A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions.

Eukaryotic translation initiates upon recruitment of the EIF2-GTP·Met-tRNAi ternary complex (TC) to the ribosomes. EIF2 (α, ß, γ subunits) is a GTPase. The GDP to GTP exchange within EIF2 is facilitated by the guanine nucleotide exchange factor EIF2B (α-ε subunits). During stress-induced conditions, phosphorylation of the α-subunit of EIF2 turns EIF2 into an inhibitor of EIF2B. In turn, inhibition of EIF2B decreases TC formation and triggers the internal stress response (ISR), which determines the cell fate. Deregulated ISR has been linked to neurodegenerative disorders and cancer, positioning EIF2B as a promising therapeutic target. Hence, a better understanding of the mechanisms/factors that regulate EIF2B activity is required. Here, combining transcript and protein level analyses, we describe an intronically polyadenylated (IPA) transcript of EIF2B's γ-subunit. We show that the IPA mRNA isoform is translated into a C-terminus truncated protein. Using structural modeling, we predict that the truncated EIF2Bγ protein has unfavorable interactions with EIF2γ, leading to a potential decrease in the stability of the nonproductive EIF2:EIF2B complex. While we discovered and confirmed the IPA mRNA isoform in breast cancer cells, the expression of this isoform is not cancer-specific and is widely present in normal tissues. Overall, our data show that a truncated EIF2Bγ protein co-exists with the canonical protein and is an additional player to regulate the equilibrium between productive and nonproductive states of the EIF2:EIF2B complex. These results may have implications in stress-induced translation control in normal and disease states. Our combinatorial approach demonstrates the need to study noncanonical mRNA and protein isoforms to understand protein interactions and intricate molecular mechanisms.

Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer.

PURPOSE: Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer that is frequently treated with chemotherapy. However, many patients exhibit either de novo chemoresistance or ultimately develop resistance to chemotherapy, leading to significantly high mortality rates. Therefore, increasing the efficacy of chemotherapy has potential to improve patient outcomes. METHODS: Here, we performed whole transcriptome sequencing (both RNA and small RNA-sequencing), coupled with network simulations and patient survival data analyses to build a novel miRNA-mRNA interaction network governing chemoresistance in TNBC. We performed cell proliferation assay, Western blotting, RNAi/miRNA mimic experiments, FN coating, 3D cultures, and ChIP assays to validate the interactions in the network, and their functional roles in chemoresistance. We developed xenograft models to test the therapeutic potential of the identified key miRNA/proteins in potentiating chemoresponse in vivo. We also analyzed several patient datasets to evaluate the clinical relevance of our findings. RESULTS: We identified fibronectin (FN1) as a central chemoresistance driver gene. Overexpressing miR-326 reversed FN1-driven chemoresistance by targeting FN1 receptor, ITGA5. miR-326 was downregulated by increased hypoxia/HIF1A and ECM stiffness in chemoresistant tumors, leading to upregulation of ITGA5 and activation of the downstream FAK/Src signaling pathways. Overexpression of miR-326 or inhibition of ITGA5 overcame FN1-driven chemotherapy resistance in vitro by inhibiting FAK/Src pathway and potentiated the efficacy of chemotherapy in vivo. Importantly, lower expression of miR-326 or higher levels of predicted miR-326 target genes was significantly associated with worse overall survival in chemotherapy-treated TNBC patients. CONCLUSION: FN1 is central in chemoresistance. In chemoresistant tumors, hypoxia and resulting ECM stiffness repress the expression of the tumor suppressor miRNA, miR-326. Hence, re-expression of miR-326 or inhibition of its target ITGA5 reverses FN1-driven chemoresistance making them attractive therapeutic approaches to enhance chemotherapy response in TNBCs.

MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets.

