Search Results - "Dickel, Diane"

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation by Preissl, Sebastian, Fang, Rongxin, Huang, Hui, Zhao, Yuan, Raviram, Ramya, Gorkin, David U., Zhang, Yanxiao, Sos, Brandon C., Afzal, Veena, Dickel, Diane E., Kuan, Samantha, Visel, Axel, Pennacchio, Len A., Zhang, Kun, Ren, Bing

“…Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in…”
Get full text

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types by Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., Dickel, Diane E.

“…Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but…”
Get full text

Genomic Patterns of De Novo Mutation in Simplex Autism by Turner, Tychele N., Coe, Bradley P., Dickel, Diane E., Hoekzema, Kendra, Nelson, Bradley J., Zody, Michael C., Kronenberg, Zev N., Hormozdiari, Fereydoun, Raja, Archana, Pennacchio, Len A., Darnell, Robert B., Eichler, Evan E.

“…To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064…”
Get full text

The changing mouse embryo transcriptome at whole tissue and single-cell resolution by He, Peng, Williams, Brian A., Trout, Diane, Marinov, Georgi K., Amrhein, Henry, Berghella, Libera, Goh, Say-Tar, Plajzer-Frick, Ingrid, Afzal, Veena, Pennacchio, Len A., Dickel, Diane E., Visel, Axel, Ren, Bing, Hardison, Ross C., Zhang, Yu, Wold, Barbara J.

“…During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we…”
Get full text

Perfect and imperfect views of ultraconserved sequences by Snetkova, Valentina, Pennacchio, Len A., Visel, Axel, Dickel, Diane E.

“…Across the human genome, there are nearly 500 ‘ultraconserved’ elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both…”
Get full text

Progressive Loss of Function in a Limb Enhancer during Snake Evolution by Kvon, Evgeny Z., Kamneva, Olga K., Melo, Uirá S., Barozzi, Iros, Osterwalder, Marco, Mannion, Brandon J., Tissières, Virginie, Pickle, Catherine S., Plajzer-Frick, Ingrid, Lee, Elizabeth A., Kato, Momoe, Garvin, Tyler H., Akiyama, Jennifer A., Afzal, Veena, Lopez-Rios, Javier, Rubin, Edward M., Dickel, Diane E., Pennacchio, Len A., Visel, Axel

“…The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major…”
Get full text

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers by Hashimoto, Hisayuki, Wang, Zhaoning, Garry, Glynnis A., Malladi, Venkat S., Botten, Giovanni A., Ye, Wenduo, Zhou, Huanyu, Osterwalder, Marco, Dickel, Diane E., Visel, Axel, Liu, Ning, Bassel-Duby, Rhonda, Olson, Eric N.

“…The cardiogenic transcription factors (TFs) Mef2c, Gata4, and Tbx5 can directly reprogram fibroblasts to induced cardiac-like myocytes (iCLMs), presenting a…”
Get full text

Ultraconserved Enhancers Are Required for Normal Development by Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth A., Harrington, Anne N., Pham, Quan T., Garvin, Tyler H., Kato, Momoe, Osterwalder, Marco, Akiyama, Jennifer A., Afzal, Veena, Rubenstein, John L.R., Pennacchio, Len A., Visel, Axel

“…Non-coding “ultraconserved” regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as…”
Get full text

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder by Long, Hannah K., Osterwalder, Marco, Welsh, Ian C., Hansen, Karissa, Davies, James O.J., Liu, Yiran E., Koska, Mervenaz, Adams, Alexander T., Aho, Robert, Arora, Neha, Ikeda, Kazuya, Williams, Ruth M., Sauka-Spengler, Tatjana, Porteus, Matthew H., Mohun, Tim, Dickel, Diane E., Swigut, Tomek, Hughes, Jim R., Higgs, Douglas R., Visel, Axel, Selleri, Licia, Wysocka, Joanna

“…Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence…”
Get full text

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers by Kosicki, Michael, Baltoumas, Fotis A, Kelman, Guy, Boverhof, Joshua, Ong, Yeongshnn, Cook, Laura E, Dickel, Diane E, Pavlopoulos, Georgios A, Pennacchio, Len A, Visel, Axel

“…Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we…”
Get full text

Spatiotemporal DNA methylome dynamics of the developing mouse fetus by He, Yupeng, Hariharan, Manoj, Gorkin, David U., Dickel, Diane E., Luo, Chongyuan, Castanon, Rosa G., Nery, Joseph R., Lee, Ah Young, Zhao, Yuan, Huang, Hui, Williams, Brian A., Trout, Diane, Amrhein, Henry, Fang, Rongxin, Chen, Huaming, Li, Bin, Visel, Axel, Pennacchio, Len A., Ren, Bing, Ecker, Joseph R.

