A. Ferdous - Academia.edu (original) (raw)

Papers by A. Ferdous

Circulation, Oct 31, 2006

Proceedings of the National Academy of Sciences, 2009

Recent studies support the existence of a common progenitor for the cardiac and endothelial cell ... more Recent studies support the existence of a common progenitor for the cardiac and endothelial cell lineages, but the underlying transcriptional networks responsible for specification of these cell fates remain unclear. Here we demonstrated that Ets-related protein 71 (Etsrp71), a newly discovered ETS family transcription factor, was a novel downstream target of the homeodomain protein, Nkx2–5. Using genetic mouse models and molecular biological techniques, we demonstrated that Nkx2–5 binds to an evolutionarily conserved Nkx2–5 response element in the Etsrp71 promoter and induces the Etsrp71 gene expression in vitro and in vivo. Etsrp71 was transiently expressed in the endocardium/endothelium of the developing embryo (E7.75-E9.5) and was extinguished during the latter stages of development. Using a gene disruption strategy, we found that Etsrp71 mutant embryos lacked endocardial/endothelial lineages and were nonviable. Moreover, using transgenic technologies and transcriptional and chr...

Circulation, 2011

Background— Recent studies suggest that the hematopoietic and cardiac lineages have close ontogen... more Background— Recent studies suggest that the hematopoietic and cardiac lineages have close ontogenic origins, and that an early mesodermal cell population has the potential to differentiate into both lineages. Studies also suggest that specification of these lineages is inversely regulated. However, the transcriptional networks that govern the cell fate specification of these progenitors are incompletely defined. Methods and Results— Here, we show that Nkx2-5 regulates the hematopoietic/erythroid fate of the mesoderm precursors early during cardiac morphogenesis. Using transgenic technologies to isolate Nkx2-5 expressing cells, we observed an induction of the erythroid molecular program, including Gata1 , in the Nkx2-5 –null embryos. We further observed that overexpression of Nkx2-5 with an Nkx2-5–inducible embryonic stem cell system significantly repressed Gata1 gene expression and suppressed the hematopoietic/erythroid potential, but not the endothelial potential, of the embryonic ...

Genes & Development, 1998

Nucleic acids symposium series, 1997

Comb-type polylysine copolymer having grafted hydrophilic side chains was newly designed as a nov... more Comb-type polylysine copolymer having grafted hydrophilic side chains was newly designed as a novel stabilizer of triplex DNAs. The comb-type copolymer elevated melting temperature of poly(dA).2poly(dT) triplex by 50 degrees C without affecting reversibility, melting and reassociation, of the triplex in buffer with physiological salt concentrations. The stabilizing effect of the copolymer was greater than spermine. Our results indicate that the molecular designing of polycation with comb-type structure is a successful strategy for creating an effective triplex stabilizer.

Nucleosides & nucleotides

Triplex-stabilizing effect of a graft copolymer under physiologically relevant conditions has bee... more Triplex-stabilizing effect of a graft copolymer under physiologically relevant conditions has been evaluated and compared with other polyamines. Here we show that the graft copolymer significantly stabilizes triplex DNAs with amazingly higher efficacy than that of physiological concentrations of spermine and spermidine.

Nucleic acids symposium series, 1997

Nucleic Acids Research, 1998

Triplex DNA formation involving unmodified triplexforming oligonucleotides (TFOs) is very unstabl... more Triplex DNA formation involving unmodified triplexforming oligonucleotides (TFOs) is very unstable under physiological conditions. Here, we report a novel strategy to stabilize both purine and pyrimidine motif triplex DNA within the rat α1 (I) collagen gene promoter under physiologically relevant conditions by a poly(L-lysine)-graft-dextran copolymer. Using an in vitro electrophoretic mobility shift assay, we show that the copolymer almost completely abrogates the inhibitory effects of physiological concentrations of monovalent cations, particularly potassium ion (K + ), on purine motif triplex formation involving very low concentrations of an unmodified guanine-rich TFO. Of importance, pH dependency in pyrimidine motif triplex formation involving an unmodified cytosine-rich TFO is also significantly overcome by the copolymer. Finally, the triplex-stabilizing efficiency of the copolymer is remarkably higher than that of other oligocations, like spermine and spermidine. We suggest that the ability of the graft copolymer to stabilize triplex DNA under physiologically relevant pH and salt concentrations will be a cue for further progress in the antigene strategy.

