Biological networks can be used to functionally annotate genes based on interaction profile similarities. Metrics known as association indices can be used to quantify interaction profile similarity. We provide an overview of commonly used association indices, including Jaccard and Pearson Correlation Coefficient, and compare their performance in different types of analyses. We introduce a web tool (‘GAIN’ - Guide for Association Index for Networks) to calculate and compare interaction profile similarities, and to define modules of genes with similar profiles.

Follicular regulatory T (Tfr) cells have specialized roles in modulating Tfh help to B cells. However, the precise role of Tfr cells in controlling antibody responses to foreign and autoantigens in vivo is still unclear due to a lack of specific tools. We developed a Tfr-deleter mouse that selectively deletes Tfr cells, facilitating temporal studies. We found Tfr cells regulate early, but not late, germinal center (GC) responses to control antigen-specific antibody and B cell memory. Deletion of Tfr cells also resulted in increased self-reactive IgG and IgE. The increased IgE levels led us to interrogate the role of Tfr cells in house dust mite (HDM) models. We found Tfr cells control Tfh13 cell-induced IgE. In vivo, loss of Tfr cells increased HDM-specific IgE and lung inflammation. Thus, Tfr cells control IgG and IgE responses to vaccines, allergens and autoantigens and exert critical immunoregulatory functions prior to GC formation. Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

A major challenge in systems biology is to understand the gene regulatory networks that drive development, physiology and pathology. Interactions between transcription factors and regulatory genomic regions provide the first level of gene control. Gateway-compatible yeast one-hybrid (Y1H) assays present a convenient method to identify and characterize the repertoire of transcription factors that can bind a DNA sequence of interest. To delineate genome-scale regulatory networks, however, large sets of DNA fragments need to be processed at high throughput and high coverage. Here, we present “enhanced” Y1H (eY1H) assays that utilize a robotic mating platform with a set of improved Y1H reagents and automated readout quantification. We demonstrate that eY1H assays provide excellent coverage and identify interacting transcription factors for multiple DNA fragments in a short amount of time. eY1H assays will be an important tool for gene regulatory network mapping in Caenorhabditis elegans and other model organisms, as well as humans.

SUMMARY Gene duplication results in two identical paralogs that diverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C. elegans transcription factors (TFs) within and across four newly delineated molecular networks. Remarkably, we find that even highly similar TFs often have different interaction degree and partners. In addition, we find that most TF families have a member that is highly connected in multiple networks. Further, different TF families have opposing correlations between network connectivity and phylogenetic age, suggesting that they are subject to different evolutionary pressures. Finally, TFs that have similar partners in one network generally do not in another, indicating a lack of pressure to retain cross-network similarity. Our multiparameter analyses provide an unprecedented glimpse into the evolutionary dynamics that shaped TF networks.

MicroRNAs (miRNAs) are small evolutionarily conserved regulatory RNAs that modulate mRNA stability and translation in a wide range of cell types. MiRNAs are involved in a broad array of biological processes, including cellular proliferation, differentiation, and apoptosis. To identify previously unidentified regulators of miRNA, we initiated a systematic discovery-type proteomic analysis of the miRNA pathway interactome in human cells. Six of 66 genes identified in our proteomic screen were capable of regulating lethal-7a (let-7a) miRNA reporter activity. Tripartite motif 65 (TRIM65) was identified as a repressor of miRNA activity. Detailed analysis indicates that TRIM65 interacts and colocalizes with trinucleotide repeat containing six (TNRC6) proteins in processing body-like structures. Ubiquitination assays demonstrate that TRIM65 is an ubiquitin E3 ligase for TNRC6 proteins. The combination of overexpression and knockdown studies establishes that TRIM65 relieves miRNA-driven suppression of mRNA expression through ubiquitination and subsequent degradation of TNRC6.RNA-induced silencing complex | protein interaction networks | GW proteinsM icroRNAs (miRNAs) are small noncoding RNAs that regulate the translation and stability of mRNA in animals and plants (1, 2). The canonical biogenesis of miRNAs starts with a hairpin-like primary miRNA (primiRNA), typically a product of RNA polymerase II (3, 4). In the nucleus, the DROSHA/DGCR8 microprocessor complex recognizes and cleaves the primiRNA hairpin, which leads to release of a precursor miRNA (premiRNA) hairpin that is ∼55-70 nt in length (5-7). The premiRNA is exported to the cytoplasm by a complex of Exportin 5 and RAN-GTP (8, 9). In the cytoplasm, the premiRNA terminal loop is cleaved by DICER in collaboration with TARBP2, yielding ∼22-nt RNA duplexes. One strand of the duplex is preferentially incorporated into the RNAinduced silencing complex (RISC), where the miRNA and mRNA interact (3). In the RISC, miRNA targets mRNA for translational repression, deadenylation, or degradation (10-12).The RISC minimally consists of two core protein components, Argonaute (AGO) and trinucleotide repeat containing six (TNRC6; also known as GW182) proteins or their paralogs, which are key factors for function of the RISC. These proteins localize in specialized cytoplasmic foci known as mRNA processing bodies (P-bodies) (13, 14). P-bodies also contain effector molecules that facilitate mRNA degradation, including decapping enzymes (DCP1 and DCP2) required for miRNA-mediated gene silencing (15) and the CCR4-NOT deadenylase complex, which removes poly(A) from messages destabilized by miRNA (15).The core proteins that participate in miRNA biogenesis and regulation have been identified (6,(16)(17)(18)(19)(20), but the global organization and coordination of this system are incompletely understood. To explore the miRNA protein-protein interaction network systematically, we initiated a global proteomic analysis of the miRNA pathway interactome (MPI) in human cells. Analysis of 40 MPI-...