scholarly journals Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 519 ◽  
Author(s):  
Mun-Kit Choy ◽  
Mehregan Movassagh ◽  
Hock-Guan Goh ◽  
Martin R Bennett ◽  
Thomas A Down ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Factor Binding ◽  
Genome Wide ◽  
Transcription Factor Binding Motifs

scholarly journals Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm

2003 ◽  
Vol 19 (Suppl 1) ◽  
pp. i169-i176 ◽  
Author(s):  
O. Johansson ◽  
W. Alkema ◽  
W. W. Wasserman ◽  
J. Lagergren
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Genome Sequences ◽  
Binding Motifs ◽  
Factor Binding ◽  
Transcription Factor Binding Motifs

scholarly journals MEDEA: analysis of transcription factor binding motifs in accessible chromatin

2020 ◽  
Vol 30 (5) ◽  
pp. 736-748
Author(s):  
Luca Mariani ◽  
Kathryn Weinand ◽  
Stephen S. Gisselbrecht ◽  
Martha L. Bulyk
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Factor Binding ◽  
Transcription Factor Binding Motifs ◽  
Accessible Chromatin

scholarly journals Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1435
Author(s):  
Yu-Chin Lien ◽  
Paul Zhiping Wang ◽  
Xueqing Maggie Lu ◽  
Rebecca A. Simmons
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Factor Binding ◽  
Intrauterine Growth ◽  
Gene Dysregulation ◽  
Genome Wide

Intrauterine growth retardation (IUGR), which induces epigenetic modifications and permanent changes in gene expression, has been associated with the development of type 2 diabetes. Using a rat model of IUGR, we performed ChIP-Seq to identify and map genome-wide histone modifications and gene dysregulation in islets from 2- and 10-week rats. IUGR induced significant changes in the enrichment of H3K4me3, H3K27me3, and H3K27Ac marks in both 2-wk and 10-wk islets, which were correlated with expression changes of multiple genes critical for islet function in IUGR islets. ChIP-Seq analysis showed that IUGR-induced histone mark changes were enriched at critical transcription factor binding motifs, such as C/EBPs, Ets1, Bcl6, Thrb, Ebf1, Sox9, and Mitf. These transcription factors were also identified as top upstream regulators in our previously published transcriptome study. In addition, our ChIP-seq data revealed more than 1000 potential bivalent genes as identified by enrichment of both H3K4me3 and H3K27me3. The poised state of many potential bivalent genes was altered by IUGR, particularly Acod1, Fgf21, Serpina11, Cdh16, Lrrc27, and Lrrc66, key islet genes. Collectively, our findings suggest alterations of histone modification in key transcription factors and genes that may contribute to long-term gene dysregulation and an abnormal islet phenotype in IUGR rats.

scholarly journals WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W412-W416 ◽  
Author(s):  
G. Wang ◽  
T. Yu ◽  
W. Zhang
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Factor Binding ◽  
Transcription Factor Binding Motifs

scholarly journals Negative selection maintains transcription factor binding motifs in human cancer

BMC Genomics ◽  
2016 ◽  
Vol 17 (S2) ◽  
Author(s):  
Ilya E. Vorontsov ◽  
Grigory Khimulya ◽  
Elena N. Lukianova ◽  
Daria D. Nikolaeva ◽  
Irina A. Eliseeva ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Negative Selection ◽  
Human Cancer ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Factor Binding ◽  
Transcription Factor Binding Motifs
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