The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex

Abstract G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1–7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.

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Duplex formation in a G-quadruplex bulge

Nucleic Acids Research ◽

10.1093/nar/gkaa738 ◽

2020 ◽

Vol 48 (18) ◽

pp. 10567-10575 ◽

Cited By ~ 1

Author(s):

Thi Quynh Ngoc Nguyen ◽

Kah Wai Lim ◽

Anh Tuân Phan

Keyword(s):

Base Pair ◽

Solution Structure ◽

Biological Significance ◽

Consensus Definition ◽

Quadruplex Structure ◽

G Quadruplex ◽

Structural Details ◽

The Stability ◽

Definition Of ◽

Duplex Formation

Abstract Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex–duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.

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Gene expression profiling of ATL patients: compilation of disease-related genes and evidence for TCF4 involvement in BIRC5 gene expression and cell viability

Blood ◽

10.1182/blood-2008-08-175901 ◽

2009 ◽

Vol 113 (17) ◽

pp. 4016-4026 ◽

Cited By ~ 56

Author(s):

Cynthia A. Pise-Masison ◽

Michael Radonovich ◽

Kathleen Dohoney ◽

John C. Morris ◽

Deirdre O'Mahony ◽

...

Keyword(s):

Gene Expression ◽

Cell Viability ◽

Cyclin B1 ◽

Leukemic Cells ◽

Leukemia Cells ◽

Nuclear Antigen ◽

Adult T Cell Leukemia ◽

Reporter Assays ◽

And Function ◽

Proliferating Cell

Abstract Adult T-cell leukemia/lymphoma (ATL) is an aggressive and fatal disease. We have examined 32 patients with smoldering, chronic, lymphoma and acute leukemia using Affymetrix HG-U133A2.0 arrays. Using the BRB array program, we identified genes differentially expressed in leukemia cells compared with normal lymphocytes. Several unique genes were identified that were overexpressed in leukemic cells, including TNFSF11, RGS13, MAFb, CSPG2, C/EBP-α, and TCF4; 200 of the most highly overexpressed ATL genes were analyzed by the Pathway Studio, version 4.0 program. ATL leukemia cells were characterized by an increase in genes linked to “central” genes CDC2/cyclin B1, SYK/LYN, proliferating cell nuclear antigen, and BIRC5. Because of its potential therapeutic importance, we focused our studies on the regulation and function of BIRC5, whose expression was increased in 13 of 14 leukemia samples. TCF4 reporter assays and transfection of DN-TCF4 demonstrated that TCF4 regulates BIRC5 gene expression. Functionally, transfection of ATL cells with BIRC5 shRNA decreased BIRC5 expression and cell viability 80%. Clinical treatment of ATL patients with Zenapax or bortezomib decreased BIRC5 expression and cell viability. These experiments represent the first direct experimental evidence that BIRC5 plays an important role in ATL cell viability and provides important insight into ATL genesis and potential targeted therapies.

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Neddylation, an Emerging Mechanism Regulating Cardiac Development and Function

Frontiers in Physiology ◽

10.3389/fphys.2020.612927 ◽

2020 ◽

Vol 11 ◽

Author(s):

Jie Li ◽

Jianqiu Zou ◽

Rodney Littlejohn ◽

Jinbao Liu ◽

Huabo Su

Keyword(s):

Quality Control ◽

Protein Quality ◽

Cardiac Development ◽

Current Knowledge ◽

Biological Significance ◽

Protein Quality Control ◽

Pathogenic Factors ◽

Health And Disease ◽

The Stability ◽

And Function

Defects in protein quality control have been increasingly recognized as pathogenic factors in the development of heart failure, a persistent devastating disease lacking efficacious therapies. Ubiquitin and ubiquitin-like proteins, a family of post-translational modifying polypeptides, play important roles in controlling protein quality by maintaining the stability and functional diversity of the proteome. NEDD8 (neural precursor cell expressed, developmentally downregulated 8), a small ubiquitin-like protein, was discovered two decades ago but until recently the biological significance of NEDD8 modifications (neddylation) in the heart has not been appreciated. In this review, we summarize the current knowledge of the biology of neddylation, highlighting several mechanisms by which neddylation regulates the function of its downstream targets, and discuss the expanding roles for neddylation in cardiac physiology and disease, with an emphasis on cardiac protein quality control. Finally, we outline challenges linked to the study of neddylation in health and disease.

