In-silico Study of Transcription Factor Binding Elements of Human PAX Gene Family Members

Rashmi; Singh, V. K.; Gangopadhyay, A. N.; Shah, G. L.; Khanna, A.; Mohapatra, T. M.; Shankar, Om; Singh, Royana
October 2013
Trends in Bioinformatics;2013, Vol. 6 Issue 3, p62
Academic Journal
PAX gene family members, tissue specific transcription factors mainly involved in the formation of tissues and organs during embryonic development and has important role in transcriptional regulation. The presence of consensus paired domain play significant role in DNA-binding transcription regulation with PAX domain. Regulatory behavior of PAX family members were determined using cis-acting elements study and repeat identification. The study helped in investigating the potential conserved motifs in the paired domain. Further, investigation of cis-acting elements was done to elucidate the function for each PAX members and then repeat analyses and their correlation with functional elements were done. The study illustrates that the cis-acting elements are involved in tissue specific developmental expression and transcriptional regulation of PAX family members. Further, based on physiochemical property study of these PAX gene family members it was found that they are mainly Ser, Pro, Gly and Ala rich amino acids. It was found that repeats containing functional DNA motifs interact with signature motifs of paired domain. The mam six signature motifs NQLGG, NGRPLP, RPC, SR, GGVSKIL and PGAIGGSKP are involved in interaction. Altogether, this study provides new insights into the regulatory behavior of upstream region of each PAX members and its effect in transcriptional regulation and developmental expression of these PAX members with involvement in disease management.


Related Articles

  • LIM homeobox protein 5 (Lhx5) is essential for mamillary body development. Miquelajáuregui, Amaya; Sandoval-Schaefer, Teresa; Martínez-Armenta, Miriam; Pérez-Martínez, Leonor; Cárabez, Alfonso; Yangu Zhao; Heide, Michael; Alvarez-Bolado, Gonzalo; Varela-Echavarría, Alfredo; Shimamura, Kenji; Morales-Delgado, Nicanor // Frontiers in Neuroanatomy;Oct2015, Vol. 9, p1 

    The mamillary body (MM) is a group of hypothalamic nuclei related to memory and spatial navigation that interconnects hippocampal, thalamic, and tegmental regions. Here we demonstrate that Lhx5, a LIM-HD domain transcription factor expressed early in the developing posterior hypothalamus, is...

  • TALEs of genome targeting. Boch, Jens // Nature Biotechnology;Feb2011, Vol. 29 Issue 2, p135 

    The article discusses two studies on the use of transcription activator-like effectors (TALEs) from the pathogenic bacterium Xanthomonas for genome targeting. The studies demonstrated how TALEs can be engineered to virtually bind any DNA sequence. They also showed how much of the protein can be...

  • The Basis for Evolution of DNA-Binding Specificity of the Aft1 Transcription Factor in Yeasts. Gonçalves, Isabelle R.; Conde e. Silva, Natalia; Garay, Cesar La Torre; Lesuisse, Emmanuel; Camadro, Jean Michel; Blaiseau, Pierre Louis // Genetics;Jan2014, Vol. 196 Issue 1, p149 

    The Saccharomyces cerevisiae Aft1 and Kluyveromyces lactis KlAft are orthologous yeast transcription activators that regulate the expression of the same group of iron-uptake genes but bind to the different DNA sites: TGCACCC for Aft1 and PuCACCC for KlAft. To establish whether the DNA-binding...

  • TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets. Glenwinkel, Lori; Di Wu; Minevich, Gregory; Hobert, Oliver // Genetics;May2014, Vol. 197 Issue 1, p61 

    The identification of the regulatory targets of transcription factors is central to our understanding of how transcription factors fulfill their many key roles in development and homeostasis. DNA-binding sites have been uncovered for many transcription factors through a number of experimental...

  • Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions. Feldmann, Angelika; Ivanek, Robert; Murr, Rabih; Gaidatzis, Dimos; Burger, Lukas; Schübeler, Dirk // PLoS Genetics;Dec2013, Vol. 9 Issue 12, p1 

    Distal regulatory elements, including enhancers, play a critical role in regulating gene activity. Transcription factor binding to these elements correlates with Low Methylated Regions (LMRs) in a process that is poorly understood. Here we ask whether and how actual occupancy of DNA-binding...

  • Morris Water Maze Training in Mice Elevates Hippocampal Levels of Transcription Factors Nuclear Factor (Erythroid-derived 2)-like 2 and Nuclear Factor Kappa B p65. Snow, Wanda M.; Pahlavan, Payam S.; Djordjevic, Jelena; McAllister, Danielle; Platt, Eric E.; Alashmali, Shoug; Bernstein, Michael J.; Miyoung Suh; Albensi, Benedict C.; Baojin Ding; Morris, Brian // Frontiers in Molecular Neuroscience;Nov2015, Vol. 8, p1 

    Research has identified several transcription factors that regulate activity-dependent plasticity and memory, with cAMP-response element binding protein (CREB) being the most well-studied. In neurons, CREB activation is influenced by the transcription factor nuclear factor kappa B (NF-kB),...

  • Targeting G with TAL Effectors: A Comparison of Activities of TALENs Constructed with NN and NK Repeat Variable Di-Residues. Christian, Michelle L.; Demorest, Zachary L.; Starker, Colby G.; Osborn, Mark J.; Nyquist, Michael D.; Yong Zhang; Carlson, Daniel F.; Bradley, Philip; Bogdanove, Adam J.; Voytas, Daniel F.; Shuang-yong Xu // PLoS ONE;Sep2012, Vol. 7 Issue 9, Special section p1 

    The DNA binding domain of Transcription Activator-Like (TAL) effectors can easily be engineered to have new DNA sequence specificities. Consequently, engineered TAL effector proteins have become important reagents for manipulating genomes in vivo. DNA binding by TAL effectors is mediated by...

  • Structure-function analyses of the human SIX1-EYA2 complex reveal insights into metastasis and BOR syndrome. Patrick, Aaron N; Cabrera, Joshua H; Smith, Anna L; Chen, Xiaojiang S; Ford, Heide L; Zhao, Rui // Nature Structural & Molecular Biology;Apr2013, Vol. 20 Issue 4, p447 

    SIX1 interacts with EYA to form a bipartite transcription factor essential for mammalian development. Loss of function of this complex causes branchio-oto-renal (BOR) syndrome, whereas re-expression of SIX1 or EYA promotes metastasis. Here we describe the 2.0-Ã… structure of SIX1 bound to...

  • Distinct DNA Binding Sites Contribute to the TCF Transcriptional Switch in C. elegans and Drosophila. Bhambhani, Chandan; Ravindranath, Aditi J.; Mentink, Remco A.; Chang, Mikyung V.; Betist, Marco C.; Yang, Yaxuan X.; Koushika, Sandhya P.; Korswagen, Hendrik C.; Cadigan, Ken M. // PLoS Genetics;Feb2014, Vol. 10 Issue 2, p1 

    Regulation of gene expression by signaling pathways often occurs through a transcriptional switch, where the transcription factor responsible for signal-dependent gene activation represses the same targets in the absence of signaling. T-cell factors (TCFs) are transcription factors in the...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics