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1. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.

Author

Leung, Wilson, Shaffer, Christopher D, Chen, Elizabeth J, Quisenberry, Thomas J, Ko, Kevin, Braverman, John M, Giarla, Thomas C, Mortimer, Nathan T, Reed, Laura K, Smith, Sheryl T, Robic, Srebrenka, McCartha, Shannon R, Perry, Danielle R, Prescod, Lindsay M, Sheppard, Zenyth A, Saville, Ken J, McClish, Allison, Morlock, Emily A, Sochor, Victoria R, Stanton, Brittney, Veysey-White, Isaac C, Revie, Dennis, Jimenez, Luis A, Palomino, Jennifer J, Patao, Melissa D, Patao, Shane M, Himelblau, Edward T, Campbell, Jaclyn D, Hertz, Alexandra L, McEvilly, Maddison F, Wagner, Allison R, Youngblom, James, Bedi, Baljit, Bettincourt, Jeffery, Duso, Erin, Her, Maiye, Hilton, William, House, Samantha, Karimi, Masud, Kumimoto, Kevin, Lee, Rebekah, Lopez, Darryl, Odisho, George, Prasad, Ricky, Robbins, Holly Lyn, Sandhu, Tanveer, Selfridge, Tracy, Tsukashima, Kara, Yosif, Hani, Kokan, Nighat P, Britt, Latia, Zoellner, Alycia, Spana, Eric P, Chlebina, Ben T, Chong, Insun, Friedman, Harrison, Mammo, Danny A, Ng, Chun L, Nikam, Vinayak S, Schwartz, Nicholas U, Xu, Thomas Q, Burg, Martin G, Batten, Spencer M, Corbeill, Lindsay M, Enoch, Erica, Ensign, Jesse J, Franks, Mary E, Haiker, Breanna, Ingles, Judith A, Kirkland, Lyndsay D, Lorenz-Guertin, Joshua M, Matthews, Jordan, Mittig, Cody M, Monsma, Nicholaus, Olson, Katherine J, Perez-Aragon, Guillermo, Ramic, Alen, Ramirez, Jordan R, Scheiber, Christopher, Schneider, Patrick A, Schultz, Devon E, Simon, Matthew, Spencer, Eric, Wernette, Adam C, Wykle, Maxine E, Zavala-Arellano, Elizabeth, McDonald, Mitchell J, Ostby, Kristine, Wendland, Peter, DiAngelo, Justin R, Ceasrine, Alexis M, Cox, Amanda H, Docherty, James EB, Gingras, Robert M, Grieb, Stephanie M, Pavia, Michael J, Personius, Casey L, Polak, Grzegorz L, Beach, Dale L, and Cerritos, Heaven L

Subjects
Chromosomes, Animals, Drosophila, Wolbachia, Histones, Retroelements, Codon, Gene Expression Profiling, Protein Processing, Post-Translational, Base Composition, Base Sequence, Genes, Insect, Female, genome size, heterochromatin, retrotransposons, Genetics, Human Genome, Generic health relevance
Abstract

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

Published
2017

6. translin Is Required for Metabolic Regulation of Sleep

Author

Murakami, Kazuma, Keene, Alex C, Bollinger, Wesley, Mehta, Aradhana, Yurgel, Maria E, Kim, Young-Joon, Gingras, Robert M, Heidker, Rebecca, Williams, Jack, DiAngelo, Justin R, Stahl, Bethany A, Masek, Pavel, and Suter, Beat

Subjects
570 Life sciences, biology
Abstract

Dysregulation of sleep or feeding has enormous health consequences. In humans, acute sleep loss is associated with increased appetite and insulin insensitivity, while chronically sleep-deprived individuals are more likely to develop obesity, metabolic syndrome, type II diabetes, and cardiovascular disease. Conversely, metabolic state potently modulates sleep and circadian behavior; yet, the molecular basis for sleep-metabolism interactions remains poorly understood. Here, we describe the identification of translin (trsn), a highly conserved RNA/DNA binding protein, as essential for starvation-induced sleep suppression. Strikingly, trsn does not appear to regulate energy stores, free glucose levels, or feeding behavior suggesting the sleep phenotype of trsn mutant flies is not a consequence of general metabolic dysfunction or blunted response to starvation. While broadly expressed in all neurons, trsn is transcriptionally upregulated in the heads of flies in response to starvation. Spatially restricted rescue or targeted knockdown localizes trsn function to neurons that produce the tachykinin family neuropeptide Leucokinin. Manipulation of neural activity in Leucokinin neurons revealed these neurons to be required for starvation-induced sleep suppression. Taken together, these findings establish trsn as an essential integrator of sleep and metabolic state, with implications for understanding the neural mechanism underlying sleep disruption in response to environmental perturbation.

