Abstract:
:An organism's genome sequence serves as a blueprint for the proteins and regulatory RNAs essential for cellular function. The genome also harbors cis-acting non-coding sequences that control gene expression and are essential to coordinate regulatory programs during embryonic development. However, the genome sequence is largely identical between cell types within a multi-cellular organism indicating that factors such as DNA accessibility and chromatin structure play a crucial role in governing cell-specific gene expression. Recent studies have identified particular chromatin modifications that define functionally distinct cis regulatory elements. Among these are forms of histone 3 that are mono- or tri-methylated at lysine 4 (H3K4me1 or H3K4me3, respectively), which bind preferentially to promoter and enhancer elements in the mammalian genome. In this work, we investigated whether these modified histones could similarly identify cis regulatory elements within the zebrafish genome. By applying chromatin immunoprecipitation followed by deep sequencing, we find that H3K4me1 and H3K4me3 are enriched at transcriptional start sites in the genome of the developing zebrafish embryo and that this association correlates with gene expression. We further find that these modifications associate with distal non-coding conserved elements, including known active enhancers. Finally, we demonstrate that it is possible to utilize H3K4me1 and H3K4me3 binding profiles in combination with available expression data to computationally identify relevant cis regulatory sequences flanking syn-expressed genes in the developing embryo. Taken together, our results indicate that H3K4me1 and H3K4me3 generally mark cis regulatory elements within the zebrafish genome and indicate that further characterization of the zebrafish using this approach will prove valuable in defining transcriptional networks in this model system.
journal_name
Dev Bioljournal_title
Developmental biologyauthors
Aday AW,Zhu LJ,Lakshmanan A,Wang J,Lawson NDdoi
10.1016/j.ydbio.2011.03.007subject
Has Abstractpub_date
2011-09-15 00:00:00pages
450-62issue
2eissn
0012-1606issn
1095-564Xpii
S0012-1606(11)00156-4journal_volume
357pub_type
杂志文章abstract::The sizes of amino acid pools in growing Xenopus laevis oocytes have been measured. The total free amino acid content per oocyte increases nearly 25-fold during oocyte growth. Together, glutamic acid and aspartic acid account for approximately 59-75% of the total amino acid pool in Xenopus oocytes. On the other hand, ...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/0012-1606(87)90480-5
更新日期:1987-11-01 00:00:00
abstract::During Drosophila oogenesis, activation of Notch signaling in the follicular epithelium (FE) around stage 6 of oogenesis is essential for entry into the endocycle and a series of other changes such as cell differentiation and migration of subsets of the follicle cells. Notch induces the expression of zinc finger prote...
journal_title:Developmental biology
pub_type: 杂志文章
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更新日期:2014-08-01 00:00:00
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journal_title:Developmental biology
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journal_title:Developmental biology
pub_type: 杂志文章
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更新日期:2018-03-01 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
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abstract::A fusion gene construct containing the bacterial chloramphenicol acetyltransferase (CAT) gene under the control of CyIIIa actin gene regulatory sequences was injected into unfertilized eggs of the urchin Strongylocentrotus purpuratus, and early pluteus stage embryos that developed from these eggs were fixed and sectio...
journal_title:Developmental biology
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abstract::A careful reanalysis of the literature indicates that the initial mechanism of activation in sea urchin eggs is remarkably similar to the mechanism established in medaka eggs: i.e., sea urchin eggs are activated by a qualitatively and quantitatively similar calcium explosion; one which is propagated in a wave sustaine...
journal_title:Developmental biology
pub_type: 杂志文章,评审
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abstract::The germ-line cells of many animals possess a characteristic cytoplasmic structure termed nuage or germinal granules. In mice, nuage that is prominent in postnatal male germ cells is also called intermitochondrial cement or chromatoid bodies. TDRD1/MTR-1, which contains Tudor domain repeats, is a specific component of...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2006.10.046
更新日期:2007-01-01 00:00:00
abstract::Leaf primordia, first visible as small bumps, are produced in a cyclical pattern at the edges of the shoot apex, a smooth region at the top of the stem. Their formation is a biomechanical process. This review first considers hypothetical construction mechanisms and then summarizes research that provides information ab...
journal_title:Developmental biology
pub_type: 杂志文章,评审
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2006.04.454
更新日期:2006-09-15 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2006.07.032
更新日期:2006-11-15 00:00:00
abstract::Although the formation and maintenance of epithelial tubes are essential for the viability of multicellular organisms, our understanding of the molecular and cellular events coordinating tubulogenesis is relatively limited. Here, we focus on the activities of Ribbon, a novel BTB-domain containing nuclear protein, in t...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2008.05.541
更新日期:2008-08-01 00:00:00
abstract::An increase in the incidence of aneuploidy is well documented with increasing maternal age, in particular in human females. Remarkably, little is known regarding the underlying molecular basis for the age-associated increase in aneuploidy, which is a major source of decreased fertility in humans. Using mouse as a mode...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2008.01.048
更新日期:2008-04-15 00:00:00
abstract::Serendipity delta (sry delta) is a member of a set of Drosophila zinc finger protein genes showing maximal transcription during oogenesis. By using transformant lines, we monitored the zygotic expression of the sry delta gene and characterized some biochemical properties of a sry delta/beta-galactosidase fusion protei...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/0012-1606(89)90272-8
更新日期:1989-12-01 00:00:00
abstract::Thrombospondin type 1 repeat (TSR) superfamily members regulate diverse biological activities ranging from cell motility to inhibition of angiogenesis. In this study, we verified that mouse protein O-fucosyltransferase-2 (POFUT2) specifically adds O-fucose to TSRs. Using two Pofut2 gene-trap lines, we demonstrated tha...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2010.07.008
更新日期:2010-10-01 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2009.11.022
更新日期:2010-01-15 00:00:00
abstract::Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2016.06.003
更新日期:2017-06-15 00:00:00
abstract::The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2018.09.023
更新日期:2019-04-15 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/0012-1606(86)90352-0
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journal_title:Developmental biology
pub_type: 杂志文章
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journal_title:Developmental biology
pub_type: 杂志文章
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更新日期:2011-08-15 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
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更新日期:2014-07-01 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2010.03.012
更新日期:2010-06-15 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2013.09.025
更新日期:2013-12-01 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/0012-1606(83)90311-1
更新日期:1983-03-01 00:00:00
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journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2019.08.006
更新日期:2019-12-01 00:00:00
abstract::Recently, it has been suggested that a mouse sperm-associated protein with properties similar to the inhibitory guanine nucleotide-binding regulatory protein Gi plays an intermediary role in the zona pellucida-induced acrosome reaction (Endo, Y., Lee, M. A., and Kopf, G. S. 1987. Dev. Biol. 119, 210-216). In the prese...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/0012-1606(88)90157-1
更新日期:1988-09-01 00:00:00
abstract::The Xenopus helix-loop-helix transcription factor Hairy2 is essential for neural crest progenitor survival and maintains cells in a mitotic undifferentiated pre-neural crest state. However, its mode of action remains largely unknown. Here we show that a Hairy2 DNA-binding mutant is unable to promote cell survival and ...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1016/j.ydbio.2008.07.026
更新日期:2008-10-15 00:00:00
abstract::Tissue specificity of cell adhesion was directly characterized in a unit cell interaction using a novel laser trapping cell manipulator in combination with a fixed micropipet. We quantified the adhesive specificity of endodermal and ectodermal epithelial cells from Hydra, which are known to sort out within hours after...
journal_title:Developmental biology
pub_type: 杂志文章
doi:10.1006/dbio.1994.1068
更新日期:1994-03-01 00:00:00