MOTIVATION: Next generation sequencing enabled the fast accumulation of genomic data at public repositories. This technology also made it possible to better understand the regulation of gene expression by transcription factors (TFs) and various chromatin-associated proteins through the integration of chromatin immunoprecipitation (ChIP-Seq). The Cistrome Project has become one of the indispensable research portals for biologists to access and analyze data generated with thousands of ChIP-Seq experiments. Integrative motif analysis on shared binding regions among a set of experiments is not yet achievable despite a set of search and analysis tools provided by Cistrome via its web interface and the Galaxy framework. RESULTS: We implemented a python command-line tool for searching binding sequences of a TF common to multiple ChIP-Seq experiments. We use the peaks in the Cistrome database as identified by MACS 2.0 for each experiment and identify shared peak regions in a genomic locus of interest. We then scan these regions for binding sequences using a binding motif of a TF obtained from the JASPAR database. MotifGenie is developed in collaboration with molecular biologists and its findings are corroborated by laboratory experiments. AVAILABILITY AND IMPLEMENTATION: MotifGenie is freely available at https://github.com/ceragoguztuzun/MotifGenie.

Cardiac Surgery 2021 Reviewed.

PubMed displayed more than 35,000 hits for the search term "cardiac surgery AND 2021." We used the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) approach and selected relevant publications for a results-oriented summary. As in recent years, we reviewed the fields of coronary and conventional valve surgery and their overlap with their interventional alternatives. COVID reduced cardiac surgical activity around the world. In the coronary field, the FAME 3 trial dominated publications by practically repeating SYNTAX, but with modern stents and fractional flow reserve (FFR)-guided percutaneous coronary interventions (PCIs). PCI was again unable to achieve non-inferiority compared with coronary artery bypass graft surgery (CABG) in patients with triple-vessel disease. Survival advantages of CABG over PCI could be linked to a reduction in myocardial infarctions and current terminology was criticized because the term "myocardial revascularization" is not precise and does not reflect the infarct-preventing collateralization effect of CABG. In structural heart disease, new guidelines were published, providing upgrades of interventional treatments of both aortic and mitral valve disease. While for aortic stenosis, transcatheter aortic valve implantation (TAVI) received a primary recommendation in older and high-risk patients; recommendations for transcatheter mitral edge-to-edge treatment were upgraded for patients considered inappropriate for surgery. For heart team discussions it is important to know that classic aortic valve replacement currently provides strong signals (from registry and randomized evidence) for a survival advantage over TAVI after 5 years. This article summarizes publications perceived as important by us. It can neither be complete nor free of individual interpretation, but provides up-to-date information for decision-making and patient information.

JOA: Joint Overlap Analysis of multiple genomic interval sets.

BACKGROUND: Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose restrictions such as not allowing nested intervals or requiring intervals to be sorted when finding overlaps in two or more interval sets. RESULTS: We proposed segment tree (ST) and indexed segment tree forest (ISTF) based solutions for intersection of multiple genomic interval sets in parallel. We developed these methods as a tool, Joint Overlap Analysis (JOA), which takes n interval sets and finds overlapping intervals with no constraints on the given intervals. The proposed indexed segment tree forest is a novel composite data structure, which leverages on indexing and natural binning of a segment tree. We also presented construction and search algorithms for this novel data structure. We compared JOA ST and JOA ISTF with each other, and with other interval intersection tools for verification of its correctness and for showing that it attains comparable execution times. CONCLUSIONS: We implemented JOA in Java using the fork/join framework which speeds up parallel processing by taking advantage of all available processor cores. We compared JOA ST with JOA ISTF and showed that segment tree and indexed segment tree forest methods are comparable with each other in terms of execution time and memory usage. We also carried out execution time comparison analysis for JOA and other tools and demonstrated that JOA has comparable execution time and is able to further reduce its running time by using more processors per node. JOA can be run using its GUI or as a command line tool. JOA is available with source code at https://github.com/burcakotlu/JOA/ . A user manual is provided at https://joa.readthedocs.org.

A New Arterial Cannulation Technique: Arterial Cannulation through Aortic Anastomosis ("Kaplan" Technique).

We performed Bentall procedure on a 65-year-old male patient. Cardiopulmonary bypass was initiated via cannulation of the aneurysmatic segment of the aorta. Distal anastomosis was performed with the open technique under deep hypothermic circulatory arrest at 18°C. We performed arterial recannulation through the anastomosis with a new technique, and cardiopulmonary bypass was reestablished. Cardiopulmonary bypass was terminated after rewarming and de-airing phases, and decannulation was performed without any problems. By this technique, the patient had no additional incisions for arterial cannulation, and there were no additional cannulation sutures left on the patient's arterial tree or the valved conduit.

Open Heart Surgery at Patient's Own Temperature Without Active Cooling.

BACKGROUND: Hypothermia is a method of myocardial protection in cardiac surgery. This protection occurs by decreasing the metabolic demands, however, it creates susceptibility to various problems. In this study, we investigated patients operated on under normothermia (at the patient's own temperature) and hypothermia for postoperative differences. METHODS: The study was conducted between June 2015 and September 2016 with 167 patients. The patients were divided into two groups in accordance with our routine clinical practice: the normothermic group (native temperature goup; intraoperative body temperature ≥ 34°C), and the hypothermic group intraoperative body temperature  < 34°C - ≥ 28°C). Preoperative and postoperative data of patients were recorded and the two groups were compared. RESULTS: There was no significant difference between the two groups in terms of cross clamp time, cardiopulmonary bypass time, awakening and extubation times, intensive care unit and hospital stay, drainage, mean serum lactate levels, arrhytmia, all causes infection, renal insufficiency, neurologic complications, myocardial infarction, or mortality (P > .05). Inotrope and transfusion requirements were found to be statistically significantly lower in the normothermic group than the hypothermic group (P < .05). CONCLUSION: Although hypothermia is commonly used in cardiac surgery, it has harmful effects. We believe that cardiac surgery can safely be performed at a patient's own temperature without active cooling to avoid these dangers.

A multiplex primer design algorithm for target amplification of continuous genomic regions.

BACKGROUND: Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is a good solution for the mentioned problems. RESULTS: We propose a novel method to design MPCR primers for a continuous genomic region, following the best practices of clinically reliable PCR design processes. On an experimental setup with 48 different combinations of factors, we have shown that multiple parameters might effect finding the first feasible solution. Increasing the length of the initial primer candidate selection sequence gives better results whereas waiting for a longer time to find the first feasible solution does not have a significant impact. CONCLUSIONS: We generated MPCR primer designs for the HBB whole gene, MEFV coding regions, and human exons between 2000 bp to 2100 bp-long. Our benchmarking experiments show that the proposed MPCR approach is able produce reliable NGS assay primers for a given sequence in a reasonable amount of time.

Comparison of tissue/disease specific integrated networks using directed graphlet signatures.

BACKGROUND: Analysis of integrated genome-scale networks is a challenging problem due to heterogeneity of high-throughput data. There are several topological measures, such as graphlet counts, for characterization of biological networks. RESULTS: In this paper, we present methods for counting small sub-graph patterns in integrated genome-scale networks which are modeled as labeled multidigraphs. We have obtained physical, regulatory, and metabolic interactions between H. sapiens proteins from the Pathway Commons database. The integrated network is filtered for tissue/disease specific proteins by using a large-scale human transcriptional profiling study, resulting in several tissue and disease specific sub-networks. We have applied and extended the idea of graphlet counting in undirected protein-protein interaction (PPI) networks to directed multi-labeled networks and represented each network as a vector of graphlet counts. Graphlet counts are assessed for statistical significance by comparison against a set of randomized networks. We present our results on analysis of differential graphlets between different conditions and on the utility of graphlet count vectors for clustering multiple condition specific networks. CONCLUSIONS: Our results show that there are numerous statistically significant graphlets in integrated biological networks and the graphlet signature vector can be used as an effective representation of a multi-labeled network for clustering and systems level analysis of tissue/disease specific networks.

3'UTR shortening and EGF signaling: implications for breast cancer.

