title: A comprehensive approach to expression of L1 loci.
abstract: L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5΄ RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads. At least 99% of L1-related sequences found in RNA do not arise from the L1 promoter, instead representing pieces of L1 incorporated in other cellular RNAs. In any given cell type a relatively few active L1 loci contribute to the 'authentic' L1 transcripts that arise from the L1 promoter, with significantly different loci seen expressed in different tissues.
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.|Department of Epidemiology, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Prescott
authors.initials: P
authors.lastname: Deininger
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Maria E
authors.initials: ME
authors.lastname: Morales
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Travis B
authors.initials: TB
authors.lastname: White
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Melody
authors.initials: M
authors.lastname: Baddoo
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hedges
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Geraldine
authors.initials: G
authors.lastname: Servant
authors.affiliation: Department of Structural and Cellular Biology, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Sudesh
authors.initials: S
authors.lastname: Srivastav
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Madison E
authors.initials: ME
authors.lastname: Smither
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.|Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Concha
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.|Department of Pathology, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Dawn L
authors.initials: DL
authors.lastname: DeHaro
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.|Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Erik K
authors.initials: EK
authors.lastname: Flemington
authors.affiliation: Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.|Department of Pathology, Tulane University, New Orleans, LA 70112, USA.
authors.forename: Victoria P
authors.initials: VP
authors.lastname: Belancio
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000737:chemistry* / Q000378:metabolism; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D056426:Genetic Loci; D015894:Genome, Human; D042822:Genomic Instability; D006367:HeLa Cells; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D051379:Mice; D041681:NIH 3T3 Cells; D021141:Nucleic Acid Amplification Techniques; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger