Paramjeet Singh Bagga,  Ph.D.

Research Projects and Important Findings

Go Home Research Projects and Important Findings Publications The Polyadenylation Complex The DSEF-1 Protein DSEF-1 Purification dsef-1 cloning strategy

Bioinformatics/Genomics of a Conserved RNA Element:

The goal of research in my lab has been to study interactions between cellular proteins and conserved ‘G’-rich sequences (GRSs) that can influence human gene expression. Altered gene expression can consequently lead to a myriad of health problems ranging from cancer, genetic disorders, developmental disorders to blood and heart diseases. Studying regulation of gene expression, therefore, is important for a better understanding of mechanisms underlying these health defects. We have previously shown that a conserved ‘G’ rich sequence found in the polyadenylation regions of human genes can mediate efficient 3’end processing of mammalian pre-mRNAs (Bagga et. al., 1995, 1998). We have also cloned a human gene the product of which, DSEF1/hnRNP H’, binds to GRS in order to influence gene expression at this level. Our preliminary bioinformatics analysis suggests that GRS is present in the polyadenylation region of a significant number of human genes (Bagga et. al., 1995, Arhin et. al., 2002).

G-quadruplex Structure and RNA Processing:

More recent bioinformatics studies performed in my lab at Ramapo College with the help of undergraduate students have revealed the presence of GRS sequences near RNA processing sites of a significant number of human and mouse genes (conference presentations by students). According to these studies, it appears that a special type of GRS, that is capable of forming a highly stable G-quadruplex structure, is involved in differential RNA processing by helping the cell decide which site should be used for processing in a tissue and time specific manner. However, detailed bioinformatics and molecular biology investigations are required to test this hypothesis.

G-quadruplexes in Untranslated Regions:

Undergraduate research in my lab has also indicated the presence of potential G-qudruplexes in the untranslated regions (UTRs) of eukaryotic mRNAs. We believe that G-quadruplex motifs may help regulate gene expression at post-transcriptional levels in the cytoplasm. Specific interactions between RNA binding proteins and cis- acting elements in 5’- and 3’- UTRs are known to be responsible for regulating essential biological activities, such as mRNA localization, mRNA turnover, and translation efficiency. Detailed bioinformatics and molecular biology investigations are required to test our hypotheses.

What is a G-quadruplex?
G-quadruplex Structure
A G-quadruplex 		The quadruplex structures formed by guanine rich nucleic acid sequences have received significant attention recently because of increasing evidence for their role in important biological processes and as therapeutic targets.The G-quadruplex structure is formed by repeated folding of either the single polynucleotide molecule or by association of two or four molecules. The structure consists of stacked G-tetrads, which are square co-planar arrays of four guanine bases each. G-quadruplex is stabilized with cyclic Hoogsteen hydrogen bonding between the four guanines within each tetrad. G-quadruplex sequence motifs have been reported in telomeric, promoter and other regions of mammalian genomes. G-quadruplex DNA has been suggested to regulate DNA replication and may control cellular proliferation. G- rich sequences capable of forming G-quadruplexes in the RNA have been implicated in a variety of important biological activities, such as mRNA turnover , Fragile X Mental Retardation Protein (FMRP) binding, translation initiation as well as repression.

Computational Tools for Studying G-quadruplexes:

Defining the role of Quadruplex forming G Rich Sequences (QGRS) in differential RNA processing and identifying the proteins that can interact with them would aid in understanding the mechanism of regulation of gene expression, especially differential gene expression. A detailed investigation into the distribution of G-quadruplex sequences near RNA processing sites can provide valuable insights. Similarly, identifying cis- regulatory G-quadruplex motifs in 5’- and 3’-UTRs of mRNAs can also help explore the role of G-quadruplex structures in the regulation of gene expression at a post-transcriptional level. However, these efforts would require a systematic large-scale analysis of mammalian genes.

My lab has adopted a computational approach to achieve our goals. We have developed computational methods (D'Antonio and Bagga, 2004) and computational tools for mapping putative QGRS (QGRS Mapper: Kikin et. al., 2006) in mammalian genes. We are also developing databases (GRSDB: Kostadinov et. al., 2006; GRSDB2 & GRS_UTRdb: Kikin et. al., 2007) for curation and further computation of the data. The computational suite is being used to conduct detailed bioinformatics studies on the distribution patterns of QGRS near biologically important sites of thousands of mammalian genes. In particular, we are investigating whether there is a correlation between the distribution pattern of QGRS and alternative processing. We are also studying the conservation of G-quadruplex motifs in untranslated regions and their association with human diseases. This project involves active participation by undergraduate students of the college, especially during the winter and summer breaks.

Top G-Q Resource QGRS Mapper GRSDB GRS_UTRdb Home

Structure-Function Analysis of DSEF-1:

The objective of these research studies has been to construct a structure-function map of DSEF-1, an auxiliary polyadenylation factor that we have cloned. Computer based structure predictions have identified three putative RNA Recognition Motifs (RRMs) and two glycine rich auxiliary domains in this protein. However, functional significance of these predicted structures in the DSEF-1 protein is still unknown. Aligning DSEF-1 protein sequence  with those of closely related proteins has helped to identify other regions which could be functionally significant as well (Bagga et. al., 1998). DSEF-1 mediates efficient 3’end processing of all the mammalian pre-mRNAs and is indicated to play a key role in regulating the gene expression at this step.

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DSEF-1 - GRS Interactions and Regulation of Mammalian Polyadenylation:

The aim of this research program has been to study RNA-protein interactions involved in the control of eukaryotic gene expression. For these studies we have chosen the interactions between a conserved sequence present in precursor as well as mature mRNAs and a human protein which specifically recognizes this downstream auxiliary sequence element.
Important findings:

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DNA Repair Mechanisms:

The aim of this research project was to study the DNA repair mechanisms that are operative in human cells. These studies involve DNA repair deficient cell lines originating from patients with heritable conditions such as Xeroderma Pigmentosum (XP) (prone to skin cancer) and Cockayne Syndrome (CS) exhibiting growth retardation and neurological degeneration. Some important accomplishments are:

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The Cellulase Enzyme Complex:

The research work performed towards my doctoral dissertation involved the analysis of production, regulation and purification of cellulase enzyme complex in Aspergillus nidulans.
Important findings:

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Go Home Research Projects and Important Findings Publications The Polyadenylation Complex The DSEF-1 Protein DSEF-1 Purification dsef-1 cloning strategy