The germinal center reaction depends on RNA methylation and divergent functions of specific methyl readers

Long-lasting immunity depends on the generation of protective antibodies through the germinal center (GC) reaction. N6-methyladenosine (m6A) modification of mRNAs by METTL3 activity modulates transcript lifetime primarily through the function of m6A readers; however, the physiological role of this molecular machinery in the GC remains unknown. Here, we show that m6A modifications by METTL3 are required for GC maintenance through the differential functions of m6A readers. Mettl3-deficient GC B cells exhibited reduced cell-cycle progression and decreased expression of proliferation- and oxidative phosphorylation-related genes. The m6A binder, IGF2BP3, was required for stabilization of Myc mRNA and expression of its target genes, whereas the m6A reader, YTHDF2, indirectly regulated the expression of the oxidative phosphorylation gene program. Our findings demonstrate how two independent gene networks that support critical GC functions are modulated by m6A through distinct mRNA binders.

Comparative transcriptomics across the prokaryotic tree of life

Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.

Core promoter sequence in yeast is a major determinant of expression level

The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription. Here, we present the first comprehensive study of yeast core promoters, providing massively parallel measurements of core promoter activity and of TSS locations and relative usage for thousands of native and designed sequences. We found core promoter activity to be highly correlated to the activity of the entire promoter and that sequence variation in different core promoter regions substantially tunes its activity in a predictable way. We also show that location, orientation, and flanking bases critically affect TATA element function, that transcription initiation in highly active core promoters is focused within a narrow region, that poly(dA:dT) orientation has a functional consequence at the 3' end of promoters, and that orthologous core promoters across yeast species have conserved activities. Our results demonstrate the importance of core promoters in the quantitative study of gene regulation.

Abstract P1-08-16: Deep sequencing of breast tumor biopsies reveals an association between pathologic complete response and reduction of TP53 clonal abundance upon brief exposure to therapy

Background: Next generation deep sequencing has revealed the existence of intra-tumor heterogeneity within subsets of breast tumors. The clinical implications of intra-tumor heterogeneity are not fully understood, however subclonal heterogeneity likely plays a role in treatment resistance. We quantify the clonal abundance of somatic mutations in breast tumor biopsies using deep targeted amplicon sequencing and assess their changes over the course of preoperative therapy (PT). We also evaluate the association of changes in clonal abundance upon brief exposure (BE) to therapy with clinical outcome.

Methods: DNA from 69 breast tumor samples obtained from BE preoperative clinical trials BrUOG 211A/211B were sequenced. Patients received a run-in dose of bevacizumab(B), nab-paclitaxel(N) or trastuzumab (T), followed by combination biologic/chemotherapy (HER2- with B/carboplatin/N; HER2+ with T/carboplatin/N). We sequenced biopsy pairs obtained pre/post 10 day exposure to run-in targeted therapy and germline and surgical tumor DNA for a subset of patients upon completion of PT. A TruSeqCustom Amplicon (Illumina) for targeted enrichment sequencing that included 1183 amplicons covering either hotspot regions or whole exonic regions from 35 commoly mutated genes in breast cancer (TCGA, Stephens, 2012; Shah); a total of 101,484 bp of the genome was represented. Sequencing was performed using IlluminaMiSeq platform and analyzed for variant calls using IlluminaBasespace. High confidence somatic mutations were identified in samples with matched germline data using VarScan2. In the absence of matched normal DNA, germline variants were eliminated using dbSNP and the 1000 Genomes Project. Minor allele frequencies (MAF) of somatic aberrations were estimated as the percentage of reads matching the variant.

Results: Approximately 5 mutations on average were found baseline and post-exposure, with a maximum mutational burden of 15 mutations in one basal breast cancer. Recurrent somatic aberrations were observed in TP53 (42%), PIK3CA (16%) and FAT4 (13%), whereas sporadic aberrations were also seen in COL1A1, PTEN, CDH1. More than 85% of samples harboring TP53 mutations exhibited MAF≥40%. Similar high clonal abundance (MAF >50%) was observed for FAT4 mutations whereas PIK3CA mutations exhibited only subclonal frequencies (MAF≤30%). We evaluated changes in clonal architecture upon BE to therapy by scoring for a change in MAF of at least 10% from baseline to post-exposure sample. We scored a total of 16 cases for clonal abundance changes in TP53 mutations upon exposure to therapy. We found 6 cases that exhibited ≥10% reduction in MAF, of which 4 achieved pCR (p = 0.03) and the remaining 2 achieved RCB I. This association was independent of therapy arm and BE regimen.

Conclusions: We found that a reduction in TP53 clonal abundance upon BE to PT is associated with clinical outcome. We are currently integrating whole genome copy-number profiles with the deep sequencing data to more accurately assess clonal architecture and changes upon exposure to therapy. Clonal changes upon BE to therapy may provide early readouts of therapy benefit and provide biological insights into mechanisms of action.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-16.

The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature

One of the hallmarks of opportunistic pathogens is their ability to adjust and respond to a wide range of environmental and host-associated conditions. The human pathogen Pseudomonas aeruginosa has an ability to thrive in a variety of hosts and cause a range of acute and chronic infections in individuals with impaired host defenses or cystic fibrosis. Here we report an in-depth transcriptional profiling of this organism when grown at host-related temperatures. Using RNA-seq of samples from P. aeruginosa grown at 28°C and 37°C we detected genes preferentially expressed at the body temperature of mammalian hosts, suggesting that they play a role during infection. These temperature-induced genes included the type III secretion system (T3SS) genes and effectors, as well as the genes responsible for phenazines biosynthesis. Using genome-wide transcription start site (TSS) mapping by RNA-seq we were able to accurately define the promoters and cis-acting RNA elements of many genes, and uncovered new genes and previously unrecognized non-coding RNAs directly controlled by the LasR quorum sensing regulator. Overall we identified 165 small RNAs and over 380 cis-antisense RNAs, some of which predicted to perform regulatory functions, and found that non-coding RNAs are preferentially localized in pathogenicity islands and horizontally transferred regions. Our work identifies regulatory features of P. aeruginosa genes whose products play a role in environmental adaption during infection and provides a reference transcriptional landscape for this pathogen.

