Creating and sustaining collaborative multi-institutional industry site visit programs: a toolkit.

Background: As more early career scientists enter into diverse career pathways, visiting local companies or organizations can support their exploration of these paths. As an efficient way to facilitate this, we developed a collaborative regional site visit program: the Enhancing Local Industry Transitions through Exploration (ELITE) Consortium.  Consortium members arrange half-day visits to local industry sites, thus providing companies and trainees the opportunity to meet and identify potential professional and career opportunities. Three different training institutions worked cooperatively in the development and maintenance of the program. The ELITE Consortium was developed with eight phased steps; guidelines and operating procedures were created for each of these steps and are provided along with sample materials for institutions interested in building similar programs. Methods: Prior to fully developing the program, trainee interests were evaluated via questionnaire. During program implementation and thereafter, program directors tracked attendance and collected career outcome data from publicly available sources to identify first job positions after training. Regression analyses and chi-squared analyses were used to examine site visit matches and career outcome data. Results: Analyses suggest a positive impact of site visits on postdoctoral and graduate trainees' career outcomes at companies or institutions that match a similar sector (e.g., for-profit) and type (e.g., biotech, pharmaceutical, contract research organization). Despite a small sample size, evidence suggests an especially positive impact on trainees who organize site visits to companies compared with those who simply participate. Conclusions: The ELITE Consortium was successful in helping trainees explore and identify a multitude of career paths. Trainees attained employment either directly or in related companies and institutions visited by ELITE participants. The joint, three-institution, flexible nature of the ELITE Consortium positively impacts the program's sustainability and reach. The toolkit provided here will help other institutions to replicate and adapt the program with minimal effort.

Determining degradation intermediates and the pathway of 3' to 5' degradation of histone mRNA using high-throughput sequencing.

The half-life of an mRNA is an important parameter contributing to the steady-state level of the mRNA. Rapid changes in mRNA levels can result from decreasing the half-life of an mRNA. Establishing the detailed pathway of mRNA degradation for a particular class of mRNAs requires the ability to isolate mRNA degradation intermediates. High-throughput sequencing provides a method for detecting these intermediates. Here we describe a method for determining the intermediates in 3' to 5' degradation. Characterizing these intermediates requires not only determining the precise 3' end of the molecule to a single nucleotide resolution, but also the ability to detect and characterize any untemplated nucleotides present on the intermediates. We achieve this by ligating a known sequence to all the 3' termini in the cell, and then sequence the 3' termini and the ligated linker to identify any alterations to the genomic reference sequence. We have applied this method to characterize the intermediates in histone mRNA metabolism, allowing us to deduce the pathway of 3' to 5' degradation. This method can potentially be applied to any RNA, and we discuss possible strategies for extending the method to include simultaneous determination of the 3' and 5' end of the same RNA molecule.

Role of oligouridylation in normal metabolism and regulated degradation of mammalian histone mRNAs.

Metazoan replication-dependent histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Histone mRNAs are present in large amounts only in S-phase cells, and their levels are coordinately regulated with the rate of DNA replication. In mammals, the stemloop at the 3' end of histone mRNA is bound to stemloop binding protein, a protein required for both synthesis and degradation of histone mRNA, and an exonuclease, 3'hExo (ERI1). Histone mRNAs are rapidly degraded when DNA synthesis is inhibited in S-phase cells and at the end of S-phase. Upf1 is also required for rapid degradation of histone mRNA as is the S-phase checkpoint. We report that Smg1 is required for histone mRNA degradation when DNA replication is inhibited, suggesting it is the PI-like kinase that activates Upf1 for histone mRNA degradation. We also show that some mutant Upf1 proteins are recruited to histone mRNAs when DNA replication is inhibited and act as dominant negative factors in histone mRNA degradation. We report that the pathway of rapid histone mRNA degradation when DNA replication is inhibited in S-phase cells that are activating the S-phase checkpoint is similar to the pathway of rapid degradation of histone mRNA at the end of S-phase.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.