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A carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteome

Scientific Reports ◽

10.1038/s41598-020-71672-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sushmitha Vijaya Kumar ◽

Paul E. Abraham ◽

Gregory B. Hurst ◽

Karuna Chourey ◽

Amber N. Bible ◽

...

Keyword(s):

Protein Composition ◽

Membrane Properties ◽

Membrane Microdomains ◽

Plant Colonization ◽

Membrane Organization ◽

Protein Distribution ◽

Cellular Functions ◽

Pellicle Formation ◽

The Stability ◽

And Function

Abstract Membrane organization plays an important role in signaling, transport, and defense. In eukaryotes, the stability, organization, and function of membrane proteins are influenced by certain lipids and sterols, such as cholesterol. Bacteria lack cholesterol, but carotenoids and hopanoids are predicted to play a similar role in modulating membrane properties. We have previously shown that the loss of carotenoids in the plant-associated bacteria Pantoea sp. YR343 results in changes to membrane biophysical properties and leads to physiological changes, including increased sensitivity to reactive oxygen species, reduced indole-3-acetic acid secretion, reduced biofilm and pellicle formation, and reduced plant colonization. Here, using whole cell and membrane proteomics, we show that the deletion of carotenoid production in Pantoea sp. YR343 results in altered membrane protein distribution and abundance. Moreover, we observe significant differences in the protein composition of detergent-resistant membrane fractions from wildtype and mutant cells, consistent with the prediction that carotenoids play a role in organizing membrane microdomains. These data provide new insights into the function of carotenoids in bacterial membrane organization and identify cellular functions that are affected by the loss of carotenoids.

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Long non-coding RNAs in regulation of adipogenesis and adipose tissue function

eLife ◽

10.7554/elife.59053 ◽

2020 ◽

Vol 9 ◽

Author(s):

Tiziana Squillaro ◽

Gianfranco Peluso ◽

Umberto Galderisi ◽

Giovanni Di Bernardo

Keyword(s):

Gene Expression ◽

Adipose Tissue ◽

Drug Targets ◽

Metabolic Diseases ◽

Tissue Development ◽

Cellular Functions ◽

Adipose Tissue Development ◽

And Function

Complex interaction between genetics, epigenetics, environment, and nutrition affect the physiological activities of adipose tissues and their dysfunctions, which lead to several metabolic diseases including obesity or type 2 diabetes. Here, adipogenesis appears to be a process characterized by an intricate network that involves many transcription factors and long noncoding RNAs (lncRNAs) that regulate gene expression. LncRNAs are being investigated to determine their contribution to adipose tissue development and function. LncRNAs possess multiple cellular functions, and they regulate chromatin remodeling, along with transcriptional and post-transcriptional events; in this way, they affect gene expression. New investigations have demonstrated the pivotal role of these molecules in modulating white and brown/beige adipogenic tissue development and activity. This review aims to provide an update on the role of lncRNAs in adipogenesis and adipose tissue function to promote identification of new drug targets for treating obesity and related metabolic diseases.

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Coordinated genomic control of ciliogenesis and cell movement by RFX2

eLife ◽

10.7554/elife.01439 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 73

Author(s):

Mei-I Chung ◽

Taejoon Kwon ◽

Fan Tu ◽

Eric R Brooks ◽

Rakhi Gupta ◽

...

Keyword(s):

Gene Expression ◽

Control Cell ◽

Cell Movement ◽

Genomic Analysis ◽

Apical Surface ◽

Biological Processes ◽

Cellular Functions ◽

Genomic Control ◽

And Function

The mechanisms linking systems-level programs of gene expression to discrete cell biological processes in vivo remain poorly understood. In this study, we have defined such a program for multi-ciliated epithelial cells (MCCs), a cell type critical for proper development and homeostasis of the airway, brain and reproductive tracts. Starting from genomic analysis of the cilia-associated transcription factor Rfx2, we used bioinformatics and in vivo cell biological approaches to gain insights into the molecular basis of cilia assembly and function. Moreover, we discovered a previously un-recognized role for an Rfx factor in cell movement, finding that Rfx2 cell-autonomously controls apical surface expansion in nascent MCCs. Thus, Rfx2 coordinates multiple, distinct gene expression programs in MCCs, regulating genes that control cell movement, ciliogenesis, and cilia function. As such, the work serves as a paradigm for understanding genomic control of cell biological processes that span from early cell morphogenetic events to terminally differentiated cellular functions.

