomes of single neurons from human brains. Because recent reports suggest frequent LINE-1 (L1) retrotransposition in human brains, we performed genome-wide L1 insertion profiling of 300 single neurons from cerebral cortex and caudate nucleus of three normal individuals, recovering >80% of germline insertions from single neurons. While we find somatic L1 insertions, we estimate <0.6 unique somatic insertions per neuron, and most neurons lack detectable somatic insertions, suggesting that L1 is not a major generator of neuronal diversity in cortex and caudate. We then genotyped single cortical cells to characterize the mosaicism of a somatic AKT3 mutation identified in a child with hemimegalencephaly. Single-neuron sequencing allows systematic assessment of genomic diversity in the human brain.
Pub.: 30 Oct '12, Pinned: 30 Aug '17
Abstract: Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons--including LINE-1, Alu and SVA elements--have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and complexity of the past and current contributions of non-LTR retrotransposons to genomic change in the human lineage.
Pub.: 19 Sep '09, Pinned: 30 Aug '17
Abstract: Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.
Pub.: 02 Aug '14, Pinned: 30 Aug '17
Abstract: Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understanding of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behaviour and are not amenable to genetic manipulation. We propose that induced pluripotent stem (iPS) cells could be a unique biological resource to determine relevant phenotypical differences between human and NHPs, and that those differences could have potential adaptation and speciation value. Here we describe the generation and initial characterization of iPS cells from chimpanzees and bonobos as new tools to explore factors that may have contributed to great ape evolution. Comparative gene expression analysis of human and NHP iPS cells revealed differences in the regulation of long interspersed element-1 (L1, also known as LINE-1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. Decreased levels of L1-restricting factors APOBEC3B (also known as A3B) and PIWIL2 (ref. 7) in NHP iPS cells correlated with increased L1 mobility and endogenous L1 messenger RNA levels. Moreover, results from the manipulation of A3B and PIWIL2 levels in iPS cells supported a causal inverse relationship between levels of these proteins and L1 retrotransposition. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPS cells in culture and may have also occurred in the germ line or embryonic cells developmentally upstream to germline specification during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have continuing adaptive significance.
Pub.: 25 Oct '13, Pinned: 30 Aug '17