21 results on '"Pauli, Florencia"'
Search Results
2. A Validated Regulatory Network for Th17 Cell Specification
- Author
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Ciofani, Maria, Madar, Aviv, Galan, Carolina, Sellars, MacLean, Mace, Kieran, Pauli, Florencia, Agarwal, Ashish, Huang, Wendy, Parkurst, Christopher N., Muratet, Michael, Newberry, Kim M., Meadows, Sarah, Greenfield, Alex, Yang, Yi, Jain, Preti, Kirigin, Francis K., Birchmeier, Carmen, Wagner, Erwin F., Murphy, Kenneth M., Myers, Richard M., Bonneau, Richard, and Littman, Dan R.
- Published
- 2012
- Full Text
- View/download PDF
3. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-α gene expression
- Author
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Monahan, Kevin, Rudnick, Noam D., Kehayova, Polina D., Pauli, Florencia, Newberry, Kimberly M., Myers, Richard M., and Maniatis, Tom
- Published
- 2012
4. An integrated encyclopedia of DNA elements in the human genome
- Author
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Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas
- Subjects
Research ,Genetic research ,Transcription (Genetics) -- Research ,Human genome -- Research ,Genetic transcription -- Research - Abstract
Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...], The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
- Published
- 2012
- Full Text
- View/download PDF
5. Architecture of the human regulatory network derived from ENCODE data
- Author
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Gerstein, Mark B., Kundaje, Anshul, Hariharan, Manoj, Landt, Stephen G., Yan, Koon-Kiu, Cheng, Chao, Mu, Xinmeng Jasmine, Khurana, Ekta, Rozowsky, Joel, Alexander, Roger, Min, Renqiang, Alves, Pedro, Abyzov, Alexej, Addleman, Nick, Bhardwaj, Nitin, Boyle, Alan P., Cayting, Philip, Charos, Alexandra, Chen, David Z., Cheng, Yong, Clarke, Declan, Eastman, Catharine, Euskirchen, Ghia, Frietze, Seth, Fu, Yao, Gertz, Jason, Grubert, Fabian, Harmanci, Arif, Jain, Preti, Kasowski, Maya, Lacroute, Phil, Leng, Jing, Lian, Jin, Monahan, Hannah, O'Geen, Henriette, Ouyang, Zhengqing, Partridge, E. Christopher, Patacsil, Dorrelyn, Pauli, Florencia, Raha, Debasish, Ramirez, Lucia, Reddy, Timothy E., Reed, Brian, Shi, Minyi, Slifer, Teri, Wang, Jing, Wu, Linfeng, Yang, Xinqiong, Yip, Kevin Y., Zilberman-Schapira, Gili, Batzoglou, Serafim, Sidow, Arend, Farnham, Peggy J., Myers, Richard M., Weissman, Sherman M., and Snyder, Michael
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Research ,Genetic aspects ,Protein-protein interactions -- Genetic aspects -- Research ,Alleles -- Research ,Transcription factors -- Research ,DNA binding proteins -- Research ,Genetic regulation -- Research ,Allelomorphism -- Research - Abstract
Author(s): Mark B. Gerstein (corresponding author) [1, 2, 3, 15]; Anshul Kundaje [4, 15]; Manoj Hariharan [5, 15]; Stephen G. Landt [5, 15]; Koon-Kiu Yan [1, 2, 15]; Chao Cheng [...], Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease.
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- 2012
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6. A small family of LLS1-related non-heme oxygenases in plants with an origin amongst oxygenic photosynthesizers
- Author
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Gray, John, Wardzala, Ellen, Yang, Manli, Reinbothe, Steffen, Haller, Steve, and Pauli, Florencia
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- 2004
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7. Allele-specific distribution of RNA polymerase II on female X chromosomes
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Kucera, Katerina S., Reddy, Timothy E., Pauli, Florencia, Gertz, Jason, Logan, Jenae E., Myers, Richard M., and Willard, Huntington F.
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- 2011
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8. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
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Reddy, Timothy E., Pauli, Florencia, Sprouse, Rebekka O., Neff, Norma F., Newberry, Kimberly M., Garabedian, Michael J., and Myers, Richard M.
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Circadian rhythms -- Research ,Corticosteroids -- Research ,Gene expression -- Analysis ,Nucleotide sequencing -- Usage ,Health - Published
- 2009
9. Some New Model Geometries for Sickled Erythrocytes
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Pauli, Florencia and Vayo, H. Westcott
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92C50 ,92C37 - Abstract
Proposed model geometries are described for six types of flattened sickled erythrocytes. These new types occur with some frequency in blood smears of patients with sickle cell disease. The six types of cells are designated as five-pointed star, witch, hypocycloid, deltoid, astroid, and semi-circular. Formulae are provided for the volume and surface area of each type and a figure showing the profile of each is included. Measurements of actual sickled cells in vitro could be used to find values for the volume and surface area of each type of cell by using parameter values for the appropriate model geometry. These would give close approximations that could be useful in clinical therapies and laboratory investigations for sickle cell anemia. Surface area to volume ratios can also be found to a close approximation for each cell type.
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- 2008
10. Evidence for multiple roles for grainyhead-like 2 in the establishment and maintenance of human mucociliary airway epithelium
- Author
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Gao, Xia, primary, Vockley, Christopher M., additional, Pauli, Florencia, additional, Newberry, Kimberly M., additional, Xue, Yan, additional, Randell, Scott H., additional, Reddy, Timothy E., additional, and Hogan, Brigid L. M., additional
- Published
- 2013
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11. Widespread plasticity in CTCF occupancy linked to DNA methylation
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Wang, Hao, primary, Maurano, Matthew T., additional, Qu, Hongzhu, additional, Varley, Katherine E., additional, Gertz, Jason, additional, Pauli, Florencia, additional, Lee, Kristen, additional, Canfield, Theresa, additional, Weaver, Molly, additional, Sandstrom, Richard, additional, Thurman, Robert E., additional, Kaul, Rajinder, additional, Myers, Richard M., additional, and Stamatoyannopoulos, John A., additional
- Published
- 2012
- Full Text
- View/download PDF
12. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Author
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Landt, Stephen G., primary, Marinov, Georgi K., additional, Kundaje, Anshul, additional, Kheradpour, Pouya, additional, Pauli, Florencia, additional, Batzoglou, Serafim, additional, Bernstein, Bradley E., additional, Bickel, Peter, additional, Brown, James B., additional, Cayting, Philip, additional, Chen, Yiwen, additional, DeSalvo, Gilberto, additional, Epstein, Charles, additional, Fisher-Aylor, Katherine I., additional, Euskirchen, Ghia, additional, Gerstein, Mark, additional, Gertz, Jason, additional, Hartemink, Alexander J., additional, Hoffman, Michael M., additional, Iyer, Vishwanath R., additional, Jung, Youngsook L., additional, Karmakar, Subhradip, additional, Kellis, Manolis, additional, Kharchenko, Peter V., additional, Li, Qunhua, additional, Liu, Tao, additional, Liu, X. Shirley, additional, Ma, Lijia, additional, Milosavljevic, Aleksandar, additional, Myers, Richard M., additional, Park, Peter J., additional, Pazin, Michael J., additional, Perry, Marc D., additional, Raha, Debasish, additional, Reddy, Timothy E., additional, Rozowsky, Joel, additional, Shoresh, Noam, additional, Sidow, Arend, additional, Slattery, Matthew, additional, Stamatoyannopoulos, John A., additional, Tolstorukov, Michael Y., additional, White, Kevin P., additional, Xi, Simon, additional, Farnham, Peggy J., additional, Lieb, Jason D., additional, Wold, Barbara J., additional, and Snyder, Michael, additional
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- 2012
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13. Dynamic MicroRNA Gene Transcription and Processing during T Cell Development
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Kirigin, Francis F., primary, Lindstedt, Kenneth, additional, Sellars, Maclean, additional, Ciofani, Maria, additional, Low, Siao Li, additional, Jones, Lachlan, additional, Bell, Fiona, additional, Pauli, Florencia, additional, Bonneau, Richard, additional, Myers, Richard M., additional, Littman, Dan R., additional, and Chong, Mark M. W., additional
- Published
- 2012
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14. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
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Reddy, Timothy E., primary, Gertz, Jason, additional, Pauli, Florencia, additional, Kucera, Katerina S., additional, Varley, Katherine E., additional, Newberry, Kimberly M., additional, Marinov, Georgi K., additional, Mortazavi, Ali, additional, Williams, Brian A., additional, Song, Lingyun, additional, Crawford, Gregory E., additional, Wold, Barbara, additional, Willard, Huntington F., additional, and Myers, Richard M., additional
- Published
- 2012
- Full Text
- View/download PDF
15. Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation
- Author
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Gertz, Jason, primary, Varley, Katherine E., additional, Reddy, Timothy E., additional, Bowling, Kevin M., additional, Pauli, Florencia, additional, Parker, Stephanie L., additional, Kucera, Katerina S., additional, Willard, Huntington F., additional, and Myers, Richard M., additional
- Published
- 2011
- Full Text
- View/download PDF
16. Some New Model Geometries for Sickled Erythrocytes
- Author
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Pauli, Florencia, primary and Vayo, H. Westcott, additional
- Published
- 2008
- Full Text
- View/download PDF
17. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes inC. elegans
- Author
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Pauli, Florencia, primary, Liu, Yueyi, additional, Kim, Yoona A., additional, Chen, Pei-Jiun, additional, and Kim, Stuart K., additional
- Published
- 2006
- Full Text
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18. Evidence for multiple roles for grainyheadlike 2 in the establishment and maintenance of human mucociliary airway epithelium.
- Author
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Xia Gao, Vockley, Christopher M., Pauli, Florencia, Newberry, Kimberly M., Yan Xue, Randell, Scott H., Reddy, Timothy E., and Hogan, Brigid L. M.
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EPITHELIUM ,PROGENITOR cells ,MORPHOGENESIS ,GENE targeting ,EPITHELIAL cells ,GENETIC transcription - Abstract
Most of the airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated basal progenitor cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia, there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in coordinating multiple cellular processes required for epithelial morphogenesis, differentiation, remodeling, and repair. However, only a few target genes have been identified, and little is known about GRHL function in the adult lung. Here we focus on the role of GRHL2 in primary human bronchial epithelial cells, both as undifferentiated progenitors and as they differentiate in air-liquid interface culture into an organized mucociliary epithelium with transepithelial resistance. Using a dominant-negative protein or shRNA to inhibit GRHL2, we follow changes in epithelial phenotype and gene transcription using RNA sequencing or microarray analysis. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2 in both undifferentiated cells and air-liquid interface cultures. Using ChIP sequencing to map sites of GRHL2 binding in the basal cells, we identify 7,687 potential primary targets and confirm that GRHL2 binding is strongly enriched near GRHL2-regulated genes. Taken together, the results support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell morphogenesis, adhesion, and motility. [ABSTRACT FROM AUTHOR]
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- 2013
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19. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-&agr; gene expression.
- Author
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Monahan, Kevin, Rudnick, Noam D., Kehayova, Polina D., Pauli, Florencia, Newberry, Kimberly M., Myers, Richard M., and Maniatis, Tom
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CADHERINS ,VERTEBRATE physiology ,NERVOUS system ,RNA splicing ,PROMOTERS (Genetics) ,GENE expression ,NUCLEOTIDE sequence ,COHESINS - Abstract
Extraordinary single-cell diversity is generated in the vertebrate nervous system by the combinatorial expression of the clustered protocadherin genes (Pcdha, -ß, and -y). This diversity is generated by a combination of stochastic promoter choice and alternative premRNA splicing. Here we show that both the insulator-binding protein CTCF and the cohesin complex subunit Rad21 bind to two highly conserved DNA sequences, the first within and the second downstream of transcriptionally active Pcdha promoters. Both CTCF and Rad21 bind to these sites in vitro and in vivo, this binding directly correlates with alternative isoform expression, and knocking down CTCF expression reduces alternative isoform expression. Remarkably, a similarly spaced pair of CTCF/Rad21 binding sites was identified within a distant enhancer element (HS5-1), which is required for normal levels of alternative isoform expression. We also identify an additional, unique regulatory role for cohesin, as Rad21 binds to another enhancer (HS7) independently of CTCF, and knockdown of Rad21 reduces expression of the constitutive, biallelically expressed Pcdha isoforms ad and ac2. We propose that CTCF and the cohesin complex initiate and maintain Pcdha promoter choice by mediating interactions between Pcdha promoters and enhancers. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
20. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans.
- Author
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Pauli, Florencia, Yueyi Liu, Kim, Yoona A., Chen, Pei-Jiun, and Kim, Stuart K.
- Subjects
- *
MESSENGER RNA , *GENE expression , *EPITOPES , *DNA microarrays , *INTESTINES - Abstract
We used mRNA tagging to identify genes expressed in the intestine of C. elegans. Animals expressing an epitope-tagged protein that binds the poly-A tail of mRNAs (FLAG::PAB-1) from an intestine-specific promoter (ges-1) were used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine. A total of 1938 intestine-expressed genes (P<0.001) were identified using DNA microarrays. First, we compared the intestine-expressed genes with those expressed in the muscle and germline, and identified 510 genes enriched in all three tissues and 624 intestine-, 230 muscle- and 1135 germ line-enriched genes. Second, we showed that the 1938 intestine-expressed genes were physically clustered on the chromosomes, suggesting that the order of genes in the genome is influenced by the effect of chromatin domains on gene expression. Furthermore, the commonly expressed genes showed more chromosomal clustering than the tissue-enriched genes, suggesting that chromatin domains may influence housekeeping genes more than tissue-specific genes. Third, in order to gain further insight into the regulation of intestinal gene expression, we searched for regulatory motifs. This analysis found that the promoters of the intestine genes were enriched for the GATA transcription factor consensus binding sequence. We experimentally verified these results by showing that the GATA motif is required in cis and that GATA transcription factors are required in trans for expression of these intestinal genes. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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21. Widespread plasticity in CTCF occupancy linked to DNA methylation.
- Author
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Hao Wang, Maurano, Matthew T., Hongzhu Qu, Varley, Katherine E., Gertz, Jason, Pauli, Florencia, Lee, Kristen, Canfield, Theresa, Weaver, Molly, Sandstrom, Richard, Thurman, Robert E., Kaul, Rajinder, Myers, Richard M., and Stamatoyannopoulos, John A.
- Subjects
- *
DNA methylation , *GENOMES , *CHROMATIN , *METHYLATION , *CELLS - Abstract
CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome- wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
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