FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns.

Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.

Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation.

Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila, maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3' UTR in a region adjacent to A-rich sequences. Using Drosophila S2R+ cultured cells we show that this binding site overlaps with a Bruno1 (Bru1) responsive element (BREs) that regulates osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3' UTR.

Improved library preparation with the new iCLIP2 protocol.

Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) is a state-of-the-art technology to map the RNA interaction sites of an RNA-binding protein (RBP) across the transcriptome. Here, we present the new iCLIP2 protocol that allows to obtain high-quality iCLIP libraries in a fast and efficient manner. The new protocol comprises separate adapter ligations, two cDNA amplification steps and bead-based size selection. The full procedure can be completed within four days. Our advances significantly increase the complexity of the iCLIP2 libraries, resulting in a more comprehensive representation of RBP binding sites. Overall, the methodological advances in iCLIP2 allow efficient library generation and thereby promote the versatile and flexible application of this important technology.

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.

The 3' untranslated regions (3' UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3' UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3' UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3' UTRs.

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation.

BACKGROUND: Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control. RESULTS: Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1. CONCLUSIONS: We propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.

Determination of nitrotyrosine concentrations in plasma samples of diabetes mellitus patients by four different immunoassays leads to contradictive results and disqualifies the majority of the tests.

BACKGROUND: In the course of type 2 diabetes mellitus, insulin resistance has a severe impact on endothelial function leading to decreased synthesis of nitric oxide (NO). Postprandial hyperglycemia leads to the generation of reactive oxygen species, which counteracts the beneficial NO effects. NO and superoxide combine very fast in solution to form peroxynitrite, which is a potent protein-oxidizing agent. The peroxynitrite concentrations can be indirectly monitored by the detection of nitrotyrosine residues in proteins, reflecting the extent of damage caused by oxidative stress. METHODS: Four commercially available nitrotyrosine-specific immunoassays were evaluated by parallel measurement of nitrotyrosine in 224 serum samples derived from 16 patients with type 2 diabetes and 12 healthy controls (13 male and 15 female, age: 33+/-11 years) following a standardized meal. RESULTS: The available ELISA tests were not applicable for nitrotyrosine determination in human plasma samples due to technical issues and implausible results. However, a competitive luminescence assay was able to provide sufficient sensitivity and lead to clinically meaningful results in our test samples. CONCLUSIONS: All three ELISA methods were disqualified and conclusions previously derived from clinical experiments using these tests should be carefully reconsidered or reconfirmed. In the absence of a liquid tandem chromatography-mass spectrometry reference method, the luminescence test appears to be the method of choice for determination of nitrotyrosine in human plasma.

Comparison of the dose accuracy of prefilled insulin pens.

BACKGROUND: Prefilled insulin pens have become a convenient and accurate way for diabetes patients to inject insulin. Their ease of use has helped to reduce the resistance of patients with type 1 diabetes and type 2 diabetes in the United States and Europe toward initiation of insulin therapy. This study compared the dosing accuracy of two prefilled insulin pens (the SoloStar((R)) from Sanofi Aventis, Berlin, Germany, and the Next Generation [NG] FlexPen((R)) from Novo Nordisk, Mainz, Germany). METHODS: The dosing accuracy was tested for both pens with x 24 10 international units of insulin (IU) and 9 x 30 IU injection volumes to investigate whether the pens comply within the acceptable International Organization for Standardization (ISO) limits of 10% (±1 IU) for 10 IU and 5% (±1.5 IU) for 30 IU. The doses were applied each with a new needle strictly according to the instructions for use of the pen manufacturers. A sensitive pharmaceutical balance was used for the assessment of the applied volumes, and the results were corrected for the specific density of the insulin formulations. We used 18 insulin pens (from two different production lots each) for the two volumes, respectively, resulting in a total of 432 doses per pen with 10 IU and 162 doses per pen with 30 IU. RESULTS: Both pens showed a very good performance, which was better for the 10 IU dose than in comparative previous studies. The NG FlexPen (mean absolute percent deviation 10 IU/30 IU: 1.63 ± 0.84%/1.23 ± 0.76%) was even more accurate than the SoloStar (2.11 ± 0.92%/1.54 ± 0.84%, p < .001/p < .05 versus the NG FlexPen). Only 0.2% of the doses were outside the ISO limit at 10 IU, with the NG FlexPen (0.6% at 30 IU). The corresponding figures for the SoloStar were 0.4% and 1.8%, respectively. CONCLUSIONS: A direct head-to-head comparison of the two prefilled insulin pens with a standardized protocol resulted in a more stable dosing accuracy of both pens as compared to previous investigations. In this investigation, the NG FlexPen was more accurate than the SoloStar at both tested doses.

Differences in the dose accuracy of insulin pens.

BACKGROUND: Modern insulin injection pens provide a convenient and accurate way for diabetes patients to inject insulin. They have widespread use among children and adults with type 1 and type 2 diabetes in the U.S. and Europe. This study compared the dosing accuracy of four commonly available insulin pens (OptiClik and SoloSTAR from sanofi-aventis, FlexPen from Novo Nordisk, and HumaPen LUXURA from Eli Lilly). METHODS: The dosing accuracy was tested for all pens with 24 x 10 IU and 9 x 30 IU injection volumes to investigate whether the pens complied with the acceptable International Organization for Standardization (ISO) limits of 10% (+/- 1 IU) for 10 IU and 5% (+/- 1.5 IU) for 30 IU. The doses were each applied with a new needle strictly according to the instructions for use by the pen manufacturers. A pharmaceutical balance was used for the assessment of the applied volumes, and the results were corrected for the specific density of the insulin formulations. Four insulin pens (two each from different production lots) were used for each of the two volumes, resulting in a total of 192 doses per pen with 10 IU, and 72 doses per pen with 30 IU. RESULTS: FlexPen (mean absolute percent deviation for 10 IU and 30 IU: 1.64 +/- 0.84% and 0.83 +/- 0.26%, respectively) and HumaPen LUXURA (1.10 +/- 0.20% and 0.62 +/- 0.19%; not significant versus FlexPen for both doses) were more accurate than the OptiClik (4.78 +/- 3.31% and 2.97 +/- 2.48%, p <.01) and the SoloSTAR (2.61 +/- 0.92% and 1.70 +/- 0.84%, p <.05). While 6.8% of doses were outside the ISO limit at 10 IU with OptiClik (13.9% at 30 IU), the corresponding figures were 0.5% and 4.1%, respectively, for SoloSTAR. No doses outside the ISO limits were seen with FlexPen or HumaPen LUXURA at 10 IU and only one 30 IU dose (1.4%) was outside the limit for FlexPen. CONCLUSIONS: A direct head-to-head comparison of four insulin pens with a standardized protocol resulted in a more stable dosing accuracy of the FlexPen and the HumaPen LUXURA in comparison to the OptiClik and SoloSTAR. Even though all insulin delivery systems undergo rigorous testing before being approved for sale, there may be reasons to be attentive to the performance of the devices in practical use.