DDX21 mediates co-transcriptional RNA m6A modification to promote transcription termination and genome stability.

N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.

OXCT1 regulates hippocampal neurogenesis and alleviates cognitive impairment via the Akt/GSK-3ß/ß-catenin pathway after subarachnoid hemorrhage.

BACKGROUND: Subarachnoid hemorrhage (SAH) is a life-threatening neurological disease that usually has a poor prognosis. Neurogenesis is a potential therapeutic target for brain injury. Ketone metabolism also plays neuroprotective roles in many neurological disorders. OXCT1 (3-Oxoacid CoA-Transferase 1) is the rate-limiting enzyme of ketone body oxidation. In this study, we explored whether increasing ketone oxidation by upregulating OXCT1 in neurons could promote neurogenesis after SAH, and evaluated the potential mechanism involved in this process. METHODS: The ß-hydroxybutyrate content was measured using an enzymatic colorimetric assay. Adeno-associated virus targeting neurons was injected to overexpress OXCT1, and the expression and localization of proteins were evaluated by western blotting and immunofluorescence staining. Adult hippocampal neurogenesis was evaluated by dual staining with doublecortin and 5-Ethynyl-2'-Deoxyuridine. LY294002 was intracerebroventricularly administered to inhibit Akt activity. The Morris water maze and Y-maze tests were employed to assess cognitive function after SAH. RESULTS: The results showed that OXCT1 expression and hippocampal neurogenesis significantly decreased in the early stage of SAH. Overexpression of OXCT1 successfully increased hippocampal neurogenesis via activation of Akt/GSK-3ß/ß-catenin signaling and improved cognitive function, both of which were reversed by administration of LY294002. CONCLUSIONS: OXCT1 regulated hippocampal ketone body metabolism and increased neurogenesis through mechanisms mediated by the Akt/GSK-3ß/ß-catenin pathway, improving cognitive impairment after SAH.

Lewis Acid Supported Nickel Nitrenoids.

Metalation of the polynucleating ligand F,tbs LH6 (1,3,5-C6 H9 (NC6 H3 -4-F-2-NSiMe2 t Bu)3 ) with two equivalents of Zn(N(SiMe3 )2 )2 affords the dinuclear product (F,tbs LH2 )Zn2 (1), which can be further deprotonated to yield (F,tbs L)Zn2 Li2 (OEt2 )4 (2). Transmetalation of 2 with NiCl2 (py)2 yields the heterometallic, trinuclear cluster (F,tbs L)Zn2 Ni(py) (3). Reduction of 3 with KC8 affords [KC222 ][(F,tbs L)Zn2 Ni] (4) which features a monovalent Ni centre. Addition of 1-adamantyl azide to 4 generates the bridging µ3 -nitrenoid adduct [K(THF)3 ][(F,tbs L)Zn2 Ni(µ3 -NAd)] (5). EPR spectroscopy reveals that the anionic cluster possesses a doublet ground state (S = 1 / 2 ${{ 1/2 }}$ ). Cyclic voltammetry of 5 reveals two fully reversible redox events. The dianionic nitrenoid [K2 (THF)9 ][(F,tbs L)Zn2 Ni(µ3 -NAd)] (6) was isolated and characterized while the neutral redox isomer was observed to undergo both intra- and intermolecular H-atom abstraction processes. Ni K-edge XAS studies suggest a divalent oxidation state for the Ni centres in both the monoanionic and dianionic [Zn2 Ni] nitrenoid complexes. However, DFT analysis suggests Ni-borne oxidation for 5.

Laparoscopic pancreaticoduodenectomy with portal or superior mesenteric vein resection and reconstruction for pancreatic cancer: A single-center experience.