Alternative polyadenylation (APA) plays a role in gene expression regulation generally by shortening of 3'UTRs (untranslated regions) upon proliferative signals and relieving microRNA-mediated repression. Owing to high proliferative indices of triple negative breast cancers (TNBCs), we hypothesized APA to cause 3'UTR length changes in this aggressive subgroup of breast cancers. Our probe-based meta-analysis approach identified 3'UTR length alterations where the significant majority was shortening events (∼70%, 113 of 165) of mostly proliferation-related transcripts in 520 TNBC patients compared with controls. Representative shortening events were further investigated for their microRNA binding potentials by computational predictions and dual-luciferase assay. In silico-predicted 3'UTR shortening events were experimentally confirmed in patient and cell line samples. To begin addressing the underlying mechanisms, we found CSTF2 (cleavage stimulation factor 2), a major regulator of 3'UTR shortening to be up-regulated in response to epidermal growth factor (EGF). EGF treatment also resulted with further shortening of the 3'UTRs. To investigate the contribution of CSTF2 and 3'UTR length alterations to the proliferative phenotype, we showed pharmacological inhibition of the EGF pathway to lead to a reduction in CSTF2 levels. Accordingly, RNAi-induced silencing of CSTF2 decreased the proliferative rate of cancer cells. Therefore, our computational and experimental approach revealed a pattern of 3'UTR length changes in TNBC patients and a potential link between APA and EGF signaling. Overall, detection of 3'UTR length alterations of various genes may help the discovery of new cancer-related genes, which may have been overlooked in conventional microarray gene expression analyses.

Open Cardiac Surgery without Blood and Blood Products Transplantation.

BACKGROUND: Blood transfusions are the most common type of tissue and organ transplantation. Perioperative and postoperative transfusions may cause morbidity and mortality and transfusion should based on only hematocrit values but also on hemodynamic and clinical parameters of the patient, which cannot be ignored. METHODS: A prospective study was conducted between January 2015 and October 2016 with adult patients undergoing elective open heart surgery. In these patients, a protocol was established, and patients were divided into two groups as transfusion (-) and transfusion (+). In the first 24 hours in the intensive care unit, patients' drainage, 24-hours urine output, awakening and extubation times, and lactate and bilirubin levels in arterial blood gases were recorded. Thirty-day mortality and morbidity, and hemodynamic and clinical data were compared between these two groups. RESULTS: We have performed a total of 138 cases; no blood and blood products were transfused in 71% (n = 98), and in 29.0% (n = 40) blood and blood products were transfused. Thirty-day mortality and morbidity (arrhythmia, infectious and pulmonary morbidity, myocardial infarction, cerebrovascular accident, renal dysfunction, sternal revision) were compared between these two groups and no statistically significant difference was observed. Patients' awakening, extubation time, cardiopulmonary bypass period, cross-clamp time, and days in intensive care unit and hospital were compared, and there was no statistically significant difference between the two groups. Conclusion: In this study, we conclude that open heart surgery without blood transfusion may be accomplished with decent peri/postoperative management. The patients who did not receive any blood or blood products were not compromised clinically or hemodynamically. No extra morbidity and mortality were seen in the non-transfusion group. Transfusion decision was based on clinical and hemodynamic parameters such as persistent hypotension or tachycardia, hyperlactatemia, low urine output, and anemic symptoms.

Stent Embolism after Coronary Angiography: Case Report.

Endovascular interventions are widely performed of late; complications including stent embolism of arteries and veins, dislocation, or malposition of medical devices are frequently seen. Peripheral stent embolisms are generally asymptomatic, but when they cause acute ischemia or severe symptoms like claudication they must be removed. Stents can be removed not only with surgical techniques but also with endovascular maneuvers. In this case report, we state that in symptomatic peripheral arterial embolization cases, surgical intervention is the first choice for treatment due to the complexity and high risk of complications when using endovascular maneuvers.

Open distal anastomosis technique for ascending aortic aneurysm repair without cerebral perfusion.

BACKGROUND: This study aimed to report the outcomes of patients who underwent proximal thoracic aortic aneurysm surgery with open distal anastomosis technique but without cerebral perfusion, instead under deep hypothermic circulatory arrest. METHODS: Thirty patients (21 male, 9 female) who underwent ascending aortic aneurysm repair with open distal anastomosis technique were included. The average age was 60.2±11.7 years. Operations were performed under deep hypothermic circulatory arrest and the cannulation for cardiopulmonary bypass was first done over the aneurysmatic segment and then moved over the graft. Intraoperative and early postoperative mortality and morbidity outcomes were reported. RESULTS: Average duration of cardiopulmonary bypass and cross-clamps were 210.8±43 and 154.9±35.4 minutes, respectively. Average duration of total circulatory arrest was 25.2±2.4 minutes. There was one hospital death (3.3%) due to chronic obstructive pulmonary disease at postoperative day 22. No neurological dysfunction was observed during the postoperative period. CONCLUSION: These results demonstrate that open distal anastomosis under less than 30 minutes of deep hypothermic circulatory arrest without antegrade or retrograde cerebral perfusion and cannulation of the aneurysmatic segment is a safe and reliable procedure in patients undergoing proximal thoracic aortic aneurysm surgery.

