Transposable Elements Donate Lineage-specific Regulatory Sequences to Host Genomes

Overview

Journal Cytogenet Genome Res

Specialty Genetics

Date 2005 Aug 12

PMID 16093685

Citations 55

Authors

L Marino-Ramirez

K C Lewis

D Landsman

I K Jordan

Affiliations

Soon will be listed here.

Abstract

The evolutionary implications of transposable element (TE) influences on gene regulation are explored here. An historical perspective is presented to underscore the importance of TE influences on gene regulation with respect to both the discovery of TEs and the early conceptualization of their potential impact on host genome evolution. Evidence that points to a role for TEs in host gene regulation is reviewed, and comparisons between genome sequences are used to demonstrate the fact that TEs are particularly lineage-specific components of their host genomes. Consistent with these two properties of TEs, regulatory effects and evolutionary specificity, human-mouse genome wide sequence comparisons reveal that the regulatory sequences that are contributed by TEs are exceptionally lineage specific. This suggests a particular mechanism by which TEs may drive the diversification of gene regulation between evolutionary lineages.

Citing Articles

Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity.

Kortsinoglou A, Wood M, Myridakis A, Andrikopoulos M, Roussis A, Eastwood D G3 (Bethesda). 2024; 14(10).

PMID: 39210673 PMC: 11457142. DOI: 10.1093/g3journal/jkae190.

Repeat Age Decomposition Informs an Ancient Set of Repeats Associated With Coleoid Cephalopod Divergence.

Marino A, Kizenko A, Wong W, Ghiselli F, Simakov O Front Genet. 2022; 13:793734.

PMID: 35368688 PMC: 8967140. DOI: 10.3389/fgene.2022.793734.

Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in .

Zhao Y, Li X, Xie J, Xu W, Chen S, Zhang X Front Plant Sci. 2022; 13:814718.

PMID: 35178060 PMC: 8843856. DOI: 10.3389/fpls.2022.814718.

An atlas of transposable element-derived alternative splicing in cancer.

Clayton E, Rishishwar L, Huang T, Gulati S, Ban D, McDonald J Philos Trans R Soc Lond B Biol Sci. 2020; 375(1795):20190342.

PMID: 32075558 PMC: 7061986. DOI: 10.1098/rstb.2019.0342.

Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Species.

Castro M, Goubert C, Monteiro F, Vieira C, Carareto C Genes (Basel). 2020; 11(2).

PMID: 32041215 PMC: 7073582. DOI: 10.3390/genes11020170.

References

Makalowski W, Mitchell G, Labuda D . Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 1994; 10(6):188-93. DOI: 10.1016/0168-9525(94)90254-2. View

Britten R, Davidson E . Gene regulation for higher cells: a theory. Science. 1969; 165(3891):349-57. DOI: 10.1126/science.165.3891.349. View

Silva J, Shabalina S, Harris D, Spouge J, Kondrashovi A . Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genet Res. 2003; 82(1):1-18. DOI: 10.1017/s0016672303006268. View

McCLINTOCK B . The significance of responses of the genome to challenge. Science. 1984; 226(4676):792-801. DOI: 10.1126/science.15739260. View

Sorek R, Ast G, Graur D . Alu-containing exons are alternatively spliced. Genome Res. 2002; 12(7):1060-7. PMC: 186627. DOI: 10.1101/gr.229302. View

Gumucio D, Gray T, Tarle S, Shelton D, Tagle D, Slightom J . Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes. Mol Cell Biol. 1992; 12(11):4919-29. PMC: 360424. DOI: 10.1128/mcb.12.11.4919-4929.1992. View

Moses A, Chiang D, Kellis M, Lander E, Eisen M . Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol. 2003; 3:19. PMC: 212491. DOI: 10.1186/1471-2148-3-19. View

Britten R . Mobile elements inserted in the distant past have taken on important functions. Gene. 1998; 205(1-2):177-82. DOI: 10.1016/s0378-1119(97)00399-5. View

Jacob F, MONOD J . Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961; 3:318-56. DOI: 10.1016/s0022-2836(61)80072-7. View

10.

van den Berg C, Demant P, Aerts P, Van Dijk H . Slp is an essential component of an EDTA-resistant activation pathway of mouse complement. Proc Natl Acad Sci U S A. 1992; 89(22):10711-5. PMC: 50411. DOI: 10.1073/pnas.89.22.10711. View

11.

Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R . Human-mouse alignments with BLASTZ. Genome Res. 2003; 13(1):103-7. PMC: 430961. DOI: 10.1101/gr.809403. View

12.

Landry J, Medstrand P, Mager D . Repetitive elements in the 5' untranslated region of a human zinc-finger gene modulate transcription and translation efficiency. Genomics. 2001; 76(1-3):110-6. DOI: 10.1006/geno.2001.6604. View

13.

Bureau T, Wessler S . Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc Natl Acad Sci U S A. 1994; 91(4):1411-5. PMC: 43168. DOI: 10.1073/pnas.91.4.1411. View

14.

Karolchik D, Baertsch R, Diekhans M, Furey T, Hinrichs A, Lu Y . The UCSC Genome Browser Database. Nucleic Acids Res. 2003; 31(1):51-4. PMC: 165576. DOI: 10.1093/nar/gkg129. View

15.

Britten R . DNA sequence insertion and evolutionary variation in gene regulation. Proc Natl Acad Sci U S A. 1996; 93(18):9374-7. PMC: 38434. DOI: 10.1073/pnas.93.18.9374. View

16.

Dermitzakis E, Clark A . Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol. 2002; 19(7):1114-21. DOI: 10.1093/oxfordjournals.molbev.a004169. View

17.

Adler A, Scheller A, Robins D . The stringency and magnitude of androgen-specific gene activation are combinatorial functions of receptor and nonreceptor binding site sequences. Mol Cell Biol. 1993; 13(10):6326-35. PMC: 364691. DOI: 10.1128/mcb.13.10.6326-6335.1993. View

18.

Brosius J . Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica. 2000; 107(1-3):209-38. View

19.

Bureau T, Ronald P, Wessler S . A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc Natl Acad Sci U S A. 1996; 93(16):8524-9. PMC: 38705. DOI: 10.1073/pnas.93.16.8524. View

20.

Thomas J, Touchman J, Blakesley R, Bouffard G, Beckstrom-Sternberg S, Margulies E . Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003; 424(6950):788-93. DOI: 10.1038/nature01858. View