BACKGROUND: Open pancreaticoduodenectomy (OPD) with portal or superior mesenteric vein resection and reconstruction has been applied in pancreatic cancer patients with tumor infiltration or adherence. However, it is controversial whether laparoscopic pancreaticoduodenectomy (LPD) with major vascular resection and reconstruction is feasible. This study aimed to evaluate the safety and feasibility of LPD with major vascular resection compared with OPD with major vascular resection. METHODS: We reviewed data for all pancreatic cancer patients undergoing LPD or OPD with vascular resection at Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, between February 2018 and May 2022. We compared the preoperative, intraoperative, and postoperative clinicopathological data of the two groups to conduct a comprehensive evaluation of LPD with major vascular resection. RESULTS: A total of 63 patients underwent pancreaticoduodenectomy (PD) with portal or superior mesenteric vein resection and reconstruction, including 25 LPDs and 38 OPDs. The LPD group had less intraoperative blood loss (200 vs. 400 mL, P < 0.001), lower proportion of intraoperative blood transfusion (16.0% vs. 39.5%, P = 0.047), longer operation time (390 vs. 334 min, P = 0.004) and shorter postoperative hospital stay (11 vs. 14 days, P = 0.005). There was no perioperative death in all patients. There was no significant difference in the incidence of total postoperative complications, grade B/C postoperative pancreatic fistula, delayed gastric emptying and abdominal infection between the two groups. No postpancreatectomy hemorrhage nor bile leakage occurred during perioperative period. There was no significant difference in R0 resection rate and number of lymph nodes harvested between the two groups. Patency of reconstructed vessels in the two groups were 96.0% and 92.1%, respectively (P = 0.927). CONCLUSIONS: LPD with portal or superior mesenteric vein resection and reconstruction was safe, feasible and oncologically acceptable for selected patients with pancreatic cancer, and it can achieve similar or even better perioperative results compared to open approach.

Anterior tibial artery pseudoaneurysm as a rare technical complication after corrective fibular osteotomy: a case report.

INTRODUCTION: Partial fibular osteotomy has been recognized as a surgical alternative to treat medial compartment osteoarthritis of the knee. Related peroneal neuropathies are of concern among the relatively few complications after this procedure. In our clinical practice, the osteotomy level has therefore been modified to avoid the above defects. However, a rare case of vascular injury was encountered. Herein we describe an accidental anterior tibial artery pseudoaneurysm as a rare technical complication after this corrective osteotomy. CASE PRESENTATION: A 55-year-old male visited our emergency room, presenting a painful swelling over his right anterolateral shin along with surrounding ecchymosis. Thirteen days ago, he just underwent a corrective fibular osteotomy over his right painful varus knee at our institute, and was discharged after an uneventful postoperative stay. Urgent angiography revealed an out-pouching vascular lesion, pseudoaneurysm, involving his right anterior tibial artery. Prompt endovascular repair with stent insertion and balloon compression successfully stopped the persistent extravasation from the injured artery. Follow-up angiography as well as outpatient review confirmed the regression of this lesion and associated symptoms without sequelae. CONCLUSION: Although corrective fibular osteotomy is a simple surgical procedure, it is not free of complications. The suggested osteotomized level in the pertinent literature predisposes patients to certain neuromuscular deficits, which could be avoided by the modified level of osteotomy. However, our case highlights surgeons' familiarity with certain risky neurovascular structures around the osteotomy site and corresponding technical considerations. A recent surgical history along with alarming symptoms/signs should arouse clinical suspicion, aid in timely identification and make appropriate interventions for potential vascular complications.

Proximal fibular osteotomy relieves pain in spontaneous osteonecrosis of the knee: A retrospective study.

Spontaneous osteonecrosis of the knee (SONK) causes knee pain and joint motion limitation. Ischemia or insufficiency fracture may be the cause, but no consensus has been developed. Proximal fibular osteotomy (PFO) has been reported to relieve pain from osteoarthritis through medial compartment decompression. We reviewed the effect of this procedure on medial compartment SONK patients and explored clinical and radiological results. Since January 2018 to January 2020, the data of 12 knees (8 right and 4 left) from 11 SONK patients (9 women and 2 men) who received PFO were analyzed. The average age was 61.5 years. The diagnosis of SONK was established through weight-bearing anterior-posterior radiographs or magnetic resonance imaging (MRI). Visual analog scale (VAS) scores, Oxford knee score (OKS), Femorotibial angle (FTA), medial joint space, and lateral joint space were documented preoperatively and at follow up visits. Outcome assessment for the clinical and radiographic data was reviewed at 12- and 24-month follow-up visits. The mean follow up period was 33 months. All patients were able to walk with or without cane assistance the day after surgery. Both VAS score and OKS (preoperative: 6.6 ± 0.9 and 24.7 ± 3.8, respectively) improved significantly at the 12-month follow-up, and to 24-month follow-up (3.6 ± 1.3 and 35.6 ± 4.5, respectively, P < .05). Medial joint space ratio increased from 0.36 to 0.50 (P < .05). Changes of FTA were insignificant at any point of follow up. Four patients underwent follow-up MRI, and a decrease in the osteonecrotic area was clearly observed in 2 patients. By achieving medial knee decompression, PFO allowed quick weight-bearing recovery, pain relief, and improvement in knee function in SONK patients.

Using a consensus acupoints regimen to explore the relationship between acupuncture sensation and lumbar spinal postoperative analgesia: A retrospective analysis of prospective clinical cooperation.