Published
2016
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7. Retrotransposons Are the Major Contributors to the Expansion of theDrosophila ananassaeMuller F Element

Author

Leung, Wilson, primary, Shaffer, Christopher D, additional, Chen, Elizabeth J, additional, Quisenberry, Thomas J, additional, Ko, Kevin, additional, Braverman, John M, additional, Giarla, Thomas C, additional, Mortimer, Nathan T, additional, Reed, Laura K, additional, Smith, Sheryl T, additional, Robic, Srebrenka, additional, McCartha, Shannon R, additional, Perry, Danielle R, additional, Prescod, Lindsay M, additional, Sheppard, Zenyth A, additional, Saville, Ken J, additional, McClish, Allison, additional, Morlock, Emily A, additional, Sochor, Victoria R, additional, Stanton, Brittney, additional, Veysey-White, Isaac C, additional, Revie, Dennis, additional, Jimenez, Luis A, additional, Palomino, Jennifer J, additional, Patao, Melissa D, additional, Patao, Shane M, additional, Himelblau, Edward T, additional, Campbell, Jaclyn D, additional, Hertz, Alexandra L, additional, McEvilly, Maddison F, additional, Wagner, Allison R, additional, Youngblom, James, additional, Bedi, Baljit, additional, Bettincourt, Jeffery, additional, Duso, Erin, additional, Her, Maiye, additional, Hilton, William, additional, House, Samantha, additional, Karimi, Masud, additional, Kumimoto, Kevin, additional, Lee, Rebekah, additional, Lopez, Darryl, additional, Odisho, George, additional, Prasad, Ricky, additional, Robbins, Holly Lyn, additional, Sandhu, Tanveer, additional, Selfridge, Tracy, additional, Tsukashima, Kara, additional, Yosif, Hani, additional, Kokan, Nighat P, additional, Britt, Latia, additional, Zoellner, Alycia, additional, Spana, Eric P, additional, Chlebina, Ben T, additional, Chong, Insun, additional, Friedman, Harrison, additional, Mammo, Danny A, additional, Ng, Chun L, additional, Nikam, Vinayak S, additional, Schwartz, Nicholas U, additional, Xu, Thomas Q, additional, Burg, Martin G, additional, Batten, Spencer M, additional, Corbeill, Lindsay M, additional, Enoch, Erica, additional, Ensign, Jesse J, additional, Franks, Mary E, additional, Haiker, Breanna, additional, Ingles, Judith A, additional, Kirkland, Lyndsay D, additional, Lorenz-Guertin, Joshua M, additional, Matthews, Jordan, additional, Mittig, Cody M, additional, Monsma, Nicholaus, additional, Olson, Katherine J, additional, Perez-Aragon, Guillermo, additional, Ramic, Alen, additional, Ramirez, Jordan R, additional, Scheiber, Christopher, additional, Schneider, Patrick A, additional, Schultz, Devon E, additional, Simon, Matthew, additional, Spencer, Eric, additional, Wernette, Adam C, additional, Wykle, Maxine E, additional, Zavala-Arellano, Elizabeth, additional, McDonald, Mitchell J, additional, Ostby, Kristine, additional, Wendland, Peter, additional, DiAngelo, Justin R, additional, Ceasrine, Alexis M, additional, Cox, Amanda H, additional, Docherty, James E B, additional, Gingras, Robert M, additional, Grieb, Stephanie M, additional, Pavia, Michael J, additional, Personius, Casey L, additional, Polak, Grzegorz L, additional, Beach, Dale L, additional, Cerritos, Heaven L, additional, Horansky, Edward A, additional, Sharif, Karim A, additional, Moran, Ryan, additional, Parrish, Susan, additional, Bickford, Kirsten, additional, Bland, Jennifer, additional, Broussard, Juliana, additional, Campbell, Kerry, additional, Deibel, Katelynn E, additional, Forka, Richard, additional, Lemke, Monika C, additional, Nelson, Marlee B, additional, O'Keeffe, Catherine, additional, Ramey, S Mariel, additional, Schmidt, Luke, additional, Villegas, Paola, additional, Jones, Christopher J, additional, Christ, Stephanie L, additional, Mamari, Sami, additional, Rinaldi, Adam S, additional, Stity, Ghazal, additional, Hark, Amy T, additional, Scheuerman, Mark, additional, Silver Key, S Catherine, additional, McRae, Briana D, additional, Haberman, Adam S, additional, Asinof, Sam, additional, Carrington, Harriette, additional, Drumm, Kelly, additional, Embry, Terrance, additional, McGuire, Richard, additional, Miller-Foreman, Drew, additional, Rosen, Stella, additional, Safa, Nadia, additional, Schultz, Darrin, additional, Segal, Matt, additional, Shevin, Yakov, additional, Svoronos, Petros, additional, Vuong, Tam, additional, Skuse, Gary, additional, Paetkau, Don W, additional, Bridgman, Rachael K, additional, Brown, Charlotte M, additional, Carroll, Alicia R, additional, Gifford, Francesca M, additional, Gillespie, Julie