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RNA modifications modulate gene expression during development

Science ◽

10.1126/science.aau1646 ◽

2018 ◽

Vol 361 (6409) ◽

pp. 1346-1349 ◽

Cited By ~ 147

Author(s):

Michaela Frye ◽

Bryan T. Harada ◽

Mikaela Behm ◽

Chuan He

Keyword(s):

Gene Expression ◽

Rna Structure ◽

Messenger Rna ◽

Normal Development ◽

Biological Processes ◽

Rna Modifications ◽

Transfer Rnas ◽

Mrna Metabolism ◽

Global Protein Synthesis ◽

And Function

RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programs. They affect diverse eukaryotic biological processes, and the correct deposition of many of these modifications is required for normal development. Messenger RNA (mRNA) modifications regulate various aspects of mRNA metabolism. For example,N6-methyladenosine (m6A) affects the translation and stability of the modified transcripts, thus providing a mechanism to coordinate the regulation of groups of transcripts during cell state maintenance and transition. Similarly, some modifications in transfer RNAs are essential for RNA structure and function. Others are deposited in response to external cues and adapt global protein synthesis and gene-specific translational accordingly and thereby facilitate proper development.

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Ultrasound Imaging of Gene Expression in Mammalian Cells

10.1101/580647 ◽

2019 ◽

Cited By ~ 4

Author(s):

Arash Farhadi ◽

Gabrielle H. Ho ◽

Daniel P. Sawyer ◽

Raymond W. Bourdeau ◽

Mikhail G. Shapiro

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

Reporter Genes ◽

Tissue Imaging ◽

Cellular Functions ◽

Cellular Processes ◽

Deep Tissue Imaging ◽

And Function ◽

Expression In Mammalian Cells

ABSTRACTThe study of cellular processes occurring inside intact organisms and the development of cell-based diagnostic and therapeutic agents requires methods to visualize cellular functions such as gene expression in deep tissues. Ultrasound is a widely used biomedical technology enabling deep-tissue imaging with high spatial and temporal resolution. However, no genetically encoded molecular reporters are available to connect ultrasound contrast to gene expression in mammalian cells. To address this limitation, we introduce the first mammalian acoustic reporter genes. Starting with an eleven-gene polycistronic gene cluster derived from bacteria, we engineered a eukaryotic genetic program whose introduction into mammalian cells results in the expression of a unique class of intracellular air-filled protein nanostructures called gas vesicles. The scattering of ultrasound by these nanostructures allows mammalian cells to be visualized at volumetric densities below 0.5%, enables the monitoring of dynamic circuit-driven gene expression, and permits high-resolution imaging of gene expression in living animals. These mammalian acoustic reporter genes enable previously impossible approaches to monitoring the location, viability and function of mammalian cellsin vivo.

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Correction to ‘The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex’

Nucleic Acids Research ◽

10.1093/nar/gkab1140 ◽

2021 ◽

Author(s):

Subramaniyam Ravichandran ◽

Maria Razzaq ◽

Nazia Parveen ◽

Ambarnil Ghosh ◽

Kyeong Kyu Kim

Keyword(s):

Gene Expression ◽

Hairpin Loop ◽

G Quadruplex ◽

Expression Activity

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The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.783889 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yang Liu ◽

Xinting Zhu ◽

Kejia Wang ◽

Bo Zhang ◽

Shuyi Qiu

Keyword(s):

Molecular Mechanisms ◽

Secondary Structures ◽

Biological Processes ◽

Cellular Functions ◽

General Introduction ◽

Rna Sequences ◽

Study Methods ◽

G Quadruplex ◽

And Function

G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.

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