Mentor: Dr. Leonard Lipovich
My research utilizes computational methods to characterize the contribution of long non-coding RNA transcripts to network regulation, development and disease etiology. LncRNAs may regulate networks through sense-antisense (SAS) interactions with transcription factors (TFs) or epigenetic modifiers (EMs). Sense-antisense (SAS) pairing occurs when exonic sequence is shared by two genes on opposite genomic strands. LncRNAs may also be co-regulated with, auto-regulate or be regulated by mRNAs with which they share bi-directional promoters (BDPs). SAS pairing and BDPs may be found on different ends of the same transcript and therefore organize multiple loci into a single, complex locus with multiple context-dependent regulatory dimensions. Cis-regulation of mRNAs by SAS or BDP lncRNAs can be through post-transcriptional or epigenetic mechanisms, while trans-regulation occurs when proteins, such as TFs, encoded by SAS or BDP mRNAs, exert their effects in the cell.
Currently, I am working on a model to describe and predict the relationship between lncRNA-mRNA SAS pairs, BDPs and regulatory networks: CUBE (Cis-trans Ubiquity & Bi-directional Expression), in which the genomic context of SAS lncRNAs creates a multidimensional regulatory space where cis-trans regulatory networks operate concurrently. We are using manual annotation as well as programmatic whole-genome automated methods to test CUBE in several species utilizing various collaborative datasets including the FANTOM5 Consortium’s comprehensive human hCAGE dataset, GENCODE’s RNA database and other non-coding, multiple individual collaborations within Wayne State University: as well as using several public data repositories including the University of Santa Cruz’s Genome Browser.
Awards and Recognitions
2010 – Dean’s Enhancement for Academic Achievement
2011 – Membership, FANTOM5 Consortium. FANTOM is an international consortium coordinated from RIKEN Omics Science Center, Yokohama Japan, whose goals are to generate both a map of the majority of human promoters and comparative models of transcriptional regulatory network models of each cellular state.
2011 – Poster Presentation at Cell Symposia: Regulatory RNAs, Chicago, IL.
Title: Presence and genomic structure of long non-coding RNA genes: no conservation between human and mouse.
2011 – Membership, ENCyclopaedia Of DNA Elements (ENCODE) Analysis Working Group. is a public research consortium project of The National Human Genome Research Institute, whose goal is to identify all functional elements in the human genome sequence.
2011 – Invited Oral Presentation at RIKENomics Science Center, Yokohama, Japan, during FANTOM5 Koyo Meeting.
Title: F5 hCAGE co-expressed sense-antisense mRNA-lncRNA pairs contain key transcriptional regulators: implications for cis- and trans-regulatory network.
2011 – Appointment to their Review Editorial Board of the journal Frontiers in Non-Coding RNA.
2011/2012 – Funded by American Center Society IRG Research Grant, PI Lipovich