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Campo V.A.,Institute Of Recherches Cliniques Of Montreal | Campo V.A.,University of Montreal | Patenaude A.-M.,Institute Of Recherches Cliniques Of Montreal | Kaden S.,ETH Zurich | And 7 more authors.
Nucleic Acids Research

The mammalian antibody repertoire is shaped by somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin (Ig) loci of B lymphocytes. SHM and CSR are triggered by non-canonical, error-prone processing of G/U mismatches generated by activation-induced deaminase (AID). In birds, AID does not trigger SHM, but it triggers Ig gene conversion (GC), a 'homeologous' recombination process involving the Ig variable region and proximal pseudogenes. Because recombination fidelity is controlled by the mismatch repair (MMR) system, we investigated whether MMR affects GC in the chicken B cell line DT40. We show here that Msh6-/- and Pms2-/- DT40 cells display cell cycle defects, including genomic re-replication. However, although IgVk GC tracts in MMR-deficient cells were slightly longer than in normal cells, Ig GC frequency, donor choice or the number of mutations per sequence remained unaltered. The finding that the avian MMR system, unlike that of mammals, does not seem to contribute towards the processing of G/U mismatches in vitro could explain why MMR is unable to initiate Ig GC in this species, despite initiating SHM and CSR in mammalian cells. Moreover, as MMR does not counteract or govern Ig GC, we report a rare example of 'homeologous' recombination insensitive to MMR. © The Author(s) 2013. Source

Bilogan C.K.,Bell Center for Regenerative Biology and Tissue Engineering | Bilogan C.K.,Brown University | Horb M.E.,Bell Center for Regenerative Biology and Tissue Engineering | Horb M.E.,Brown University

Pancreas-specific transcription factor 1a (Ptf1a), a bHLH transcription factor, has two temporally distinct functions during pancreas development; initially it is required for early specification of the entire pancreas, while later it is required for proper differentiation and maintenance of only acinar cells. The importance of Ptf1a function was revealed by the fact that loss of Ptf1a leads to pancreas agenesis in humans. While Ptf1a is one of the most important pancreatic transcription factors, little is known about the differences between the regulatory networks it controls during initial specification of the pancreas as opposed to acinar cell development, and to date no comprehensive analysis of its downstream targets has been published. In this article, we use Xenopus embryos to identify putative downstream targets of Ptf1a. We isolated anterior endoderm tissue overexpressing Ptf1a at two early stages, NF32 and NF36, and compared their gene expression profiles using microarrays. Our results revealed that Ptf1a regulates genes with a wide variety of functions, providing insight into the complexity of the regulatory network required for pancreas specification. © 2012 Wiley Periodicals, Inc. Source

Bilogan C.K.,Bell Center for Regenerative Biology and Tissue Engineering | Horb M.E.,Bell Center for Regenerative Biology and Tissue Engineering

Defining the regulatory molecular networks involved in patterning the developing anterior endoderm is essential to understand how the pancreas, liver, stomach, and duodenum are discretely specified from each other. In this study, we analyzed the expression and function of the double-stranded RNA-binding protein Staufen2 in Xenopus laevis endoderm. We found that staufen2 was broadly expressed within the developing endoderm beginning at gastrulation becoming localized to the anterior endoderm at later stages. Through morpholino-mediated knockdown, we demonstrate that Staufen2 function is required for proper formation of the stomach, liver, and pancreas. We define that its function is required during gastrulation for proper patterning of the dorsal-ventral axis and that it acts to regulate expression of BMP signaling components. © 2011 Wiley Periodicals, Inc. Source

Fischer A.H.L.,Bell Center for Regenerative Biology and Tissue Engineering | Smith J.,Bell Center for Regenerative Biology and Tissue Engineering
Integrative and Comparative Biology

Advanced genomics tools enable powerful new strategies for understanding complex biological processes, including development. By extension, we should be able to use these methods in a comparative fashion to capture evolutionary mechanisms. This requires a capacity to go deep and broad, to analyze developmental gene regulatory networks in many organisms, especially nontraditional models. As we usher in a new era of next-generation GRN (gene regulatory network) analysis, it is important to ask how to evaluate the evolution of network interactions. Particularly problematic, as always, is defining "independence": Are two character traits found together because they are functionally linked or because of historical accident? The same basic question applies to understanding developmental GRN evolution. However, the essential difference here is that a GRN defines a causal chain of events. An understanding of causal relations - how Genes A and B work in concert to drive expression of Genes C and D to create a new Territory E - gives hope for establishing "trait independence" in a way that purely correlative arguments - the association of the expression of Gene D in Territory E - never could. Insight into causality provides the key to interpretation, as seen in this simplified scenario. Real-world networks bring new degrees of complexity, but the elucidation of causal relations remains the same. Has the day arrived when a single laboratory has the wherewithal to conduct multiorganism gene network projects in parallel? No. However, we argue that day is closer than one might suppose. We describe how a speedboat GRN project in one's favorite nonmodel organism(s) might look and provide a framework for comparative network analysis. © 2012 The Author 2012. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com. Source

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