Nucleic Acids Research, 1996

We have developed a simple method to purify sequence-specific DNA-binding proteins directly from ... more We have developed a simple method to purify sequence-specific DNA-binding proteins directly from crude cell extracts by using DNA affinity latex beads. The method enabled us to purify not only DNA-binding proteins, but also their associated proteins. Using beads bearing the ATF/E4TF3 site from the adenovirus E4 gene promoter, a protein kinase activity was copurified with the ATF/E4TF3 family. We found that the kinase interacted with ATF1 in vitro efficiently. The kinase did not bind directly to DNA. The kinase mainly phosphorylated ATF1 on serine 36, which was one of target amino acids for casein kinase (CK) II. Biological features of the kinase were the same as those of CKII and an anti-CKII serum reacted with the kinase, indicating that the kinase was CKII. Moreover, it was clearly shown that one of CKII subunits, the CKII α protein bound to glutathione-S-transferase (GST) fusion ATF1 but not GST in vitro. It has been reported that a specific CKII inhibitor, 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) inhibits transcription by RNA polymerase II [Zandomeni et al., (1986) J. Biol. Chem. 261, 3414-3419]. Taken together, these results suggest that ATF/E4TF3 may recruit the CKII activity to a transcription initiation machinery and stimulate transcription.

Molecular Cell, 2001

that was first purified by Reinberg and coworkers based upon its ability to stimulate elongation ... more that was first purified by Reinberg and coworkers based upon its ability to stimulate elongation on chromatin templates (LeRoy et al., 1998). Subsequent biochemical studies by Handa and coworkers (Wada et al., 2000) revealed that FACT also stimulates elongation, even on nonchromatin templates, by at least one other mecha-University of Texas nism. FACT operates in concert with another factor, Southwestern Medical Center P-TEFb (positive transcription elongation factor) (Mar-5323 Harry Hines Boulevard shall et al., 1996) to counteract inhibition of elongation Dallas, Texas 75390-8573 by two negative factors DSIF (DRB sensitivity-inducing factor) (Wada et al., 1998) and NELF (negative elongation factor) (Yamaguchi et al., 1999). Summary Analysis of the two polypeptides that comprise mammalian FACT (Orphanides et al., 1999) revealed that they It is generally thought that the primary or even sole are the homologs of the yeast Cdc68/Spt16 (Malone et activity of the 19S regulatory particle of the 26S proteaal., 1991; Rowley et al., 1991) and Pob3 (Wittmeyer and some is to facilitate the degradation of polyubiquiti-Formosa, 1997) proteins. Cdc68 and Pob3 are known nated proteins by the 20S-core subunit. However, we to form a stable, nuclear-localized heterodimer in yeast present evidence that the 19S complex is required for (Wittmeyer et al., 1999). Genetic experiments in yeast efficient elongation of RNA polymerase II (RNAP II) in support the idea that FACT (Cdc68/Pob3) functions in vitro and in vivo. First, yeast strains carrying alleles of transcription elongation in vivo. Suppressor studies SUG1 and SUG2, encoding 19S components, exhibit demonstrated a genetic interaction between the Cdc68 phenotypes indicative of elongation defects. Second, and the elongation factors TFIIS and Spt4 (Orphanides in vitro transcription is inhibited by antibodies raised et al., 1999). The latter protein and an associated factor, against Sug1, or by heat-inactivating temperature-Spt5, are the yeast analogs of human DSIF (Hartzog et sensitive Sug1 mutants with restoration of elongation al., 1996) and regulate transcription elongation in vivo by addition of immunopurified 19S complex. Finally, (Hartzog et al., 1998). Thus, the genetic and biochemical Cdc68, a known elongation factor, coimmunoprecipidata present a consistent picture of these positive and tates with the 19S complex, indicating a physical internegative regulatory factors modulating elongation. action. Inhibition of the 20S proteolytic core of the The recent realization that Cdc68 is a transcription proteasome has no effect on elongation. This work elongation factor suggests another layer of complexity defines a nonproteolytic role for the 19S complex in in elongation. Xu et al. (1995) had demonstrated that the RNAP II transcription.

Journal of Pharmaceutical Sciences, 1998

0 By employing a reductive amination reaction between the -amino groups of poly(L-lysine) (PLL) a... more 0 By employing a reductive amination reaction between the -amino groups of poly(L-lysine) (PLL) and the reductive ends of the hydrophilic dextran (Dex) side chain, we have prepared different comb-type copolymers which varied in the degree of grafting and the length of the hydrophilic Dex chains. The resulting copolymers, poly-(L-lysine)-graft-dextran (PLL-g-Dex), were tested for their ability to stabilize triplex DNA in vitro under physiologically relevant conditions. Thermal denaturation (UV−T m ) and circular dichroism experiments revealed that the graft copolymer with the higher degree of grafting of long Dex chains significantly increased the thermal stability of triplex structure of poly(dA)‚2poly(dT) by more than 50°C without affecting the transition between triplex and single-stranded DNA or the native structure of DNA. Of importance is that when triplex formation involving a 30-mer target duplex from rat R1 (I) collagen promoter was analyzed by an in vitro electrophoretic mobility shift assay, the graft copolymer also remarkably diminished potassium inhibition of the purine motif triplex formation up to 200 mM as well as pH-dependence of the pyrimidine motif triplex formation. Moreover the triplex-stabilizing efficiency of the copolymer was significantly higher than that of other oligocations like spermine and spermidine. We suggest that a molecular design of comb-type copolymers consisting of various types of polycation backbones (e.g., PLL) grafted with different hydrophilic side chains (e.g., Dex) is a novel strategy to create efficient triplex stabilizers that will certainly shed light on possible in vivo application of the antigene strategy.

