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1.  Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers 
BMC Genomics  2014;15(1):868.
Background
Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), or Type II. However, the whole genome DNA methylation changes in these two classical types of endometrial cancer is still unknown.
Results
Here we described complete genome-wide DNA methylome maps of EAC, UPSC, and normal endometrium by applying a combined strategy of methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme digestion sequencing (MRE-seq). We discovered distinct genome-wide DNA methylation patterns in EAC and UPSC: 27,009 and 15,676 recurrent differentially methylated regions (DMRs) were identified respectively, compared with normal endometrium. Over 80% of DMRs were in intergenic and intronic regions. The majority of these DMRs were not interrogated on the commonly used Infinium 450K array platform. Large-scale demethylation of chromosome X was detected in UPSC, accompanied by decreased XIST expression. Importantly, we discovered that the majority of the DMRs harbored promoter or enhancer functions and are specifically associated with genes related to uterine development and disease. Among these, abnormal methylation of transposable elements (TEs) may provide a novel mechanism to deregulate normal endometrium-specific enhancers derived from specific TEs.
Conclusions
DNA methylation changes are an important signature of endometrial cancer and regulate gene expression by affecting not only proximal promoters but also distal enhancers.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-868) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-868
PMCID: PMC4198682  PMID: 25286960
3.  An encyclopedia of mouse DNA elements (Mouse ENCODE) 
Stamatoyannopoulos, John A | Snyder, Michael | Hardison, Ross | Ren, Bing | Gingeras, Thomas | Gilbert, David M | Groudine, Mark | Bender, Michael | Kaul, Rajinder | Canfield, Theresa | Giste, Erica | Johnson, Audra | Zhang, Mia | Balasundaram, Gayathri | Byron, Rachel | Roach, Vaughan | Sabo, Peter J | Sandstrom, Richard | Stehling, A Sandra | Thurman, Robert E | Weissman, Sherman M | Cayting, Philip | Hariharan, Manoj | Lian, Jin | Cheng, Yong | Landt, Stephen G | Ma, Zhihai | Wold, Barbara J | Dekker, Job | Crawford, Gregory E | Keller, Cheryl A | Wu, Weisheng | Morrissey, Christopher | Kumar, Swathi A | Mishra, Tejaswini | Jain, Deepti | Byrska-Bishop, Marta | Blankenberg, Daniel | Lajoie1, Bryan R | Jain, Gaurav | Sanyal, Amartya | Chen, Kaun-Bei | Denas, Olgert | Taylor, James | Blobel, Gerd A | Weiss, Mitchell J | Pimkin, Max | Deng, Wulan | Marinov, Georgi K | Williams, Brian A | Fisher-Aylor, Katherine I | Desalvo, Gilberto | Kiralusha, Anthony | Trout, Diane | Amrhein, Henry | Mortazavi, Ali | Edsall, Lee | McCleary, David | Kuan, Samantha | Shen, Yin | Yue, Feng | Ye, Zhen | Davis, Carrie A | Zaleski, Chris | Jha, Sonali | Xue, Chenghai | Dobin, Alex | Lin, Wei | Fastuca, Meagan | Wang, Huaien | Guigo, Roderic | Djebali, Sarah | Lagarde, Julien | Ryba, Tyrone | Sasaki, Takayo | Malladi, Venkat S | Cline, Melissa S | Kirkup, Vanessa M | Learned, Katrina | Rosenbloom, Kate R | Kent, W James | Feingold, Elise A | Good, Peter J | Pazin, Michael | Lowdon, Rebecca F | Adams, Leslie B
Genome Biology  2012;13(8):418.
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.
doi:10.1186/gb-2012-13-8-418
PMCID: PMC3491367  PMID: 22889292
ENCODE Project; mouse genome; DNaseI hypersensitive sites; histone modifications; transcriptome; transcription factor binding sites; comparative genomics; ChIP-seq; RNA-seq
4.  Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project 
Gerstein, Mark B. | Lu, Zhi John | Van Nostrand, Eric L. | Cheng, Chao | Arshinoff, Bradley I. | Liu, Tao | Yip, Kevin Y. | Robilotto, Rebecca | Rechtsteiner, Andreas | Ikegami, Kohta | Alves, Pedro | Chateigner, Aurelien | Perry, Marc | Morris, Mitzi | Auerbach, Raymond K. | Feng, Xin | Leng, Jing | Vielle, Anne | Niu, Wei | Rhrissorrakrai, Kahn | Agarwal, Ashish | Alexander, Roger P. | Barber, Galt | Brdlik, Cathleen M. | Brennan, Jennifer | Brouillet, Jeremy Jean | Carr, Adrian | Cheung, Ming-Sin | Clawson, Hiram | Contrino, Sergio | Dannenberg, Luke O. | Dernburg, Abby F. | Desai, Arshad | Dick, Lindsay | Dosé, Andréa C. | Du, Jiang | Egelhofer, Thea | Ercan, Sevinc | Euskirchen, Ghia | Ewing, Brent | Feingold, Elise A. | Gassmann, Reto | Good, Peter J. | Green, Phil | Gullier, Francois | Gutwein, Michelle | Guyer, Mark S. | Habegger, Lukas | Han, Ting | Henikoff, Jorja G. | Henz, Stefan R. | Hinrichs, Angie | Holster, Heather | Hyman, Tony | Iniguez, A. Leo | Janette, Judith | Jensen, Morten | Kato, Masaomi | Kent, W. James | Kephart, Ellen | Khivansara, Vishal | Khurana, Ekta | Kim, John K. | Kolasinska-Zwierz, Paulina | Lai, Eric C. | Latorre, Isabel | Leahey, Amber | Lewis, Suzanna | Lloyd, Paul | Lochovsky, Lucas | Lowdon, Rebecca F. | Lubling, Yaniv | Lyne, Rachel | MacCoss, Michael | Mackowiak, Sebastian D. | Mangone, Marco | McKay, Sheldon | Mecenas, Desirea | Merrihew, Gennifer | Miller, David M. | Muroyama, Andrew | Murray, John I. | Ooi, Siew-Loon | Pham, Hoang | Phippen, Taryn | Preston, Elicia A. | Rajewsky, Nikolaus | Rätsch, Gunnar | Rosenbaum, Heidi | Rozowsky, Joel | Rutherford, Kim | Ruzanov, Peter | Sarov, Mihail | Sasidharan, Rajkumar | Sboner, Andrea | Scheid, Paul | Segal, Eran | Shin, Hyunjin | Shou, Chong | Slack, Frank J. | Slightam, Cindie | Smith, Richard | Spencer, William C. | Stinson, E. O. | Taing, Scott | Takasaki, Teruaki | Vafeados, Dionne | Voronina, Ksenia | Wang, Guilin | Washington, Nicole L. | Whittle, Christina M. | Wu, Beijing | Yan, Koon-Kiu | Zeller, Georg | Zha, Zheng | Zhong, Mei | Zhou, Xingliang | Ahringer, Julie | Strome, Susan | Gunsalus, Kristin C. | Micklem, Gos | Liu, X. Shirley | Reinke, Valerie | Kim, Stuart K. | Hillier, LaDeana W. | Henikoff, Steven | Piano, Fabio | Snyder, Michael | Stein, Lincoln | Lieb, Jason D. | Waterston, Robert H.
Science (New York, N.Y.)  2010;330(6012):1775-1787.
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
doi:10.1126/science.1196914
PMCID: PMC3142569  PMID: 21177976

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