Identifying coordinately regulated genes and their control by environmentally-initiated signal transduction pathways is important for understanding bacterial virulence mechanisms. The work reported here provides a comprehensive, high resolution, transcriptome map of the opportunistic pathogen Pseudomonas aeruginosa using RNA-seq. The results suggest that P. aeruginosa senses the temperature during the transition from its natural environment to a mammalian host, and this plays a key role in regulating the coordinated expression of several virulence factors. A large number of antisense transcripts and non-coding RNAs were identified, with preferential clustering in the regions acquired through horizontal gene transfer, suggesting that a part of the non-coding genome has a distinct evolutionary origin. We created an online data viewer, the Pseudomonas transcriptome browser, to facilitate access to the transcriptome data from this study as well as the subsequent results of work deposited by other investigators. The resources generated through our analyses provide a valuable tool to the P. aeruginosa research community and set the foundation for a systems biology approach towards understanding the complexity of the regulatory networks controlling the multiple lifestyles of this highly versatile organism.

Transcriptome-wide discovery of circular RNAs in Archaea

Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted tRNA genes. Despite their potentially important biological roles, discovery of circular RNAs has so far been mostly serendipitous. We have developed circRNA-seq, a combined experimental/computational approach that enriches for circular RNAs and allows profiling their prevalence in a whole-genome, unbiased manner. Application of this approach to the archaeon Sulfolobus solfataricus P2 revealed multiple circular transcripts, a subset of which was further validated independently. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but were also enriched with non-coding RNAs, including C/D box RNAs and RNase P, as well as circular RNAs of unknown function. Many of the identified circles were conserved in Sulfolobus acidocaldarius, further supporting their functional significance. Our results suggest that circular RNAs, and particularly circular non-coding RNAs, are more prevalent in archaea than previously recognized, and might have yet unidentified biological roles. Our study establishes a specific and sensitive approach for identification of circular RNAs using RNA-seq, and can readily be applied to other organisms.

Genomic fossils as a snapshot of the human transcriptome

Processed pseudogenes (PPGs) are cDNA sequences that were generated through reverse transcription of mature, spliced mRNAs and have subsequently been reinserted at a new genomic location. These cDNA sequences are usually no longer transcribed and are considered "dead on arrival." Here we show that PPGs can be used to generate a map of the transcriptome. By analyzing thousands of human PPGs, we were able to discover hundreds of transcript variants so far unidentified. An experimental verification of a subset of these variants by RT-PCR indicates that most of them are still active in the human transcriptome. Furthermore, we demonstrate that PPGs can enable the identification of ancient splice variants that were expressed ancestrally but are now extinct. Our results show that the genome itself carries a "virtual cDNA library" that can readily be used to analyze both present and ancestral transcripts. Our approach can be applied to sequenced metazoan genomes to computationally annotate splicing variation even when expressed sequences are unavailable.

Transcription-mediated gene fusion in the human genome

Transcription of a gene usually ends at a regulated termination point, preventing the RNA-polymerase from reading through the next gene. However, sporadic reports suggest that chimeric transcripts, formed by transcription of two consecutive genes into one RNA, can occur in human. The splicing and translation of such RNAs can lead to a new, fused protein, having domains from both original proteins. Here, we systematically identified over 200 cases of intergenic splicing in the human genome (involving 421 genes), and experimentally demonstrated that at least half of these fusions exist in human tissues. We showed that unique splicing patterns dominate the functional and regulatory nature of the resulting transcripts, and found intergenic distance bias in fused compared with nonfused genes. We demonstrate that the hundreds of fused genes we identified are only a subset of the actual number of fused genes in human. We describe a novel evolutionary mechanism where transcription-induced chimerism followed by retroposition results in a new, active fused gene. Finally, we provide evidence that transcription-induced chimerism can be a mechanism contributing to the evolution of protein complexes.

Cyclin S: a new member of the cyclin family plays a role in long-term memory

Memory is thought to be subserved by structural and functional alteration in synaptic connectivity. But although neuronal plasticity requires gene expression, the identity of the proteins involved is largely unknown. Using the chick 1-day-old passive avoidance learning paradigm and differential display RNA fingerprinting, we identified 13 candidate genes which are upregulated in the intermediate medial hyperstriatum ventrale (IMHV), an area that has been correlated with the initial processing of memory formation. One of the induced genes is a new member of the cyclin family, with high homology to cyclin L (ania-6a). Analysis of the expression pattern of this gene after training revealed two time waves of induction: the first correlated with learning and initial memory process in the IMHV; the second correlated with memory consolidation, first in the IMHV, and then in the lobus paraolefactoris. There is a correlation between methylanthranilate (MeA) concentrations (the malaise substrate in the passive avoidance training procedure), the duration of memory and the expression level of cyclin S. While training chicks on low concentrations of MeA causes short-term memory and low expression level of cyclin S, high concentration of MeA induces long-term memory and high expression level of cyclin S in the IMHV. The role of cyclins in the regulation of neuronal-plasticity-related gene expression was overlooked, and it might serve as a key step in long-term memory formation.