scholarly journals Comparative genomics and evolution of regulons of the LacI-family transcription factors

2014 ◽  
Vol 5 ◽  
Author(s):  
Dmitry A. Ravcheev ◽  
Matvei S. Khoroshkin ◽  
Olga N. Laikova ◽  
Olga V. Tsoy ◽  
Natalia V. Sernova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Comparative Genomics ◽  
Laci Family

Deciphering the enigma of missing DNA binding domain of LacI family transcription factors

2021 ◽  
Vol 713 ◽  
pp. 109060
Author(s):  
Neetu Neetu ◽  
Madhusudhanarao Katiki ◽  
Jai Krishna Mahto ◽  
Monica Sharma ◽  
Anoop Narayanan ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Laci Family

scholarly journals Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

2008 ◽  
Vol 38 (1) ◽  
pp. 1-31 ◽  
Author(s):  
Lakshminarayan M. Iyer ◽  
Vivek Anantharaman ◽  
Maxim Y. Wolf ◽  
L. Aravind
Keyword(s):  
Transcription Factors ◽  
Comparative Genomics ◽  
Chromatin Proteins

scholarly journals Phylogenetic analysis of TALE superclass homeobox genes in amphipod crustaceans

2021 ◽  
Author(s):  
Wai Hoong Chang ◽  
Alvina G Lai
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Comparative Genomics ◽  
Homeobox Genes ◽  
Crustacean Species ◽  
Animal Development ◽  
Amphipod Crustacean

TALE class genes are a group of developmentally conserved transcription factors found in animals. Here, we describe the identification and phylogenetic analysis of TALE class genes in amphipod crustaceans. We identified 241 putative TALE class genes from 56 amphipod crustacean species. Phylogenetic analysis of the genes revealed six subclasses. We provide a list of FASTA sequences of the genes identified. Results from this work may inform future evolutionary and comparative genomics studies on animal development.

scholarly journals 3P305 Comparative Genomics of Eukaryotic Transcription Factors

2005 ◽  
Vol 45 (supplement) ◽  
pp. S280
Author(s):  
Y. Minezaki ◽  
K. Nishikawa
Keyword(s):  
Transcription Factors ◽  
Comparative Genomics ◽  
Eukaryotic Transcription

scholarly journals Engineering transcription factors with novel DNA-binding specificity using comparative genomics

2009 ◽  
Vol 37 (8) ◽  
pp. 2493-2503 ◽  
Author(s):  
Tasha A. Desai ◽  
Dmitry A. Rodionov ◽  
Mikhail S. Gelfand ◽  
Eric J. Alm ◽  
Christopher V. Rao
Keyword(s):  
Transcription Factors ◽  
Comparative Genomics ◽  
Dna Binding ◽  
Binding Specificity ◽  
Dna Binding Specificity

scholarly journals Machine learning study of DNA binding by transcription factors from the LacI family

2011 ◽  
Vol 45 (4) ◽  
pp. 667-679 ◽  
Author(s):  
G. G. Fedonin ◽  
A. B. Rakhmaninova ◽  
Yu. D. Korostelev ◽  
O. N. Laikova ◽  
M. S. Gelfand
Keyword(s):  
Machine Learning ◽  
Transcription Factors ◽  
Dna Binding ◽  
Learning Study ◽  
Laci Family

scholarly journals Comparative genomics reveals evolutionary drivers of sessile life and left-right shell asymmetry in bivalves

2021 ◽  
Author(s):  
Yang Zhang ◽  
Fan Mao ◽  
Shu Xiao ◽  
Haiyan Yu ◽  
Zhiming Xiang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Comparative Genomics ◽  
High Resolution ◽  
Larval Development ◽  
Expression Profiles ◽  
Homeobox Gene ◽  
Gene Families ◽  
Pinctada Fucata ◽  
Shell Formation ◽  
Related Gene

Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Evidence from comparative transcriptomics shows that the left-right asymmetrical C. hongkongensis plausibly diverged from the symmetrical Pinctada fucata in expression profiles marked by elevated activities of orthologous transcription factors and lineage-specific shell-related gene families including tyrosinases, which may cooperatively govern asymmetrical shell formation in Ostreoida oysters.

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