Limits...
Identification and characterization of novel human tissue-specific RFX transcription factors.

Aftab S, Semenec L, Chu JS, Chen N - BMC Evol. Biol. (2008)

Bottom Line: Five regulatory factor X (RFX) transcription factors (TFs)-RFX1-5-have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies.Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5.The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. saaftab@sfu.ca

ABSTRACT

Background: Five regulatory factor X (RFX) transcription factors (TFs)-RFX1-5-have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies.

Results: In this study, we have identified two additional RFX genes-RFX6 and RFX7-in the current human genome sequences. Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5. Phylogenetic analysis suggests that the RFX family in the human genome has undergone at least three gene duplications in evolution and the seven human RFX genes can be clearly categorized into three subgroups: (1) RFX1-3, (2) RFX4 and RFX6, and (3) RFX5 and RFX7. Our functional genomics analysis suggests that RFX6 and RFX7 have distinct expression profiles. RFX6 is expressed almost exclusively in the pancreatic islets, while RFX7 has high ubiquitous expression in nearly all tissues examined, particularly in various brain tissues.

Conclusion: The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.

Show MeSH

Related in: MedlinePlus

Mammalian RFX DBDs are highly conserved. DBDs from six mammalian RFX genes were aligned using ClustalW. The conservation of amino acid is depicted by a color gradient from the color yellow, which indicates low conservation, to red, which indicates high conservation. Nine residues that make direct or water-mediated DNA contacts are indicated with arrow heads. The species names included in this figure are abbreviated. They are: Mus–mouse (Mus musculus); Rno–Rat (Rattus norvegicus); Cfa–dog (Canis familiaris); Ptr–chimpanzee (Pan troglodytes); Mmu–monkey (Macaca mulatta) and Hsa–human (Homo sapiens).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2533330&req=5

Figure 1: Mammalian RFX DBDs are highly conserved. DBDs from six mammalian RFX genes were aligned using ClustalW. The conservation of amino acid is depicted by a color gradient from the color yellow, which indicates low conservation, to red, which indicates high conservation. Nine residues that make direct or water-mediated DNA contacts are indicated with arrow heads. The species names included in this figure are abbreviated. They are: Mus–mouse (Mus musculus); Rno–Rat (Rattus norvegicus); Cfa–dog (Canis familiaris); Ptr–chimpanzee (Pan troglodytes); Mmu–monkey (Macaca mulatta) and Hsa–human (Homo sapiens).

Mentions: To confirm that the two novel human RFX genes–RFX6 and RFX7 are indeed RFX TFs, we further examined their DBDs by aligning them with DBDs from RFX1-5 protein sequences. As expected, the DBDs of RFX6 and RFX7 align well with those of RFX1-5 (Figure 1). RFX TFs belong to the winged-helix family of DNA binding proteins because their DBDs are related in structure and function to the helix-turn-helix bacterial transcriptional regulatory proteins [30]. DBDs from RFX6 and RFX7 each contain one wing (W1), which is the same as DBDs from RFX1-5. W1 interacts with the major groove and another conserved fold H3 (helix 3) interacts with the minor groove of DNA. In particular, the nine residues in DBDs (Figure 1, indicated with arrow heads) that make direct or water-mediated DNA contacts [31] are almost entirely conserved in RFX6 and RFX7 (Figure 1) with a couple of minor exceptions. Of the nine residues, the human RFX7 DBD has two residues different from most of the other RFX DBDs. The first different residue is the first of the nine indicated residues. It is Lys in RFX7 DBD and RFX5 DBD, compared to Arg in DBDs of other RFX genes. Thus this difference is shared with the RFX5 DBD. The other different residue is the third of the nine residues. It is Lys in RFX7, compared to Arg at this site for DBDs of all other RFX genes. Because both Lys and Arg are basic amino acids, such substitutions are not expected to have dramatic impacts on the binding between the DBDs and their cognate binding sites. This high degree of conservation suggests that RFX6 and RFX7 may bind to similar if not identical cis-regulatory elements, i.e., the X-box motif [1]. Hence RFX6 and RFX7 are new members of the human RFX gene family with conserved DBDs.


