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Transposable Elements

Transposable Elements (BIOL 6301) - Syllabus

Resources - PLP Summary examplePeer evaluation formPaper schedulePaper lis

Manuscripts for Transposable Elements (BIOL 6301), Fall 2016

Review Paper 1 Transposable element basics =================
Piegu et al. 2015: A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity
Potential Primary Literature Papers (choose two from the list below)
Nishihara et al. 2016: MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals
Guyot et al. 2016: Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories
Kines et al. 2016: The endonuclease domain of the LINE-1 ORF2 protein can tolerate multiple mutations
Jiang et al. 2016: Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome
Roffler et al. 2015: The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants
Roffler and Wicker 2015: Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons

RP2 TEs and genome size and composition =================
Canapa et al. 2016: Transposons, genome size, and evolutionary insights in animals
Potential PLPs (* = mandatory paper)
*Gordon et al. 2016: Long-read sequence assembly of the gorilla genome
Sun et al. 2012: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders
Blass et al. 2012: Accumulation and rapid decay of Non-LTR retrotransposons in the genome of the Three-Spine Stickleback
Gao et al. 2016: The contribution of transposable elements to size variations between four teleost genomes

RP3 TE impacts on human biology =================
Hancks and Kazazian 2016: Roles for retrotransposon insertions in human disease
PLPs
Scott et al. 2016: A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer
Iskow et al. 2010: Natural mutagenesis of human genomes by endogenous retrotransposons

RP4 TEs and human biology =================
Erwin et al. 2014: Mobile DNA elements in the generation of diversity and complexity in the brain
Potential PLPs
Morales et al. 2015: The contribution of Alu elements to mutagenic DNA double strand break repair
Gu et al. 2015: Alu-mediate divers and complex pathogenic copy-number variants within human chromosome 17 at p13.3
Konkel et al. 2015: Sequence analysis and characterization of active human Alu subfamilies based on the 1000 genomes pilot project
Huen et al. 2015: DNA methylation of LINE-1 and Alu repetitive elements in relation to sex hormones and pubertal timing in Mexican-American children
White et al. 2016: Modulation of LINE-1 retrotransposition by a human SAMHD1 polymorphism
Kagawa et al. 2015: Recessive inheritance of population-specific intronic LINE-1 insertion causes a Rotor Syndrome phenotype
Mavragani et al. 2016: Long interspersed nuclear element-1 retroelements are expressed in patients with systemic autoimmune disease and induce type I interferon

RP5 TEs and evolutionary change =================
Koonin 2016: Viruses and mobile elements as drivers of evolutionary transitions
Potential PLPs
*van’t Hof et al. 2016: The industrial melanism mutation in British peppered moths is a transposable element
Ding et al. 2015: Natural courtship song variation caused by an intronic retroelement in an ion channel gene
Platt et al. 2014: Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats

RP6 TEs and evolutionary change =================
Oliver and Greene 2012: Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis
Potential PLPs
Staton and Burke 2015: Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance
Sundaram et al. 2014: Widespread contribution of transposable elements to the innovation of gene regulatory networks
http://genome.cshlp.org/content/early/2014/10/08/gr.168872.113.abstract
Jurka et al. 2011: Families of transposable elements, population structure and the origin of species

RP7 TEs and evolutionary change =================
Warren et al. 2015: Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates
PLPs
Lynch et al. 2015: Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy
Chuong et al. 2016: Regulatory evolution of innate immunity through co-option of endogenous retroviruses

RP8 TEs in population genetics and ecology =================
Stapley et al. 2015: Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species
PLPs
Ortiz et al. 2014: An evaluation of the ecological relationship between Drosophila species and their parasitoid wasps as an opportunity for horizontal transposon transfer
Kofler et al. 2016: PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq

RP9 Horizontal transfer =================
Ivancevic et al. 2013: Jumping the fine LINE between species:  Horizontal transfer of transposable elements in animals catalyses genome evolution
PLPs
Suh et al. 2016: Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes
Fawcett and Innan 2016: High similarity between distantly related species of a plant SINE family is consistent with a scenario of vertical transmission without horizontal transfers

RP10 TE identification =================
Ewing 2015: Transposable element detection from whole genome sequence data
PLPs
*Platt et al. 2016: Accurate transposable element annotation is vital when analyzing new genome assemblies
Gallus et al. 2015: Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian Devil
Ha et al. 2016: Identification of polymorphic SVA retrotransposons using a mobile element scanning method for SVA (ME-Scan-SVA)

RP11 TE control =================
Goodier 2016: Restricting retrotransposons: a review
Potential PLPs
Lee 2015: The role of piRNA-mediated epigenetic silencing in the population dynamics of transposable elements in Drosophila melanogaster
Panda et al. 2016: Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation
Gong et al. 2015: A cluster of recently inserted transposable elements associated with siRNAs in Gossypium raimondii

RP12 Retrotransposition mechanics =================
Richardson et al. 2014: The influence of LINE-1 and SINE retrotransposons on mammalian genomes
PLPs
Hayashi et al. 2014: Mechanism by which a LINE protein recognizes its 3’ tail
Doucet et al. 2015: A 3’ poly(A) tract is required for LINE-1 retrotransposition