scholarly journals Patchy Interspecific Sequence Similarities Efficiently Identify Positive cis-Regulatory Elements in the Sea Urchin

2002 ◽  
Vol 246 (1) ◽  
pp. 148-161 ◽  
Author(s):  
Chiou-Hwa Yuh ◽  
C.Titus Brown ◽  
Carolina B. Livi ◽  
Lee Rowen ◽  
Peter J.C. Clarke ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Regulatory Elements ◽  
Sequence Similarities

scholarly journals Correct Expression of spec2a in the Sea Urchin Embryo Requires Both Otx and Other cis-Regulatory Elements

2001 ◽  
Vol 232 (2) ◽  
pp. 424-438 ◽  
Author(s):  
Chiou-Hwa Yuh ◽  
Xiaotao Li ◽  
Eric H Davidson ◽  
William H Klein
Keyword(s):  
Sea Urchin ◽  
Regulatory Elements ◽  
Sea Urchin Embryo ◽  
Correct Expression

scholarly journals Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene

2004 ◽  
Vol 273 (2) ◽  
pp. 436-453 ◽  
Author(s):  
Sandeep Dayal ◽  
Takae Kiyama ◽  
Jeffrey T. Villinski ◽  
Ning Zhang ◽  
Shuguang Liang ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Repetitive Sequence ◽  
Regulatory Elements

scholarly journals Cis-regulatory control of the SM50 gene, an early marker of skeletogenic lineage specification in the sea urchin embryo

Development ◽  
1995 ◽  
Vol 121 (7) ◽  
pp. 1957-1970 ◽  
Author(s):  
K.W. Makabe ◽  
C.V. Kirchhamer ◽  
R.J. Britten ◽  
E.H. Davidson
Keyword(s):  
Transcription Start Site ◽  
Sea Urchin ◽  
Regulatory Elements ◽  
Regulatory Control ◽  
Control Element ◽  
Start Site ◽  
Transcription Start ◽  
Sequence Element ◽  
Spatial Control ◽  
Sea Urchin Embryo

The SM50 gene encodes a minor matrix protein of the sea urchin embryo spicule. We carried out a detailed functional analysis of a cis-regulatory region of this gene, extending 440 bp upstream and 120 bp downstream of the transcription start site, that had been shown earlier to confer accurate skeletogenic expression of an injected expression vector. The distal portion of this fragment contains elements controlling amplitude of expression, while the region from −200 to +105 contains spatial control elements that position expression accurately in the skeletogenic lineages of the embryo. A systematic mutagenesis analysis of this region revealed four adjacent regulatory elements, viz two copies of a positively acting sequence (element D) that are positioned just upstream of the transcription start site; an indispensable spatial control element (element C) that is positioned downstream of the start site; and further downstream, a second positively acting sequence (element A). We then constructed a series of synthetic expression constructs. These contained oligonucleotides representing normal and mutated versions of elements D, C, and A, in various combinations. We also changed the promoter of the SM50 gene from a TATA-less to a canonical TATA box form, without any effect on function. Perfect spatial regulation was also produced by a final series of constructs that consisted entirely of heterologous enhancers from the CyIIIa gene, the SV40 early promoter, and synthetic D, C, and A elements. We demonstrate that element C exercises the primary spatial control function of the region we analyzed. We term this a ‘locator’ element. This differs from conventional ‘tissue-specific enhancers’ in that while it is essential for expression, it has no transcriptional activity on its own, and it requires other, separable, positive regulatory elements for activity. In the normal configuration these ancillary positive functions are mediated by elements A and D. Only positively acting control elements were observed in the SM50 regulatory domain throughout this analysis.

scholarly journals Identification of cis-regulatory elements involved in transcriptional regulation of the sea urchin SpFoxB gene

2005 ◽  
Vol 47 (7) ◽  
pp. 461-470 ◽  
Author(s):  
Elizabeth-Sharon Fung ◽  
Carey Thurm ◽  
Rae Reuille ◽  
Barbara Brede ◽  
Brian T. Livingston
Keyword(s):  
Transcriptional Regulation ◽  
Sea Urchin ◽  
Regulatory Elements

scholarly journals Identification and prediction of developmental enhancers in sea urchin embryos

2021 ◽  
Author(s):  
Cesar Arenas-Mena ◽  
Sofija Miljovska ◽  
Sevinc Ercan ◽  
Tanvi Shashikant ◽  
Charles G. Danko ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Transcriptional Activation ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Model Organisms ◽  
Enhancer Activity ◽  
Pol Ii ◽  
Sea Urchin Embryos ◽  
Genomic Regions

The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins. We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos. ATAC-seq, PRO-seq, and Pol II ChIP-seq from early and late blastula embryos are manually contrasted with experimental cis-regulatory analyses available in sea urchin embryos, with particular attention to common developmental regulatory elements known to have enhancer and silencer functions differentially deployed among embryonic territories. Using the three functional genomic data types, machine learning models are trained and tested to classify and quantitatively predict the enhancer activity of several hundred genomic regions previously validated with reporter constructs in vivo. Overall, chromatin accessibility and transcription have substantial power for predicting enhancer activity. For promoter-overlapping cis-regulatory elements in particular, the distribution of Pol II is the best predictor of enhancer activity in blastula embryos. Furthermore, ATAC- and PRO-seq predictive value is stage dependent for the promoter-overlapping subset. This suggests that the sequence of regulatory mechanisms leading to transcriptional activation have distinct relevance at different levels of the developmental gene regulatory hierarchy deployed during embryogenesis.

Proximal cis-regulatory elements of sea urchin arylsulfatase gene

1998 ◽  
Vol 40 (5) ◽  
pp. 537-544 ◽  
Author(s):  
Hiroko Koike ◽  
Koji Akasaka ◽  
Keiko Mitsunaga-Nakatsubo ◽  
Hiraku Shimada
Keyword(s):  
Sea Urchin ◽  
Regulatory Elements
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