Beth, additional, Herman, Susan E, additional, Holtcamp, Krystal L, additional, Host, Misha A, additional, Hussey, Gabrielle, additional, Kramer, Danielle M, additional, Lawrence, Joan Q, additional, Martin, Madeline M, additional, Niemiec, Ellen N, additional, O'Reilly, Ashleigh P, additional, Pahl, Olivia A, additional, Quintana, Guadalupe, additional, Rettie, Elizabeth A S, additional, Richardson, Torie L, additional, Rodriguez, Arianne E, additional, Rodriguez, Mona O, additional, Schiraldi, Laura, additional, Smith, Joanna J, additional, Sugrue, Kelsey F, additional, Suriano, Lindsey J, additional, Takach, Kaitlyn E, additional, Vasquez, Arielle M, additional, Velez, Ximena, additional, Villafuerte, Elizabeth J, additional, Vives, Laura T, additional, Zellmer, Victoria R, additional, Hauke, Jeanette, additional, Hauser, Charles R, additional, Barker, Karolyn, additional, Cannon, Laurie, additional, Parsamian, Perouza, additional, Parsons, Samantha, additional, Wichman, Zachariah, additional, Bazinet, Christopher W, additional, Johnson, Diana E, additional, Bangura, Abubakarr, additional, Black, Jordan A, additional, Chevee, Victoria, additional, Einsteen, Sarah A, additional, Hilton, Sarah K, additional, Kollmer, Max, additional, Nadendla, Rahul, additional, Stamm, Joyce, additional, Fafara-Thompson, Antoinette E, additional, Gygi, Amber M, additional, Ogawa, Emmy E, additional, Van Camp, Matt, additional, Kocsisova, Zuzana, additional, Leatherman, Judith L, additional, Modahl, Cassie M, additional, Rubin, Michael R, additional, Apiz-Saab, Susana S, additional, Arias-Mejias, Suzette M, additional, Carrion-Ortiz, Carlos F, additional, Claudio-Vazquez, Patricia N, additional, Espada-Green, Debbie M, additional, Feliciano-Camacho, Marium, additional, Gonzalez-Bonilla, Karina M, additional, Taboas-Arroyo, Mariela, additional, Vargas-Franco, Dorianmarie, additional, Montañez-Gonzalez, Raquel, additional, Perez-Otero, Joseph, additional, Rivera-Burgos, Myrielis, additional, Rivera-Rosario, Francisco J, additional, Eisler, Heather L, additional, Alexander, Jackie, additional, Begley, Samatha K, additional, Gabbard, Deana, additional, Allen, Robert J, additional, Aung, Wint Yan, additional, Barshop, William D, additional, Boozalis, Amanda, additional, Chu, Vanessa P, additional, Davis, Jeremy S, additional, Duggal, Ryan N, additional, Franklin, Robert, additional, Gavinski, Katherine, additional, Gebreyesus, Heran, additional, Gong, Henry Z, additional, Greenstein, Rachel A, additional, Guo, Averill D, additional, Hanson, Casey, additional, Homa, Kaitlin E, additional, Hsu, Simon C, additional, Huang, Yi, additional, Huo, Lucy, additional, Jacobs, Sarah, additional, Jia, Sasha, additional, Jung, Kyle L, additional, Wai-Chee Kong, Sarah, additional, Kroll, Matthew R, additional, Lee, Brandon M, additional, Lee, Paul F, additional, Levine, Kevin M, additional, Li, Amy S, additional, Liu, Chengyu, additional, Liu, Max Mian, additional, Lousararian, Adam P, additional, Lowery, Peter B, additional, Mallya, Allyson P, additional, Marcus, Joseph E, additional, Ng, Patrick C, additional, Nguyen, Hien P, additional, Patel, Ruchik, additional, Precht, Hashini, additional, Rastogi, Suchita, additional, Sarezky, Jonathan M, additional, Schefkind, Adam, additional, Schultz, Michael B, additional, Shen, Delia, additional, Skorupa, Tara, additional, Spies, Nicholas C, additional, Stancu, Gabriel, additional, Vivian Tsang, Hiu Man, additional, Turski, Alice L, additional, Venkat, Rohit, additional, Waldman, Leah E, additional, Wang, Kaidi, additional, Wang, Tracy, additional, Wei, Jeffrey W, additional, Wu, Dennis Y, additional, Xiong, David D, additional, Yu, Jack, additional, Zhou, Karen, additional, McNeil, Gerard P, additional, Fernandez, Robert W, additional, Menzies, Patrick Gomez, additional, Gu, Tingting, additional, Buhler, Jeremy, additional, Mardis, Elaine R, additional, and Elgin, Sarah C R, additional

Published
2017
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8. translin Is Required for Metabolic Regulation of Sleep

Author

Murakami, Kazuma, primary, Yurgel, Maria E., additional, Stahl, Bethany A., additional, Masek, Pavel, additional, Mehta, Aradhana, additional, Heidker, Rebecca, additional, Bollinger, Wesley, additional, Gingras, Robert M., additional, Kim, Young-Joon, additional, Ja, William W., additional, Suter, Beat, additional, DiAngelo, Justin R., additional, and Keene, Alex C., additional

Published
2016
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