Abstract:
:We present new approaches to cis-regulatory module (CRM) discovery in the common scenario where relevant transcription factors and/or motifs are unknown. Beginning with a small list of CRMs mediating a common gene expression pattern, we search genome-wide for CRMs with similar functionality, using new statistical scores and without requiring known motifs or accurate motif discovery. We cross-validate our predictions on 31 regulatory networks in Drosophila and through correlations with gene expression data. Five predicted modules tested using an in vivo reporter gene assay all show tissue-specific regulatory activity. We also demonstrate our methods' ability to predict mammalian tissue-specific enhancers. Finally, we predict human CRMs that regulate early blood and cardiovascular development. In vivo transgenic mouse analysis of two predicted CRMs demonstrates that both have appropriate enhancer activity. Overall, 7/7 predictions were validated successfully in vivo, demonstrating the effectiveness of our approach for insect and mammalian genomes.
journal_name
Dev Celljournal_title
Developmental cellauthors
Kantorovitz MR,Kazemian M,Kinston S,Miranda-Saavedra D,Zhu Q,Robinson GE,Göttgens B,Halfon MS,Sinha Sdoi
10.1016/j.devcel.2009.09.002subject
Has Abstractpub_date
2009-10-01 00:00:00pages
568-79issue
4eissn
1534-5807issn
1878-1551pii
S1534-5807(09)00384-0journal_volume
17pub_type
杂志文章abstract::The Frizzled (Fz) receptor is required cell autonomously in Wnt/beta-catenin and planar cell polarity (PCP) signaling. In addition to these requirements, Fz acts nonautonomously during PCP establishment: wild-type cells surrounding fz(-) patches reorient toward the fz(-) cells. The molecular mechanism(s) of nonautonom...
journal_title:Developmental cell
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doi:10.1016/j.devcel.2008.08.004
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abstract::For 20 years, researchers have thought that circadian clocks are defined by feedback loops of transcription and translation. The rediscovery of posttranslational circadian oscillators in diverse organisms forces us to rethink this paradigm. Meanwhile, the original "basic" feedback loops of canonical circadian clocks h...
journal_title:Developmental cell
pub_type: 杂志文章,评审
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abstract::Unravelling the role of cytoskeleton regulators may be complicated by adaptations to experimental manipulations. In this issue of Developmental Cell, Cerikan et al. (2016) reveal how acute effects of DOCK6 RhoGEF depletion on RAC1 and CDC42 activation are reversed over time by compensatory mechanisms that re-establish...
journal_title:Developmental cell
pub_type: 评论,杂志文章
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journal_title:Developmental cell
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doi:10.1016/s1534-5807(03)00188-6
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abstract::Neurite fasciculation through contact-dependent signaling is important for the wiring and function of the neuronal circuits. Here, we describe a type of axon-dendrite fasciculation in C. elegans, where proximal dendrites of the nociceptor PVD adhere to the axon of the ALA interneuron. This axon-dendrite fasciculation ...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2018.10.028
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journal_title:Developmental cell
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doi:10.1016/j.devcel.2012.12.015
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abstract::We use the Dpp morphogen gradient in the Drosophila wing disc as a model to address the fundamental question of how a gradient of a growth factor can produce uniform growth. We first show that proper expression and subcellular localization of components in the Fat tumor-suppressor pathway, which have been argued to de...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2010.11.007
更新日期:2011-01-18 00:00:00
abstract::Nuclear size plays pivotal roles in gene expression, embryo development, and disease. A central hypothesis in organisms ranging from yeast to vertebrates is that nuclear size scales to cell size. This implies that nuclei may reach steady-state sizes set by limiting cytoplasmic pools of size-regulating components. By m...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2020.05.003
更新日期:2020-08-10 00:00:00
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journal_title:Developmental cell
pub_type: 评论,杂志文章
doi:10.1016/j.devcel.2017.08.007
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abstract::Eukaryotic genomes are organized within the nucleus through interactions with inner nuclear membrane (INM) proteins. How chromatin tethering to the INM is controlled in interphase and how this process contributes to subsequent mitotic nuclear envelope (NE) remodeling remains unclear. We have probed these fundamental q...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2020.01.028
