Modulation of Gene Expression by Gene Architecture and Promoter Structure

Kumar, Aditya; Bansal, Manju

doi:10.5772/intechopen.76051

Cited by 3 publications

(4 citation statements)

References 107 publications

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“…at a well-defined location relative to the transcription initial sites. 20 The origins of replication have a similar chromatin environment and share some genetic features to that of transcription-activating sequences or promoters. 2 Mounting evidence showed that the Oris are inclined to sequence positions in the vicinity of transcriptional start sites (TSSs).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…DNA duplex stability or free energy of the fragment of DNA depends on hydrogen bonds between bases and the stacking interaction between consecutive bases and can be computed by summing the free energy of the constituent dinucleotides. 20 The melting temperature of a DNA fragment directly depends on DNA stability. A dinucleotide descriptor based on the collection of melting studies of 108 oligonucleotides 57 has been used for computing DNA stability.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…Smoothing windows with the size of 15 nucleotides (corresponding to 14 dinucleotide steps) for dinucleotide models and 30 nucleotides for tri or tetranucleotide structural descriptors were employed based on our previous studies. 18,20,21 Computation of Structural Motifs. A DNA G-quadruplex is defined as a four-stranded DNA structure that is composed of stacked guanine tetrads.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Delving into Eukaryotic Origins of Replication Using DNA Structural Features

et al. 2020

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DNA replication in eukaryotes is an intricate process, which is precisely synchronized by a set of regulatory proteins, and the replication fork emanates from discrete sites on chromatin called origins of replication (Oris). These spots are considered as the gateway to chromosomal replication and are stereotyped by sequence motifs. The cognate sequences are noticeable in a small group of entire origin regions or totally absent across different metazoans. Alternatively, the use of DNA secondary structural features can provide additional information compared to the primary sequence. In this article, we report the trends in DNA sequence-based structural properties of origin sequences in nine eukaryotic systems representing different families of life. Biologically relevant DNA secondary structural properties, namely, stability, propeller twist, flexibility, and minor groove shape were studied in the sequences flanking replication start sites. Results indicate that Oris in yeasts show lower stability, more rigidity, and narrow minor groove preferences compared to genomic sequences surrounding them. Yeast Oris also show preference for A-tracts and the promoter element TATA box in the vicinity of replication start sites. On the contrary, Drosophila melanogaster, humans, and Arabidopsis thaliana do not have such features in their Oris, and instead, they show high preponderance of G-rich sequence motifs such as putative G-quadruplexes or i-motifs and CpG islands. Our extensive study applies the DNA structural feature computation to delve into origins of replication across organisms ranging from yeasts to mammals and including a plant. Insights from this study would be significant in understanding origin architecture and help in designing new algorithms for predicting DNA trans-acting factor recognition events.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Delving into Eukaryotic Origins of Replication Using DNA Structural Features

et al. 2020

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“…BGN4+G1 exhibited the highest hydrolytic activity regardless of the incubation time, for which the enzyme activity was continuously 2.5 to 4.2 times higher than that of BGN4. Many previous studies reported that the consensus sequences (−35 and −10 regions) [38,39], spacer sequences [39,40], TG motif [41], UP elements [42] and the promoters' structural properties [43] can all affect the promoter strength. The promoters used in this study seem to differ in strength due to differences in those factors.…”

Section: Comparison Of Hydrolytic Activities Between Transformants An...mentioning

confidence: 99%

Cloning and Heterologous Expression of the ¥ -Galactosidase Gene from Bifidobacterium longum RD47 in B. bifidum BGN4

Park¹,

Park²,

Ji³

2019

Journal of Microbiology and Biotechnology

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The gene encoding β-galactosidase was cloned from Bifidobacterium longum RD47 with combinations of several bifidobacterial promoters, and expressed in B. bifidum BGN4. Among the recombinant bifidobacteria, BGN4+G1 showed the highest β-galactosidase level, for which the hydrolytic activity was continuously 2.5 to 4.2 times higher than that of BGN4 and 4.3 to 9.6 times higher than that of RD47. The β-galactosidase activity of BGN4+G1 was exceedingly superior to that of any of the other 35 lactic acid bacteria. When commercial whole milk and BGN4+G1 were reacted, BGN4+G1 removed nearly 50% of the lactose in the milk by the 63-h time point, and a final 61% at 93 h. These figures are about twice the lactose removal rate of conventional fermented milk. As for the reaction of commercial whole milk and crude enzyme extract from BGN4+G1, the β-galactosidase of BGN4+G1 eliminated 51% of the lactose in milk in 2 h. As shown below, we also compared the strengths and characteristics of the strong bifidobacterial promoters reported by previous studies.

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Association of Augmented Immune-Staining of G-Quadruplex Tertiary DNA Structure in Chemo-Tolerant TNBC with Downregulation of WNT/Epidermal Growth Factor Receptor Pathway Receptor Genes

Panda¹,

Islam²,

Basu³

et al. 2023

Journal of Radiation and Cancer Research

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Purpose: The aim of the study is to understand the involvement of G-Quadruplex (G-Q) structures in altering the expression profile of WNT/epidermal growth factor receptor (EGFR) pathway receptor genes in chemo-tolerant Triple Negative Breast Cancer (TNBC) samples. Materials and Methods: At first, Gene Expression Omnibus datasets were mined where the expression profile of WNT/EGFR pathway genes in TNBC samples and MDA-MB-231, a TNBC cell line, were checked in response to doxorubicin, a chemotherapeutic drug. Next, to unveil the probable mechanism of regulation, the presence of G-Q structure was checked in in silico study and later validated by immunohistochemical analyses in our pool of sample. These observed results were correlated with patient's demography and survival status. Results: Expression of the receptors (FZD7, LRP6, EGFR) of the WNT/EGFR pathway were found to be differentially expressed in TNBC samples; further emphasized in our samples (n = 61). Notably, these G-Q structures were found in the promoter region of the WNT pathway receptor genes (FZD7, LRP6, and EGFR). Validating in our patient sample pool, a significant increase in G-Q immunostaining was observed in samples, after neoadjuvant chemotherapy (NACT) samples (n = 17) than the pretherapeutic samples (n = 44). Similar pattern of G-Q immunostaining was noticed in doxorubicin-treated MDA-MB-231 cell line. Intriguingly, low staining of G-Q among the pretherapeutic samples, but NACT TNBC samples, was found to be significantly correlated with lymph node metastasis. Conclusions: This study showed that the augmented immunostaining of G-Q structure might have an important involvement in regulating the expression pattern of the WNT/EGFR pathway genes in response to doxorubicin treatment of TNBC.

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Modulation of Gene Expression by Gene Architecture and Promoter Structure

Cited by 3 publications

References 107 publications

Delving into Eukaryotic Origins of Replication Using DNA Structural Features

Delving into Eukaryotic Origins of Replication Using DNA Structural Features

Cloning and Heterologous Expression of the ¥ -Galactosidase Gene from Bifidobacterium longum RD47 in B. bifidum BGN4

Association of Augmented Immune-Staining of G-Quadruplex Tertiary DNA Structure in Chemo-Tolerant TNBC with Downregulation of WNT/Epidermal Growth Factor Receptor Pathway Receptor Genes

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