Estrogen-induced upregulation and 3'-UTR shortening of CDC6.

3'-Untranslated region (UTR) shortening of mRNAs via alternative polyadenylation (APA) has important ramifications for gene expression. By using proximal APA sites and switching to shorter 3'-UTRs, proliferating cells avoid miRNA-mediated repression. Such APA and 3'-UTR shortening events may explain the basis of some of the proto-oncogene activation cases observed in cancer cells. In this study, we investigated whether 17 ß-estradiol (E2), a potent proliferation signal, induces APA and 3'-UTR shortening to activate proto-oncogenes in estrogen receptor positive (ER+) breast cancers. Our initial probe based screen of independent expression arrays suggested upregulation and 3'-UTR shortening of an essential regulator of DNA replication, CDC6 (cell division cycle 6), upon E2 treatment. We further confirmed the E2- and ER-dependent upregulation and 3'UTR shortening of CDC6, which lead to increased CDC6 protein levels and higher BrdU incorporation. Consequently, miRNA binding predictions and dual luciferase assays suggested that 3'-UTR shortening of CDC6 was a mechanism to avoid 3'-UTR-dependent negative regulations. Hence, we demonstrated CDC6 APA induction by the proliferative effect of E2 in ER+ cells and provided new insights into the complex regulation of APA. E2-induced APA is likely to be an important but previously overlooked mechanism of E2-responsive gene expression.

Differential expression of mRNA 3'-end isoforms in cervical and ovarian cancers.

Early diagnosis and therapeutic targeting are continuing challenges for gynecological cancers. Here, we focus on cancer transcriptomes and describe the differential expression of 3'UTR isoforms in patients using an algorithm to detect differential poly(A) site usage. We find primarily 3'UTR shortening cases in cervical cancers compared with the normal cervix. We show differential expression of alternate 3'-end isoforms of FOXP1, VPS4B, and OGT in HPV16-positive patients who develop high-grade cervical lesions compared with the infected but non-progressing group. In contrast, in ovarian cancers, 3'UTR lengthening is more evident compared with normal ovary tissue. Nevertheless, highly malignant ovarian tumors have unique 3'UTR shortening events (e.g., CHRAC1, SLC16A1, and TOP2A), some of which correlate with upregulated protein levels in tumors. Overall, our study shows isoform level deregulation in gynecological cancers and highlights the complexity of the transcriptome. This transcript diversity could help identify novel cancer genes and provide new possibilities for diagnosis and therapy.

Slide type landslide susceptibility assessment of the Büyük Menderes watershed using artificial neural network method.

The Büyük Menderes watershed is the largest drainage watershed in Western Anatolia with an area of approximately 26,000 km2. In the study area, almost 863 landslides occurred, extending over 222 km2 with a mean landslide area of 0.21 km2. In this study, landslide susceptibility assessments were carried out using artificial neural network method, which is one of the data-driven methods. In this study, that will contribute to the mitigation or control of the landslides caused by the reasons controlling the spatial and temporal distribution of landslides created in the GIS and MATLAB environment by using scientific and technological approaches within the framework. Since derivative activation function is also used in back-propagation artificial neural networks, its derivative is easily calculated in order not to slow down the calculation. Levenberg-Marquardt back-propagation (LM), resilient back propagation back-propagation (trainrp), scaled conjugate gradient back-propagation (trainscg), conjugate gradient with Powell/Beale restarts back-propagation (traincgb), and Fletcher-Powell conjugate gradient back-propagation (traincgf) algorithms are used, which constantly interrogate the link between the input parameter and the result output, and at least one cell's output is given as an input to any other cell. Geology, digital elevation model, slope, topographic wetness index, roughness index, plan, profile curvatures, and proximity to active faults and rivers were used as landslide conditioning factors. In susceptibility assessments, landslides were separated by 70% analysis, 15% test, and 15% validation datasets by random selection method. The performances of the landslide susceptibility maps were assessed by the area under the ROC curve (AUC), accuracy (ACC), precision, recall, F1 score, Kappa test error histogram, and confusion matrix, respectively. The area under the receiver operating characteristic curves, analysis, testing, validation, landslides, and study areas were found between 0.873 and 0.911. The susceptibility map had a high prediction rate in which high and very high susceptible zones corresponded to 26% of the study area including 82% of the recorded landslides.

