Molecular archeology of L1 insertions in the human genome

“The BLASTX program [45] was used to translate our set of full-length L1 DNA sequences in all three reading frames and compare them to the L1.”

“DNA sequence logos [59] of TSDs were generated using binary code downloaded from the site [60].”

“L1 poly(A) tails During the process of TPRT, whereby a copy of an L1 is inserted into the genome, reverse transcription is believed to be primed on the poly(A) tail of the L1 transcript [12,14,17,27].”

“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3 ́-terminal Zn finger-like domain [14].”

“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3 ́-terminal Zn finger-like domain [14].”

“Furthermore, the concentration of L1s with TSDs on the p arm of the X chromosome is lower than that on the q arm (Figure 8). Lahn and Page [ 52 ] have hypothesized that the distal p arm is the site of the youngest evolutionary strata on the X chromosome, indicating that the X and Y chromosomes actively recombined at t…”

“This modest majority may reflect a weak selection against L1s in the same orientation; such insertions could result in premature truncation of a gene’s mRNA due to the L1 polyadenylation signal [27,48,49].”

“Also, L1-encoded proteins were almost certainly involved in the insertion of most of the Alu elements and processed pseudogenes in the genome [6-10]; thus, L1s are probably responsible, directly or indirectly, for the genesis of most of the transposed fraction of human DNA.”

“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3 ́-terminal Zn finger-like domain [14].”

“Nevertheless, this large fraction is a testament to the efficiency with which these elements, now mostly fossil sequences [2-5], have been able to propagate, and it is clear that they played a large part in determining the structure”

“This quality is consistent with previous computational [6] and biochemical [12,34] observations of A-rich target sequences of L1s and Alu sequences.”

“Several instances of disease have been attributed to the disruption of genes by an L1 insertion (for a review see [ 42 ]).”

“A full-length, active human L1 is approximately 6,000 nucleotides long and consists of a 5 ́ UTR with an internal promoter, two open reading frames (ORFs) separated by a 63-nucleotide intergenic region, and a 3 ́ UTR terminating in a poly(A) tail [11] (Figure 1a).”

“It is estimated that 30-60 full-length active L1s reside in the average human genome [ 37 ].”

“It has been suggested that the high concentration of L1s on the X chromosome may have a role in X inactivation of select genes [39].”

“The most variable features of L1s are the poly(A) tail, which has a variable length and can contain simple repeats, the polyadenylation signal, and the 3 ́ UTR, but many changes have also been reported in the coding regions of young L1s, especially in a segment of ORF1 [21-24].”

“(NAD+) gamma, biglycan, tafazzin, deoxyribonuclease I-like 1, and emerin [51].”

“Characteristics of 5 truncated L1 elements The majority of L1s in the human genome are significantly 5 truncated [25]; indeed, only 5% of the 3 intact L1s in our study were full-length (Table 1).”

“L1.3 is one of the most active L1s in a cell-culture assay [37] and is a member of the human-specific Ta-1 subfamily of L1s which encompasses the vast majority of active, young L1 elements in the human genome [ 22 ].”

“Consequently, the 3 TSD of the resulting L1 insertion event can be located hundreds of nucleotides downstream of the L1 sequence itself [29,30].”

“Consequently, the 3 TSD of the resulting L1 insertion event can be located hundreds of nucleotides downstream of the L1 sequence itself [29,30].”

“The poly(A) tails found in I factors, a transposable element in Drosophila melanogaster similar to L1s, contain several copies of the simple repeat TAA instead of a traditional poly(A) tail [40,41].”

“Also, L1-encoded proteins were almost certainly involved in the insertion of most of the Alu elements and processed pseudogenes in the genome [6-10]; thus, L1s are probably responsible, directly or indirectly, for the genesis of most of the transposed fraction of human DNA.”

“Instead, our findings support the recently proposed twin-priming model for inversion [47]; as we showed above, the 3 end topstrand cleavage product has a modest bias to be a ‘T’ nucleotide (Figure 3b) and we indeed see a modest preference for a complementary ‘A’ nucleotide at the corresponding position of the inversio…”

“This quality is consistent with previous computational [6] and biochemical [12,34] observations of A-rich target sequences of L1s and Alu sequences.”

“Also, 3 transduction events associated with L1 insertions add an additional structural variation [27,28]; such elements are generated when the element’s transcript includes some downstream flanking sequences that become transduced, along with the L1 sequence, to a new genomic locus.”

“A new L1 insertion is usually flanked by short direct repeats derived from the target DNA locus upon L1 integration [19]; these repeats are referred to as target site duplications (TSDs), and can range from just a few to more than 200 nucleotides in length [14].”

“This observation is consistent with previous reports that the density of L1s on the X chromosome is almost double that on the autosomes [1,38,39].”

“The progenitor elements of these insertions were always fulllength or near full-length L1s with intact ORFs that were active in retrotransposition assays [11,14,35-37].”

“They propagate by being transcribed from an internal RNA polymerase II promoter [ 15 ,16], and then use their endonuclease and reverse transcriptase respectively to nick a target site and reverse transcribe L1 RNA, integrating the L1 into a new genomic locus [12,17,18]; this process is known as target-site-primed reve…”

“Nevertheless, this large fraction is a testament to the efficiency with which these elements, now mostly fossil sequences [2-5], have been able to propagate, and it is clear that they played a large part in determining the structure”

“An extra 131 nucleotides are found in the 5 UTR of some L1 elements, starting at nucleotide position 777 [26].”

“Nevertheless, this large fraction is a testament to the efficiency with which these elements, now mostly fossil sequences [2-5], have been able to propagate, and it is clear that they played a large part in determining the structure”

“The most variable features of L1s are the poly(A) tail, which has a variable length and can contain simple repeats, the polyadenylation signal, and the 3 ́ UTR, but many changes have also been reported in the coding regions of young L1s, especially in a segment of ORF1 [21-24].”

“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3´-terminal Zn finger-like domain [14].”

“The progenitor elements of these insertions were always fulllength or near full-length L1s with intact ORFs that were active in retrotransposition assays [11,14,35-37].”

“3 reference sequence, ensuring the presence of an intact L1 internal promoter [16,43,44].”

“There is evidence that the related sequence-specific R1 element endonuclease makes both cuts in the target DNA [18].”

“Also, L1-encoded proteins were almost certainly involved in the insertion of most of the Alu elements and processed pseudogenes in the genome [6-10]; thus, L1s are probably responsible, directly or indirectly, for the genesis of most of the transposed fraction of human DNA.”

“[6,8,53].”

“3 reference sequence, ensuring the presence of an intact L1 internal promoter [16,43,44].”

“Finally, residues 472(G) and 474(D) in the conserved Z motif in ORF2 are required for reverse transcriptase activity [46].”

“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3 ́-terminal Zn finger-like domain [14].”

“This modest majority may reflect a weak selection against L1s in the same orientation; such insertions could result in premature truncation of a gene’s mRNA due to the L1 polyadenylation signal [27,48,49].”

“Indeed, as a result of TPRT and decay over time, most L1 copies are inactivated by truncations, internal rearrangements and mutation”

“Most LINE-1 s in the human genome are grossly truncated at their 5′-end [6, 36, 37].”