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abstract::Epithelial reorganization involves coordinated changes in cell shapes and movements. This restructuring occurs during formation of placodes, ectodermal thickenings that initiate the morphogenesis of epithelial organs including hair, mammary gland, and tooth. Signaling pathways in ectodermal placode formation are well ...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2014.02.003
更新日期:2014-03-10 00:00:00
abstract::Cells entering mitosis become rounded, lose attachment to the substrate, and increase their cortical rigidity. Pivotal to these events is the dismantling of focal adhesions (FAs). How mitotic reshaping is linked to commitment to divide is unclear. Here, we show that DEPDC1B, a protein that accumulates in G2, coordinat...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2014.09.009
更新日期:2014-11-24 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2008.01.011
更新日期:2008-02-01 00:00:00
abstract::The effect of intracellular vesicle trafficking on stem-cell behavior is largely unexplored. We screened the Drosophila sorting nexins (SNXs) and discovered that one, SH3PX1, profoundly affects gut homeostasis and lifespan. SH3PX1 restrains intestinal stem cell (ISC) division through an endocytosis-autophagy network t...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2019.03.029
更新日期:2019-05-20 00:00:00
abstract::Transcriptional mediators of cell stress pathways, including HIF1α, ATF4, and p53, are key to normal development and play critical roles in disease, including ischemia and cancer. Despite their importance, mechanisms by which pathways mediated by these transcription factors interact with one another are not fully unde...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2015.04.021
更新日期:2015-06-08 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2009.05.002
更新日期:2009-05-01 00:00:00
abstract::The conserved Hippo kinase pathway plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. Whereas the function of the core kinase cascade, consisting of the serine/threonine kinases Hippo and Warts, in phosphorylating and thereby inactivating the transcri...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2009.12.013
更新日期:2010-02-16 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2011.06.013
更新日期:2011-07-19 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章,评审
doi:10.1016/j.devcel.2017.09.020
更新日期:2017-10-09 00:00:00
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journal_title:Developmental cell
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doi:10.1016/j.devcel.2005.02.010
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journal_title:Developmental cell
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doi:10.1016/j.devcel.2012.09.016
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2007.08.003
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journal_title:Developmental cell
pub_type: 评论,杂志文章
doi:10.1016/j.devcel.2008.10.010
更新日期:2008-11-01 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2020.01.005
更新日期:2020-02-10 00:00:00
abstract::A century ago, Oscar Hertwig discovered that cells orient their cleavage plane orthogonal to their long axis. Reporting recently in Nature, Bosveld et al. (2016) shed light on how, showing that NuMA/Mud localization at tricellular junctions provides mitotic cells with the memory of interphase shape used to orient clea...
journal_title:Developmental cell
pub_type: 评论,杂志文章
doi:10.1016/j.devcel.2016.03.005
更新日期:2016-03-21 00:00:00
abstract::Early leaf growth is sustained by cell proliferation and subsequent cell expansion that initiates at the leaf tip and proceeds in a basipetal direction. Using detailed kinematic and gene expression studies to map these stages during early development of the third leaf of Arabidopsis thaliana, we showed that the cell-c...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2011.11.011
更新日期:2012-01-17 00:00:00
abstract::The majority of excitatory synaptic transmission in the brain occurs at dendritic spines, which are actin-rich protrusions on the dendrites. The asymmetric nature of these structures suggests that proteins regulating cell polarity might be involved in their formation. Indeed, the polarity protein PAR-3 is required for...
journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2007.11.020
更新日期:2008-02-01 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
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更新日期:2001-09-01 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2006.08.009
更新日期:2006-10-01 00:00:00
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journal_title:Developmental cell
pub_type: 杂志文章
doi:10.1016/j.devcel.2020.10.019
更新日期:2020-12-07 00:00:00