Surgical mitral valve repair technique considerations based on the available evidence.

Mitral valve regurgitation is the second most common valve disease in the western world. Surgery is currently the best tool for generating a long-lasting elimination of mitral valve regurgitation. However, the mitral valve apparatus is a complex anatomical and functional structure, and repair results and durability show substantial heterogeneity. This is not only due to differences in the underlying mitral valve regurgitation pathophysiology but also due to differences in repair techniques. Repair philosophies differ substantially from one surgeon to the other, and consensus for the technically best repair strategy has not been reached yet. We had previously addressed this topic by suggesting that ring sizing is "voodoo". We now review the available evidence regarding the various repair techniques described for structural and functional mitral valve regurgitation. Herein, we illustrate that for structural mitral valve regurgitation, resuspension of prolapsing valve segments or torn chordae with polytetrafluoroethylene sutures and annuloplasty can generate the most durable results paired with the best achievable hemodynamics. For functional mitral valve regurgitation, the evidence suggests that annuloplasty alone is insufficient in most cases to generate durable results, and additional subvalvular strategies are associated with improved durability and possibly improved clinical outcomes. This review addresses current strategies but also implausibilities in mitral valve repair and informs the mitral valve surgeon about the current evidence. We believe that this information may help improve outcomes in mitral valve repair as the heterogeneity of mitral valve regurgitation pathophysiology does not allow a one-size-fits-all concept.

Detection and tracking of sea-surface targets in infrared and visual band videos using the bag-of-features technique with scale-invariant feature transform.

Sea-surface targets are automatically detected and tracked using the bag-of-features (BOF) technique with the scale-invariant feature transform (SIFT) in infrared (IR) and visual (VIS) band videos. Features corresponding to the sea-surface targets and background are first clustered using a training set offline, and these features are then used for online target detection using the BOF technique. The features corresponding to the targets are matched to those in the subsequent frame for target tracking purposes with a set of heuristic rules. Tracking performance is compared with an optical-flow-based method with respect to the ground truth target positions for different real IR and VIS band videos and synthetic IR videos. Scenarios are composed of videos recorded/generated at different times of day, containing single and multiple targets located at different ranges and orientations. The experimental results show that sea-surface targets can be detected and tracked with plausible accuracies by using the BOF technique with the SIFT in both IR and VIS band videos.

Identification of an mRNA isoform switch for HNRNPA1 in breast cancers.

Roles of HNRNPA1 are beginning to emerge in cancers; however, mechanisms causing deregulation of HNRNPA1 function remain elusive. Here, we describe an isoform switch between the 3'-UTR isoforms of HNRNPA1 in breast cancers. We show that the dominantly expressed isoform in mammary tissue has a short half-life. In breast cancers, this isoform is downregulated in favor of a stable isoform. The stable isoform is expressed more in breast cancers, and more HNRNPA1 protein is synthesized from this isoform. High HNRNPA1 protein levels correlate with poor survival in patients. In support of this, silencing of HNRNPA1 causes a reversal in neoplastic phenotypes, including proliferation, clonogenic potential, migration, and invasion. In addition, silencing of HNRNPA1 results in the downregulation of microRNAs that map to intragenic regions. Among these miRNAs, miR-21 is known for its transcriptional upregulation in breast and numerous other cancers. Altogether, the cancer-specific isoform switch we describe here for HNRNPA1 emphasizes the need to study gene expression at the isoform level in cancers to identify novel cases of oncogene activation.

A CpG island promoter drives the CXXC5 gene expression.

CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5' untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5'-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G-C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.