TY - JOUR
T1 - Many LINE1 elements contribute to the transcriptome of human somatic cells
AU - Rangwala, Sanjida H.
AU - Zhang, Lili
AU - Kazazian, Haig H.
N1 - Funding Information:
We acknowledge the DNA Sequencing Facility at the University of Pennsylvania School of Medicine for generating Sanger and 454 sequence for this study. We thank Scott Sherrill-Mix and Adam D Ewing for preliminary bio-informatics analysis of 454 sequence reads. We are grateful to Adam D Ewing and Jens Mayer and our anonymous reviewers for helpful comments on the manuscript. This study was supported by grants to HHK from the Penn Genome Frontiers Institute (PGFI) and the National Institutes of Health (NIH). The above funding bodies did not significantly contribute to the collection, analysis, and interpretation of data, the writing of the manuscript, or the decision to submit the manuscript for publication.
PY - 2009/9/22
Y1 - 2009/9/22
N2 - Background: While LINE1 (L1) retroelements comprise nearly 20% of the human genome, the majority are thought to have been rendered transcriptionally inactive, due to either mutation or epigenetic suppression. How many L1 elements 'escape' these forms of repression and contribute to the transcriptome of human somatic cells? We have cloned out expressed sequence tags corresponding to the 5' and 3' flanks of L1 elements in order to characterize the population of elements that are being actively transcribed. We also examined expression of a select number of elements in different individuals.Results: We isolated expressed sequence tags from human lymphoblastoid cell lines corresponding to 692 distinct L1 element sites, including 410 full-length elements. Four of the expression tagged sites corresponding to full-length elements from the human specific L1Hs subfamily were examined in European-American individuals and found to be differentially expressed in different family members.Conclusions: A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence.
AB - Background: While LINE1 (L1) retroelements comprise nearly 20% of the human genome, the majority are thought to have been rendered transcriptionally inactive, due to either mutation or epigenetic suppression. How many L1 elements 'escape' these forms of repression and contribute to the transcriptome of human somatic cells? We have cloned out expressed sequence tags corresponding to the 5' and 3' flanks of L1 elements in order to characterize the population of elements that are being actively transcribed. We also examined expression of a select number of elements in different individuals.Results: We isolated expressed sequence tags from human lymphoblastoid cell lines corresponding to 692 distinct L1 element sites, including 410 full-length elements. Four of the expression tagged sites corresponding to full-length elements from the human specific L1Hs subfamily were examined in European-American individuals and found to be differentially expressed in different family members.Conclusions: A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence.
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U2 - 10.1186/gb-2009-10-9-r100
DO - 10.1186/gb-2009-10-9-r100
M3 - Article
C2 - 19772661
AN - SCOPUS:76249132036
SN - 1474-7596
VL - 10
JO - Genome Biology
JF - Genome Biology
IS - 9
M1 - R100
ER -