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What Drives Positive Selection in the Drosophila piRNA Machinery? The Genomic Autoimmunity Hypothesis.
Blumenstiel JP, Erwin AA, Hemmer LW. Blumenstiel JP, et al. Yale J Biol Med. 2016 Dec 23;89(4):499-512. eCollection 2016 Dec. Yale J Biol Med. 2016. PMID: 28018141 Free PMC article. Review.
We propose that recurrent positive selection in the piRNA machinery can be partly explained by an ongoing tension between selection for sensitivity required by genome defense and selection for specificity to avoid the off-target effects of maladaptive genic silencing by pi …
We propose that recurrent positive selection in the piRNA machinery can be partly explained by an ongoing tension between selection for sens …
The interplay of homologous recombination and horizontal gene transfer in bacterial speciation.
Lawrence JG, Retchless AC. Lawrence JG, et al. Methods Mol Biol. 2009;532:29-53. doi: 10.1007/978-1-60327-853-9_3. Methods Mol Biol. 2009. PMID: 19271178 Review.
In the context of the Biological Species concept, allelic exchange purges genic variability within bacterial populations as gene exchange mediates selective sweeps. ...
In the context of the Biological Species concept, allelic exchange purges genic variability within bacterial populations as gene exch …
Two major chromosome evolution events with unrivaled conserved gene content in pomegranate.
Akparov Z, Hajiyeva S, Abbasov M, Kaur S, Hamwieh A, Alsamman AM, Hajiyev E, Babayeva S, Izzatullayeva V, Mustafayeva Z, Mehdiyeva S, Mustafayev O, Shahmuradov I, Kosarev P, Solovyev V, Salamov A, Jighly A. Akparov Z, et al. Front Plant Sci. 2023 Mar 13;14:1039211. doi: 10.3389/fpls.2023.1039211. eCollection 2023. Front Plant Sci. 2023. PMID: 36993855 Free PMC article.
Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan-genic content was represented by Tunisia and Taishanhong only. We also revisited the divergence between soft- and hard-seeded cultivars …
Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan- …
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution.
Lee YCG, Karpen GH. Lee YCG, et al. Elife. 2017 Jul 11;6:e25762. doi: 10.7554/eLife.25762. Elife. 2017. PMID: 28695823 Free PMC article.
Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs. Interestingly, the …
Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend …
Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host-Pathogen Genetic Interactions.
Syme RA, Martin A, Wyatt NA, Lawrence JA, Muria-Gonzalez MJ, Friesen TL, Ellwood SR. Syme RA, et al. Front Genet. 2018 Apr 18;9:130. doi: 10.3389/fgene.2018.00130. eCollection 2018. Front Genet. 2018. PMID: 29720997 Free PMC article.
Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive gen …
Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a proc …
All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs.
Schork AJ, Thompson WK, Pham P, Torkamani A, Roddey JC, Sullivan PF, Kelsoe JR, O'Donovan MC, Furberg H; Tobacco and Genetics Consortium; Bipolar Disorder Psychiatric Genomics Consortium; Schizophrenia Psychiatric Genomics Consortium; Schork NJ, Andreassen OA, Dale AM. Schork AJ, et al. PLoS Genet. 2013 Apr;9(4):e1003449. doi: 10.1371/journal.pgen.1003449. Epub 2013 Apr 25. PLoS Genet. 2013. PMID: 23637621 Free PMC article.
We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combinati …
We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new …
piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis.
Erwin AA, Galdos MA, Wickersheim ML, Harrison CC, Marr KD, Colicchio JM, Blumenstiel JP. Erwin AA, et al. PLoS Genet. 2015 Aug 4;11(8):e1005332. doi: 10.1371/journal.pgen.1005332. eCollection 2015 Aug. PLoS Genet. 2015. PMID: 26241928 Free PMC article.
Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic …
Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expressio …
G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation.
Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME, Lawrence CJ, Bass HW. Andorf CM, et al. J Genet Genomics. 2014 Dec 20;41(12):627-47. doi: 10.1016/j.jgg.2014.10.004. Epub 2014 Nov 4. J Genet Genomics. 2014. PMID: 25527104 Free article.
G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5' UTR and the other at the 5' end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures i …
G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5' UTR and the other at the …
Characterization of HPV and host genome interactions in primary head and neck cancers.
Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network. Parfenov M, et al. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13. Proc Natl Acad Sci U S A. 2014. PMID: 25313082 Free PMC article.
Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript …
Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for geni …