“…Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited 1…”
Get full text

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants by Kvon, Evgeny Z., Zhu, Yiwen, Kelman, Guy, Novak, Catherine S., Plajzer-Frick, Ingrid, Kato, Momoe, Garvin, Tyler H., Pham, Quan, Harrington, Anne N., Hunter, Riana D., Godoy, Janeth, Meky, Eman M., Akiyama, Jennifer A., Afzal, Veena, Tran, Stella, Escande, Fabienne, Gilbert-Dussardier, Brigitte, Jean-Marçais, Nolwenn, Hudaiberdiev, Sanjarbek, Ovcharenko, Ivan, Dobbs, Matthew B., Gurnett, Christina A., Manouvrier-Hanu, Sylvie, Petit, Florence, Visel, Axel, Dickel, Diane E., Pennacchio, Len A.

“…Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter…”
Get full text

The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome by Spurrell, Cailyn H., Dickel, Diane E., Visel, Axel

“…Coupling chromosome conformation capture to molecular enrichment for promoter-containing DNA fragments enables the systematic mapping of interactions between…”
Get full text

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation by Turco, Gina M, Rodriguez-Medina, Joel, Siebert, Stefan, Han, Diane, Valderrama-Gómez, Miguel Á, Vahldick, Hannah, Shulse, Christine N, Cole, Benjamin J, Juliano, Celina E, Dickel, Diane E, Savageau, Michael A, Brady, Siobhan M

“…Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation…”
Get full text

Genomic analyses implicate noncoding de novo variants in congenital heart disease by Richter, Felix, Morton, Sarah U., Kim, Seong Won, Kitaygorodsky, Alexander, Wasson, Lauren K., Chen, Kathleen M., Zhou, Jian, Qi, Hongjian, Patel, Nihir, DePalma, Steven R., Parfenov, Michael, Homsy, Jason, Gorham, Joshua M., Manheimer, Kathryn B., Velinder, Matthew, Farrell, Andrew, Marth, Gabor, Schadt, Eric E., Kaltman, Jonathan R., Newburger, Jane W., Giardini, Alessandro, Goldmuntz, Elizabeth, Brueckner, Martina, Kim, Richard, Porter, George A., Bernstein, Daniel, Chung, Wendy K., Srivastava, Deepak, Tristani-Firouzi, Martin, Troyanskaya, Olga G., Dickel, Diane E., Shen, Yufeng, Seidman, Jonathan G., Seidman, Christine E., Gelb, Bruce D.

“…A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants…”
Get full text

Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development by Liu, Zhidong, Ypsilanti, Athéna R, Markenscoff-Papadimitriou, Eirene, Dickel, Diane E, Sanders, Stephan J, Dong, Shan, Pennacchio, Len A, Visel, Axel, Rubenstein, John L

“…There is evidence that transcription factor (TF) encoding genes, which temporally control development in multiple cell types, can have tens of enhancers that…”
Get full text

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation by Sethi, Anurag, Gu, Mengting, Gumusgoz, Emrah, Chan, Landon, Yan, Koon-Kiu, Rozowsky, Joel, Barozzi, Iros, Afzal, Veena, Akiyama, Jennifer A., Plajzer-Frick, Ingrid, Yan, Chengfei, Novak, Catherine S., Kato, Momoe, Garvin, Tyler H., Pham, Quan, Harrington, Anne, Mannion, Brandon J., Lee, Elizabeth A., Fukuda-Yuzawa, Yoko, Visel, Axel, Dickel, Diane E., Yip, Kevin Y., Sutton, Richard, Pennacchio, Len A., Gerstein, Mark

“…Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays…”
Get full text

Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons by Lindtner, Susan, Catta-Preta, Rinaldo, Tian, Hua, Su-Feher, Linda, Price, James D., Dickel, Diane E., Greiner, Vanille, Silberberg, Shanni N., McKinsey, Gabriel L., McManus, Michael T., Pennacchio, Len A., Visel, Axel, Nord, Alex S., Rubenstein, John L.R.

“…DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of…”
Get full text

Increased enhancer–promoter interactions during developmental enhancer activation in mammals by Chen, Zhuoxin, Snetkova, Valentina, Bower, Grace, Jacinto, Sandra, Clock, Benjamin, Dizehchi, Atrin, Barozzi, Iros, Mannion, Brandon J., Alcaina-Caro, Ana, Lopez-Rios, Javier, Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Kvon, Evgeny Z.

“…Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains…”
Get full text

Genome-wide compendium and functional assessment of in vivo heart enhancers by Dickel, Diane E., Barozzi, Iros, Zhu, Yiwen, Fukuda-Yuzawa, Yoko, Osterwalder, Marco, Mannion, Brandon J., May, Dalit, Spurrell, Cailyn H., Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth, Garvin, Tyler H., Kato, Momoe, Akiyama, Jennifer A., Afzal, Veena, Lee, Ah Young, Gorkin, David U., Ren, Bing, Rubin, Edward M., Visel, Axel, Pennacchio, Len A.

“…Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations…”
Get full text