A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks

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Title: A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks
Author: Bhinge, Akshay Anant
Abstract: It has been suggested that organismal complexity correlates with the complexity of gene regulation . Transcriptional control of gene expression is mediated by binding of regulatory proteins to cis -acting sequences on the genome . Hence , it is crucial to identify the chromosomal targets of transcription factors (TFs ) to delineate transcriptional regulatory networks underlying gene expression programs . The development of ChIP -chip technology has enabled high throughput mapping of TF binding sites across the genome . However , there are many limitations to the technology including the availability of whole genome arrays for complex organisms such human or mouse . To circumvent these limitations , we developed the Sequence Tag Analysis of Genomic Enrichment (STAGE ) methodology that is based on extracting short DNA sequences or “tags” from ChIP -enriched DNA . With improvements in sequencing technologies , we applied the recently developed ChIP -Seq technique i .e . ChIP followed by ultra high throughput sequencing , to identify binding sites for the TF E2F4 across the human genome . We identified previously uncharacterized E2F4 binding sites in intergenic regions and found that several microRNAs are potential E2F4 targets . Binding of TFs to their respective chromosomal targets requires access of the TF to its regulatory element , which is strongly influenced by nucleosomal remodeling . In order to understand nucleosome remodeling in response to transcriptional perturbation , we used ultra high throughput sequencing to map nucleosome positions in yeast that were subjected to heat shock or were grown normally . We generated nucleosome remodeling profiles across yeast promoters and found that specific remodeling patterns correlate with specific TFs active during the transcriptional reprogramming . Another important aspect of gene regulation operates at the post -transcriptional level . MicroRNAs (miRNAs ) are ~22 nucleotide non -coding RNAs that suppress translation or mark mRNAs for degradation . MiRNAs regulate TFs and in turn can be regulated by TFs . We characterized a TF -miRNA network involving the oncofactor Myc and the miRNA miR -22 that suppresses the interferon pathway as primary fibroblasts enter a stage of rapid proliferation . We found that miR -22 suppresses the interferon pathway by inhibiting nuclear translocation of the TF NF -kappaB . Our results show how the oncogenic TF Myc cross -talks with other TF regulatory pathways via a miRNA intermediary .
URI: http : / /hdl .handle .net /2152 /6533
Date: 2009-10-15

Citation

A functional genomics approach to map transcriptional and post-transcriptional gene regulatory networks. Doctoral dissertation, The University of Texas at Austin. Available electronically from http : / /hdl .handle .net /2152 /6533 .

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