Identification and characterization of novel human tissue-specific RFX transcription factors.

Aftab S, Semenec L, Chu JS, Chen N - BMC Evol. Biol. (2008)

Mammalian RFX DBDs are highly conserved. DBDs from six mammalian RFX genes were aligned using ClustalW. The conservation of amino acid is depicted by a color gradient from the color yellow, which indicates low conservation, to red, which indicates high conservation. Nine residues that make direct or water-mediated DNA contacts are indicated with arrow heads. The species names included in this figure are abbreviated. They are: Mus–mouse (Mus musculus); Rno–Rat (Rattus norvegicus); Cfa–dog (Canis familiaris); Ptr–chimpanzee (Pan troglodytes); Mmu–monkey (Macaca mulatta) and Hsa–human (Homo sapiens).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2533330&req=5

Figure 1: Mammalian RFX DBDs are highly conserved. DBDs from six mammalian RFX genes were aligned using ClustalW. The conservation of amino acid is depicted by a color gradient from the color yellow, which indicates low conservation, to red, which indicates high conservation. Nine residues that make direct or water-mediated DNA contacts are indicated with arrow heads. The species names included in this figure are abbreviated. They are: Mus–mouse (Mus musculus); Rno–Rat (Rattus norvegicus); Cfa–dog (Canis familiaris); Ptr–chimpanzee (Pan troglodytes); Mmu–monkey (Macaca mulatta) and Hsa–human (Homo sapiens).
Mentions: To confirm that the two novel human RFX genes–RFX6 and RFX7 are indeed RFX TFs, we further examined their DBDs by aligning them with DBDs from RFX1-5 protein sequences. As expected, the DBDs of RFX6 and RFX7 align well with those of RFX1-5 (Figure 1). RFX TFs belong to the winged-helix family of DNA binding proteins because their DBDs are related in structure and function to the helix-turn-helix bacterial transcriptional regulatory proteins [30]. DBDs from RFX6 and RFX7 each contain one wing (W1), which is the same as DBDs from RFX1-5. W1 interacts with the major groove and another conserved fold H3 (helix 3) interacts with the minor groove of DNA. In particular, the nine residues in DBDs (Figure 1, indicated with arrow heads) that make direct or water-mediated DNA contacts [31] are almost entirely conserved in RFX6 and RFX7 (Figure 1) with a couple of minor exceptions. Of the nine residues, the human RFX7 DBD has two residues different from most of the other RFX DBDs. The first different residue is the first of the nine indicated residues. It is Lys in RFX7 DBD and RFX5 DBD, compared to Arg in DBDs of other RFX genes. Thus this difference is shared with the RFX5 DBD. The other different residue is the third of the nine residues. It is Lys in RFX7, compared to Arg at this site for DBDs of all other RFX genes. Because both Lys and Arg are basic amino acids, such substitutions are not expected to have dramatic impacts on the binding between the DBDs and their cognate binding sites. This high degree of conservation suggests that RFX6 and RFX7 may bind to similar if not identical cis-regulatory elements, i.e., the X-box motif [1]. Hence RFX6 and RFX7 are new members of the human RFX gene family with conserved DBDs.

Bottom Line: Five regulatory factor X (RFX) transcription factors (TFs)-RFX1-5-have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies.Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5.The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. saaftab@sfu.ca

ABSTRACT

Background: Five regulatory factor X (RFX) transcription factors (TFs)-RFX1-5-have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies.

Results: In this study, we have identified two additional RFX genes-RFX6 and RFX7-in the current human genome sequences. Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5. Phylogenetic analysis suggests that the RFX family in the human genome has undergone at least three gene duplications in evolution and the seven human RFX genes can be clearly categorized into three subgroups: (1) RFX1-3, (2) RFX4 and RFX6, and (3) RFX5 and RFX7. Our functional genomics analysis suggests that RFX6 and RFX7 have distinct expression profiles. RFX6 is expressed almost exclusively in the pancreatic islets, while RFX7 has high ubiquitous expression in nearly all tissues examined, particularly in various brain tissues.

Conclusion: The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.

Show MeSH
Related in: MedlinePlus