Search Results - "Scacheri, Peter C"

Enhancer variants: evaluating functions in common disease by Corradin, Olivia, Scacheri, Peter C

“…Gene enhancer elements are noncoding segments of DNA that play a central role in regulating transcriptional programs that control development, cell identity,…”
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Functional Enhancers Shape Extrachromosomal Oncogene Amplifications by Morton, Andrew R., Dogan-Artun, Nergiz, Faber, Zachary J., MacLeod, Graham, Bartels, Cynthia F., Piazza, Megan S., Allan, Kevin C., Mack, Stephen C., Wang, Xiuxing, Gimple, Ryan C., Wu, Qiulian, Rubin, Brian P., Shetty, Shashirekha, Angers, Stephane, Dirks, Peter B., Sallari, Richard C., Lupien, Mathieu, Rich, Jeremy N., Scacheri, Peter C.

“…Non-coding regions amplified beyond oncogene borders have largely been ignored. Using a computational approach, we find signatures of significant…”
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Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits by Corradin, Olivia, Saiakhova, Alina, Akhtar-Zaidi, Batool, Myeroff, Lois, Willis, Joseph, Cowper-Sal lari, Richard, Lupien, Mathieu, Markowitz, Sanford, Scacheri, Peter C

“…DNA variants (SNPs) that predispose to common traits often localize within noncoding regulatory elements such as enhancers. Moreover, loci identified by…”
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Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency by Factor, Daniel C., Corradin, Olivia, Zentner, Gabriel E., Saiakhova, Alina, Song, Lingyun, Chenoweth, Josh G., McKay, Ronald D., Crawford, Gregory E., Scacheri, Peter C., Tesar, Paul J.

“…Naive mouse embryonic stem cells (mESCs) and primed epiblast stem cells (mEpiSCs) represent successive snapshots of pluripotency during embryogenesis. Using…”
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Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases by Lu, Leina, Liu, Xiaoxiao, Huang, Wei-Kai, Giusti-Rodríguez, Paola, Cui, Jian, Zhang, Shanshan, Xu, Wanying, Wen, Zhexing, Ma, Shufeng, Rosen, Jonathan D., Xu, Zheng, Bartels, Cynthia F., Kawaguchi, Riki, Hu, Ming, Scacheri, Peter C., Rong, Zhili, Li, Yun, Sullivan, Patrick F., Song, Hongjun, Ming, Guo-li, Li, Yan, Jin, Fulai

“…Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C”…”
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CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing by Tie, Feng, Banerjee, Rakhee, Stratton, Carl A, Prasad-Sinha, Jayashree, Stepanik, Vincent, Zlobin, Andrei, Diaz, Manuel O, Scacheri, Peter C, Harte, Peter J

“…Trimethylation of histone H3 lysine 27 (H3K27me3) by Polycomb repressive complex 2 (PRC2) is essential for transcriptional silencing of Polycomb target genes,…”
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The Chromatin Fingerprint of Gene Enhancer Elements by Zentner, Gabriel E., Scacheri, Peter C.

“…Different cell types within a single organism are generally distinguished by strikingly different patterns of gene expression, which are dynamic throughout…”
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Transcription elongation factors represent in vivo cancer dependencies in glioblastoma by Miller, Tyler E., Liau, Brian B., Wallace, Lisa C., Morton, Andrew R., Xie, Qi, Dixit, Deobrat, Factor, Daniel C., Kim, Leo J. Y., Morrow, James J., Wu, Qiulian, Mack, Stephen C., Hubert, Christopher G., Gillespie, Shawn M., Flavahan, William A., Hoffmann, Thomas, Thummalapalli, Rohit, Hemann, Michael T., Paddison, Patrick J., Horbinski, Craig M., Zuber, Johannes, Scacheri, Peter C., Bernstein, Bradley E., Tesar, Paul J., Rich, Jeremy N.

“…An in vivo RNA interference screening strategy in glioblastoma enabled the identification of a host of epigenetic targets required for glioblastoma cell…”
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Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer by Akhtar-Zaidi, Batool, Cowper-Sal-lari, Richard, Corradin, Olivia, Saiakhova, Alina, Bartels, Cynthia F., Balasubramanian, Dheepa, Myeroff, Lois, Lutterbaugh, James, Jarrar, Awad, Kalady, Matthew F., Willis, Joseph, Moore, Jason H., Tesar, Paul J., Laframboise, Thomas, Markowitz, Sanford, Lupien, Mathieu, Scacheri, Peter C.

“…Cancer is characterized by gene expression aberrations. Studies have largely focused on coding sequences and promoters, even though distal regulatory elements…”
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Integrative genomic analysis of human ribosomal DNA by Zentner, Gabriel E., Saiakhova, Alina, Manaenkov, Pavel, Adams, Mark D., Scacheri, Peter C.

