Comparative studies of gene regulatory networks involved in brain development

Abstract

Human genome is enriched with thousands of conserved non-coding elements (CNEs). Medium throughput strategies were employed to analyze the ability of human CNEs to drive tissue specific expression during mouse embryogenesis. These data led to the establishment of publicly available genome wide catalog of functionally defined human enhancers. Scattering of enhancers over larger regions in vertebrate genomes seriously impede attempts to pinpoint their precise target genes. Such associations are prerequisite to explore the significance of this in vivo characterized catalog of human enhancers in development, disease and evolution. Recent high throughput strategies like next generation sequencing and interpretation of epigenomic marks resulted in the rapid expansion of tissue specific genome wide cis-regulatory repertoire. The next step is to recruit for trans-regulatory elements for the development of specific tissue on the basis of this cis-regulatory repertoire. Results: This study is an attempt to systematically identify the target gene-bodies for functionally defined human CNE-enhancers. For the purpose we adopted the orthology/paralogy mapping approach and compared the CNE induced reporter expression with reported endogenous expression pattern of neighboring genes. This procedure pinpointed specific target gene-bodies for the total of 192 human CNE-enhancers. This enables us to gauge the maximum genomic search space for enhancer hunting: 4 Mb of genomic sequence around the gene of interest (2 Mb on either side). Narrowing down of our research we opted for forebrain as it is considered as a hub of evolution from non human primates to human because it is responsible for all the unique humanly attributes like speech, memory, thinking, intelligence etc. We devised a pipeline that uses computational and experimental information (high throughput data) to pin down transcription factors (TFs) that interact and interplay with each other in the prototyping of forebrain. For this purpose we used forebrain specific CNE-enhancers to infer that the forebrain specific gene expression is closely associated with the cooperative interaction among at least 23 distinct transcription factors. Conclusion: In conclusion, the systematic wiring of cis-acting sites and their target gene bodies is an important step to unravel the role of in vivo characterized catalog of human enhancers in development, physiology and medicine. Discovered forebrain specific TF code could be used as trained data set to hunt for genome wide forebrain specific cis regulatory elements. This automated pipe line could also be used to define any tissue specific TF code.