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Transposable Elements

Transposable Elements (BIOL 6301) - Syllabus

Resources - PLP Summary examplePeer evaluation form, Intro to Unix, Running RepeatMasker, Running RepeatMasker in SGE Mode, Intro lecture by D Ray

Manuscripts and presentation schedule for Transposable Elements (BIOL 6301), Fall 2016

Review Papers - Transposable element basics =================
Jenna 9/5 -- 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
Nan 9/10 -- Sotero-Caio et al. 2017: Evolution and Diversity of Transposable Elements in Vertebrate Genomes
Jack 9/17 -- Arkhipova 2017: Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

RP2 TEs and genome size and composition =================
Jenna 9/19 -- Arkhipova 2018: Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution
PLP
Jack 9/24 -- Kapusta et al. 2017: Dynamics of genome size evolution in birds and mammals

RP3 TE impacts on phenotype  =================
Nan 9/26 -- Hancks and Kazazian 2016: Roles for retrotransposon insertions in human disease
PLP
Jenna 10/1 -- Murphy et al. 2018: Length variations within the Merle retrotransposon of canine PMEL: correlating genotype with phenotype

RP4 TEs and human biology =================
Jack 10/3 -- Burns 2017: Transposable elements in cancer
PLP
Nan 10/8 -- Guichard et al. 2018: Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans

RP5 TE Domestication =================
Jenna 10/10 -- Joly-Lopez and Bureau 2018: Exaptation of transposable element coding sequences
Jack 10/15 -- Jangam et al. 2017: Transposable Element Domestication as an Adaptation to Evolutionary Conflicts
PLP
Nan 10/17 -- Simonti et al. 2017: Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints

RP6 TEs and regulatory change =================
Jenna 10/22 -- Chuong et al. 2017: Regulatory activities of transposable elements: from conflicts to benefits
PLP
Jack 10/24 -- Krishnan et al. 2018: Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat

RP7 TEs and adaptive evolution =================
Nan 10/29 -- Schrader and Schmitz 2018:  The impact of transposable elements in adaptive evolution
Potential PLPs
Jenna 10/31 -- Plague et al. 2017: Transposable Elements Mediate Adaptive Debilitation of Flagella in Experimental Escherichia coli Populations
Jack 11/7 -- Li et al. 2018: Transposable elements contribute to the adaptation of Arabidopsis thaliana

RP8 TE control =================
Nan 11/12 -- Iwasaki et al. 2015: PIWI-Interacting RNA: Its Biogenesis and Functions
PLP
Jenna 11/14 -- Wang, et al. 2018: Hijacking oogenesis enables massive propagation of LINE and retroviral transposons
Jack 11/19 — Moon et al. 2018: A robust transposon-endogenizing response from germline stem cells

RP9 TE population biology/ecology =================
Cancelled Jack 11/19 -- Kent et al. 2017: Coevolution between transposable elements and recombination
PLP
Cancelled Nan 11/26 -- Lu et al. 2017: Tracking the genome-wide outcomes of a transposable element burst over decades of amplification
11/26 — Kofler et al. 2018: Molecular dissection of a natural transposable element invasion 

TE project presentations ================
Jenna 11/28 -- [Title]
Jack 12/3 -- [Title]
Nan 12/5 -- [Title]

I was too ambitious. Extra topics and papers if you want to read them.

RP 10 Retrotransposon evolution =================
TBD
PLP
Sookdeo et al. 2018: Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinctionSuh et al. 2017: De-novo emergence of SINE retroposons during the early evolution of passerine birds

RP11 Horizontal transfer =================
Peccoud et al. 2017: Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects
PLPs
Metzger et al. 2018: Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla

RP11 TE identification =================
Ewing 2015: Transposable element detection from whole genome sequence data
PLP
Gardner et al. 2017: The Mobile Element Locator Tool (MELT): Population-scale mobile element discovery and biology
Daron and Slotkin 2017: EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels

RP12 Retrotransposition mechanics =================
Richardson et al. 2014: The influence of LINE-1 and SINE retrotransposons on mammalian genomes
PLP
Christian et al. 2017: Involvement of Conserved Amino Acids in the C-Terminal Region of LINE-1 ORF2p in Retrotransposition