Journal of Biological Chemistry, 1999

Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use f... more Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use for artificial control of gene expression in vivo. Stabilization of the pyrimidine motif triplex at physiological pH is therefore of great importance in improving its therapeutic potential. To this end, isothermal titration calorimetry interaction analysis system and electrophoretic mobility shift assay have been used to explore the thermodynamic and kinetic effects of our previously reported triplex stabilizer, poly (L-lysine)-graft-dextran (PLL-g-Dex) copolymer, on pyrimidine motif triplex formation at physiological pH. Both the thermodynamic and kinetic analyses have clearly indicated that in the presence of the PLL-g-Dex copolymer, the binding constant of the pyrimidine motif triplex formation at physiological pH was about 100 times higher than that observed without any triplex stabilizer. Of importance, the triplex-promoting efficiency of the copolymer was more than 20 times higher than that of physiological concentrations of spermine, a putative intracellular triplex stabilizer. Kinetic data have also demonstrated that the observed copolymer-mediated promotion of the triplex formation at physiological pH resulted from the considerable increase in the association rate constant rather than the decrease in the dissociation rate constant. Our results certainly support the idea that the PLL-g-Dex copolymer could be a key material and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo.

Genes & Development, 2007

Recent studies have shown that the intersection between transcription and proteins involved in th... more Recent studies have shown that the intersection between transcription and proteins involved in the ubiquitin-proteasome pathway encompasses both proteolytic and nonproteolytic functions. Examples of the latter type include evidence that monoubiquitylation of some transcriptional activators stimulates their activity. In addition, the proteasomal ATPases are recruited to many active promoters through binding to activators and play an important, nonproteolytic role in promoter escape and elongation. In this study, we report the discovery of a new nonproteolytic activity of the proteasome (specifically the proteasomal ATPases): the active destabilization of activator-promoter complexes. This reaction depends on the presence of an activation domain and ATP. Destabilization is inhibited in vitro and in vivo if the protein is monoubiquitylated or if ubiquitin is genetically fused to the activator. The fact that monoubiquitylated activator is resistant to the "stripping" activity of the proteasomal ATPases may explain, in part, why some activators require this modification in order to function efficiently.

Genes & Development, 1998

Article cited in:

Development, 2011

Er71 mutant embryos are nonviable and lack hematopoietic and endothelial lineages. To further def... more Er71 mutant embryos are nonviable and lack hematopoietic and endothelial lineages. To further define the functional role for ER71 in cell lineage decisions, we generated genetically modified mouse models. We engineered an Er71-EYFP transgenic mouse model by fusing the 3.9 kb Er71 promoter to the EYFP reporter gene. Using FACS and transcriptional profiling, we examined the EYFP + population of cells in Er71 mutant and wild-type littermates. In the absence of ER71, we observed an increase in the number of EYFP-expressing cells, increased expression of the cardiac molecular program and decreased expression of the hematoendothelial program, as compared with wild-type littermate controls. We also generated a novel Er71-Cre transgenic mouse model using the same 3.9 kb Er71 promoter. Genetic fate-mapping studies revealed that the ER71-expressing cells give rise to the hematopoietic and endothelial lineages in the wild-type background. In the absence of ER71, these cell populations contributed to alternative mesodermal lineages, including the cardiac lineage. To extend these analyses, we used an inducible embryonic stem/embryoid body system and observed that ER71 overexpression repressed cardiogenesis. Together, these studies identify ER71 as a critical regulator of mesodermal fate decisions that acts to specify the hematopoietic and endothelial lineages at the expense of cardiac lineages. This enhances our understanding of the mechanisms that govern mesodermal fate decisions early during embryogenesis.

Circulation, Oct 31, 2006

Proceedings of the National Academy of Sciences, 2009

Circulation, 2011

Genes & Development, 1998

Nucleic acids symposium series, 1997

Nucleosides & nucleotides

Nucleic acids symposium series, 1997

Nucleic Acids Research, 1998

Nucleic Acids Research, 1996

Molecular Cell, 2001

Journal of Pharmaceutical Sciences, 1998

Journal of Biological Chemistry, 1999

Genes & Development, 2007

Genes & Development, 1998

Article cited in:

Development, 2011