“…The transcription of ribosomal RNA (rRNA) is critical to life. Despite its importance, ribosomal DNA (rDNA) is not included in current genome assemblies and,…”
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Histone Demethylase UTX and Chromatin Remodeler BRM Bind Directly to CBP and Modulate Acetylation of Histone H3 Lysine 27 by Tie, Feng, Banerjee, Rakhee, Conrad, Patricia A., Scacheri, Peter C., Harte, Peter J.

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome by Zentner, Gabriel E., Layman, Wanda S., Martin, Donna M., Scacheri, Peter C.

“…CHARGE syndrome [coloboma of the eye, heart defects, atresia of the choanae, retardation of growth and/or development, genital and/or urinary abnormalities,…”
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Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome by Cohen, Andrea J., Saiakhova, Alina, Corradin, Olivia, Luppino, Jennifer M., Lovrenert, Katreya, Bartels, Cynthia F., Morrow, James J., Mack, Stephen C., Dhillon, Gursimran, Beard, Lydia, Myeroff, Lois, Kalady, Matthew F., Willis, Joseph, Bradner, James E., Keri, Ruth A., Berger, Nathan A., Pruett-Miller, Shondra M., Markowitz, Sanford D., Scacheri, Peter C.

“…In addition to mutations in genes, aberrant enhancer element activity at non-coding regions of the genome is a key driver of tumorigenesis. Here, we perform…”
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CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression by Schnetz, Michael P, Handoko, Lusy, Akhtar-Zaidi, Batool, Bartels, Cynthia F, Pereira, C Filipe, Fisher, Amanda G, Adams, David J, Flicek, Paul, Crawford, Gregory E, Laframboise, Thomas, Tesar, Paul, Wei, Chia-Lin, Scacheri, Peter C

“…CHD7 is one of nine members of the chromodomain helicase DNA-binding domain family of ATP-dependent chromatin remodeling enzymes found in mammalian cells. De…”
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Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer by Shang, Stephen, Yang, Jiekun, Jazaeri, Amir A, Duval, Alexander James, Tufan, Turan, Lopes Fischer, Natasha, Benamar, Mouadh, Guessous, Fadila, Lee, Inyoung, Campbell, Robert M, Ebert, Philip J, Abbas, Tarek, Landen, Charles N, Difeo, Analisa, Scacheri, Peter C, Adli, Mazhar

“…Chemoresistance is driven by unique regulatory networks in the genome that are distinct from those necessary for cancer development. Here, we investigate the…”
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Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis by Forrest, Megan E., Saiakhova, Alina, Beard, Lydia, Buchner, David A., Scacheri, Peter C., LaFramboise, Thomas, Markowitz, Sanford, Khalil, Ahmad M.

“…Long non-coding RNAs (lncRNAs) are frequently dysregulated in many human cancers. We sought to identify candidate oncogenic lncRNAs in human colon tumors by…”
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Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis by Pontius, W. Dean, Hong, Ellen S., Faber, Zachary J., Gray, Jeremy, Peacock, Craig D., Bayles, Ian, Lovrenert, Katreya, Chin, Diana H., Gryder, Berkley E., Bartels, Cynthia F., Scacheri, Peter C.

“…The metastasis-invasion cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor and ultimately grow…”
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Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns by Schnetz, Michael P, Bartels, Cynthia F, Shastri, Kuntal, Balasubramanian, Dheepa, Zentner, Gabriel E, Balaji, Ravishankar, Zhang, Xiaodong, Song, Lingyun, Wang, Zhenghe, Laframboise, Thomas, Crawford, Gregory E, Scacheri, Peter C

“…CHD7 is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes. De novo mutation of the CHD7 gene is a…”
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Upregulation of Glucose-Regulated Protein 78 in Metastatic Cancer Cells Is Necessary for Lung Metastasis Progression by Lizardo, Michael M, Morrow, James J, Miller, Tyler E, Hong, Ellen S, Ren, Ling, Mendoza, Arnulfo, Halsey, Charles H, Scacheri, Peter C, Helman, Lee J, Khanna, Chand

“…Abstract Metastasis is the cause of more than 90% of all cancer deaths. Despite this fact, most anticancer therapeutics currently in clinical use have limited…”
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ITCH K63-Ubiquitinates the NOD2 Binding Protein, RIP2, to Influence Inflammatory Signaling Pathways by Tao, MingFang, Scacheri, Peter C., Marinis, Jill M., Harhaj, Edward W., Matesic, Lydia E., Abbott, Derek W.

“…The inability to coordinate the signaling pathways that lead to proper cytokine responses characterizes the pathogenesis of inflammatory diseases such as…”
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