scholarly journals Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development

2006 ◽  
Vol 300 (1) ◽  
pp. 74-89 ◽  
Author(s):  
Meredith Howard-Ashby ◽  
Stefan C. Materna ◽  
C. Titus Brown ◽  
Lili Chen ◽  
R. Andrew Cameron ◽  
...  
2018 ◽  
Vol 61 (2) ◽  
pp. 85-96 ◽  
Author(s):  
Hongwei Xun ◽  
Zhibing Zhang ◽  
Yunxiao Zhou ◽  
Xueyan Qian ◽  
Yingshan Dong ◽  
...  

2019 ◽  
Author(s):  
Olivera Grujic ◽  
Tanya N. Phung ◽  
Soo Bin Kwon ◽  
Adriana Arneson ◽  
Yuju Lee ◽  
...  

AbstractAnnotations of evolutionarily constraint provide important information for variant prioritization. Genome-wide maps of epigenomic marks and transcription factor binding provide complementary information for interpreting a subset of such prioritized variants. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the human genome being in a constrained non-exonic element from over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting constrained non-exonic bases from such data. However, a subset of such bases are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) using conservation state and constrained element annotations that is predictive of those bases. Using human genetic variation, regulatory sequence motifs, mouse epigenomic data, and retrospectively considered additional human data we further characterize the nature of constrained non-exonic bases with low CNEP scores.


2018 ◽  
Vol 86 (2) ◽  
pp. 235-249 ◽  
Author(s):  
Haoqiang Yu ◽  
Wenqi Feng ◽  
Fuai Sun ◽  
YuanYuan Zhang ◽  
JingTao Qu ◽  
...  

Development ◽  
2000 ◽  
Vol 127 (11) ◽  
pp. 2447-2459 ◽  
Author(s):  
S.M. Robertson ◽  
M. Kennedy ◽  
J.M. Shannon ◽  
G. Keller

In this report, we describe the identification and characterization of an early embryoid body-derived colony, termed the transitional colony, which contains cell populations undergoing the commitment of mesoderm to the hematopoietic and endothelial lineages. Analysis of individual transitional colonies indicated that they express Brachyury as well as flk-1, SCL/tal-1, GATA-1, (beta)H1 and (beta)major reflecting the combination of mesodermal, hematopoietic and endothelial populations. This pattern differs from that found in the previously described hemangioblast-derived blast cell colonies in that they typically lacked Brachyury expression, consistent with their post-mesodermal stage of development (Kennedy, M., Firpo, M., Choi, K., Wall, C., Robertson, S., Kabrun, N. and Keller, G. (1997) Nature 386, 488–493). Replating studies demonstrated that transitional colonies contain low numbers of primitive erythroid precursors as well as a subset of precursors associated with early stage definitive hematopoiesis. Blast cell colonies contain higher numbers and a broader spectrum of definitive precursors than found in the transitional colonies. ES cells homozygous null for the SCL/tal-1 gene, a transcription factor known to be essential for development of the primitive and definitive hematopoietic systems, were not able to form blast colonies but did form transitional colonies. Together these findings suggest that the transitional colony represents a stage of development earlier than the blast cell colony and one that uniquely defines the requirement for a functional SCL/tal-1 gene for the progression to hematopoietic commitment.


2006 ◽  
Vol 282 (8) ◽  
pp. 5761-5769 ◽  
Author(s):  
Charles A. S. Banks ◽  
Stephanie E. Kong ◽  
Henrik Spahr ◽  
Laurence Florens ◽  
Skylar Martin-Brown ◽  
...  

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