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Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate.

Kim TM, Hong SJ, Rhyu MG - J. Korean Med. Sci. (2004)

Bottom Line: Overall, the peaks of autonomous LINE (young and old L1s and L2s) peaks and non-autonomous SINE (Alus and MIRs) have alternated repeatedly for 150 million years.In addition, a single burst of LTR parallels the Cretaceous-Tertiary (K-T) boundary, an exceptional global event.These findings suggest that the periodic explosive expansions of LINEs and SINEs and an exceptional burst of LTR comprise the genome dynamics underlying the macroevolution of the hominoid primate lineage.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.

ABSTRACT
Five retroelement families, L1 and L2 (long interspersed nuclear element, LINE), Alu and MIR (short interspersed nuclear element, SINE), and LTR (long terminal repeat), comprise almost half of the human genome. This genome-wide analysis on the time-scaled expansion of retroelements sheds light on the chronologically synchronous amplification peaks of each retroelement family in variable heights across human chromosomes. Especially, L1s and LTRs in the highest density on sex chromosomes Xq and Y, respectively, disclose peak activities that are obscured in autosomes. The periods of young L1, Alu, LTR, and old L1 peak activities calibrated based on sequence divergence coincide with the divergence of the three major hominoid divergence as well as early eutherian radiation while the amplification peaks of old MIR and L2 account for the marsupial-placental split. Overall, the peaks of autonomous LINE (young and old L1s and L2s) peaks and non-autonomous SINE (Alus and MIRs) have alternated repeatedly for 150 million years. In addition, a single burst of LTR parallels the Cretaceous-Tertiary (K-T) boundary, an exceptional global event. These findings suggest that the periodic explosive expansions of LINEs and SINEs and an exceptional burst of LTR comprise the genome dynamics underlying the macroevolution of the hominoid primate lineage.

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Time-scaled expansion curves of L1, Alu, and LTR retroelements. The chromosomal fractions of retroelement family are plotted against percent of sequence divergence. The expansion curves of L1s most prominent on chromosome Xq, Alus on chromosome 19, and LTRs on chromosome Y are compared with those of autosomal average and counterpart sex chromosomes. The sex chromosomes disclose the L1s and LTRs peak activities, both of which are obscured in autosomes. The peak curves of L1s and Alus on chromosome Y tend to be skewed toward the higher divergence than those on other chromosomes.
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Figure 2: Time-scaled expansion curves of L1, Alu, and LTR retroelements. The chromosomal fractions of retroelement family are plotted against percent of sequence divergence. The expansion curves of L1s most prominent on chromosome Xq, Alus on chromosome 19, and LTRs on chromosome Y are compared with those of autosomal average and counterpart sex chromosomes. The sex chromosomes disclose the L1s and LTRs peak activities, both of which are obscured in autosomes. The peak curves of L1s and Alus on chromosome Y tend to be skewed toward the higher divergence than those on other chromosomes.

Mentions: The chromosomal fractions of five retroelement families were plotted according to the degree of sequence divergence for the analysis of time-scaled accumulation (Fig. 2, 3). L1s in the highest density on chromosome Xq make the most prominent expansion curve with two amplification peaks at the sequence divergences of 3% and 18% (Fig. 2). The dominant amplification peak at 18% is unique on chromosome Xq, and the height is three times higher than that of the average amplification peak on autosomes. The over-accumulation of L1s on Xq continues throughout the lifetime of L1s, encompassing the divergence range from 1% to 30%. Chromosome Y contains an L1 amplification peak at 5% divergence, which is as prominent as that on chromosome Xq, but has no L1 peak at 18% divergence.


Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate.

Kim TM, Hong SJ, Rhyu MG - J. Korean Med. Sci. (2004)

Time-scaled expansion curves of L1, Alu, and LTR retroelements. The chromosomal fractions of retroelement family are plotted against percent of sequence divergence. The expansion curves of L1s most prominent on chromosome Xq, Alus on chromosome 19, and LTRs on chromosome Y are compared with those of autosomal average and counterpart sex chromosomes. The sex chromosomes disclose the L1s and LTRs peak activities, both of which are obscured in autosomes. The peak curves of L1s and Alus on chromosome Y tend to be skewed toward the higher divergence than those on other chromosomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2822296&req=5

Figure 2: Time-scaled expansion curves of L1, Alu, and LTR retroelements. The chromosomal fractions of retroelement family are plotted against percent of sequence divergence. The expansion curves of L1s most prominent on chromosome Xq, Alus on chromosome 19, and LTRs on chromosome Y are compared with those of autosomal average and counterpart sex chromosomes. The sex chromosomes disclose the L1s and LTRs peak activities, both of which are obscured in autosomes. The peak curves of L1s and Alus on chromosome Y tend to be skewed toward the higher divergence than those on other chromosomes.
Mentions: The chromosomal fractions of five retroelement families were plotted according to the degree of sequence divergence for the analysis of time-scaled accumulation (Fig. 2, 3). L1s in the highest density on chromosome Xq make the most prominent expansion curve with two amplification peaks at the sequence divergences of 3% and 18% (Fig. 2). The dominant amplification peak at 18% is unique on chromosome Xq, and the height is three times higher than that of the average amplification peak on autosomes. The over-accumulation of L1s on Xq continues throughout the lifetime of L1s, encompassing the divergence range from 1% to 30%. Chromosome Y contains an L1 amplification peak at 5% divergence, which is as prominent as that on chromosome Xq, but has no L1 peak at 18% divergence.

Bottom Line: Overall, the peaks of autonomous LINE (young and old L1s and L2s) peaks and non-autonomous SINE (Alus and MIRs) have alternated repeatedly for 150 million years.In addition, a single burst of LTR parallels the Cretaceous-Tertiary (K-T) boundary, an exceptional global event.These findings suggest that the periodic explosive expansions of LINEs and SINEs and an exceptional burst of LTR comprise the genome dynamics underlying the macroevolution of the hominoid primate lineage.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.

ABSTRACT
Five retroelement families, L1 and L2 (long interspersed nuclear element, LINE), Alu and MIR (short interspersed nuclear element, SINE), and LTR (long terminal repeat), comprise almost half of the human genome. This genome-wide analysis on the time-scaled expansion of retroelements sheds light on the chronologically synchronous amplification peaks of each retroelement family in variable heights across human chromosomes. Especially, L1s and LTRs in the highest density on sex chromosomes Xq and Y, respectively, disclose peak activities that are obscured in autosomes. The periods of young L1, Alu, LTR, and old L1 peak activities calibrated based on sequence divergence coincide with the divergence of the three major hominoid divergence as well as early eutherian radiation while the amplification peaks of old MIR and L2 account for the marsupial-placental split. Overall, the peaks of autonomous LINE (young and old L1s and L2s) peaks and non-autonomous SINE (Alus and MIRs) have alternated repeatedly for 150 million years. In addition, a single burst of LTR parallels the Cretaceous-Tertiary (K-T) boundary, an exceptional global event. These findings suggest that the periodic explosive expansions of LINEs and SINEs and an exceptional burst of LTR comprise the genome dynamics underlying the macroevolution of the hominoid primate lineage.

Show MeSH