OBJECTIVE: This study evaluated the effectiveness of acupuncture treatment on postoperative pain in patients with degenerative lumbar spine disease, and explored the relationship between the postoperative analgesic effect of acupuncture and the sensation of acupuncture experienced by the patients. METHODS: This retrospective study analyzed the medical records of 97 patients who had undergone an operation by the same surgeon due to degenerative lumbar disease. These patients were divided into acupuncture group (n = 32), patient-controlled analgesia (PCA) group (n = 27), and oral analgesia group (n = 38) according to the different postoperative analgesic methods. During their hospitalization, patients completed daily evaluations of their pain using a visual analogue scale (VAS), and injection times of supplemental meperidine were recorded. Also, the Chinese version of the Massachusetts General Hospital Acupuncture Sensation Scale (C-MASS) was used in the acupuncture group. RESULTS: Each of the three treatment groups showed significant reductions in postoperative pain, as shown by reduced VAS scores. The acupuncture group, however, had less rebound pain (P < 0.05) than the other two groups. Both the acupuncture and PCA groups experienced acute analgesic effects that were superior to those in the oral analgesia group. In addition, the higher the C-MASS index on the second day after surgery, the lower the VAS score on the fourth day after surgery. There was also a significant difference in the "dull pain" in the acupuncture sensation. CONCLUSION: The results demonstrated that acupuncture was beneficial for postoperative pain and discomfort after simple surgery for degenerative spinal disease. It is worth noting that there was a disproportionate relevance between the patient's acupuncture sensation and the improvement of pain VAS score.

Structurally Precise Two-Transition-Metal Water Oxidation Catalysts: Quantifying Adjacent 3d Metals by Synchrotron X-Radiation Anomalous Dispersion Scattering.

Mixed 3d metal oxides are some of the most promising water oxidation catalysts (WOCs), but it is very difficult to know the locations and percent occupancies of different 3d metals in these heterogeneous catalysts. Without such information, it is hard to quantify catalysis, stability, and other properties of the WOC as a function of the catalyst active site structure. This study combines the site selective synthesis of a homogeneous WOC with two adjacent 3d metals, [Co2Ni2(PW9O34)2]10- (Co2Ni2P2) as a tractable molecular model for CoNi oxide, with the use of multiwavelength synchrotron X-radiation anomalous dispersion scattering (synchrotron XRAS) that quantifies both the location and percent occupancy of Co (∼97% outer-central-belt positions only) and Ni (∼97% inner-central-belt positions only) in Co2Ni2P2. This mixed-3d-metal complex catalyzes water oxidation an order of magnitude faster than its isostructural analogue, [Co4(PW9O34)2]10- (Co4P2). Four independent and complementary lines of evidence confirm that Co2Ni2P2 and Co4P2 are the principal WOCs and that Co2+(aq) is not. Density functional theory (DFT) studies revealed that Co4P2 and Co2Ni2P2 have similar frontier orbitals, while stopped-flow kinetic studies and DFT calculations indicate that water oxidation by both complexes follows analogous multistep mechanisms, including likely Co-OOH formation, with the energetics of most steps being lower for Co2Ni2P2 than for Co4P2. Synchrotron XRAS should be generally applicable to active-site-structure-reactivity studies of multi-metal heterogeneous and homogeneous catalysts.

Electroacupuncture attenuates vascular hyporeactivity in a rat model of portal hypertension induced by bile duct ligation.

BACKGROUND: A hyperdynamic circulation and impaired vascular responsiveness to vasoconstrictors are observed in portal hypertension (PHT) rats. Inflammation is a major contributor to the hyperdynamic circulation state in murine models of PHT. Electroacupuncture (EA) may ameliorate the inflammatory response and limit arterial vasodilatation and portal pressure. This study investigated the possible mechanisms underlying putative hemodynamics effects of EA in normal and PHT rats. METHODS: PHT was induced by bile duct ligation (BDL) surgery over 4 weeks in rats. Sham-operated and BDL rats were treated with low-frequency EA (2 Hz) at ST36 10 min three times weekly for one or two consecutive weeks (for a total of 3 or 7 treatments, respectively). Serum tumor necrosis factor-α (TNF-α), nitrite/nitrate (NOx) and 6-keto-prostaglandin F1α (6-keto-PGF1α) were analyzed, and hemodynamic variation and contractile responses to phorbol-12,13-dibutyrate and phenylephrine in aortic and superior mesenteric arterial rings were recorded. Inducible (i) and endothelial (3) nitric oxide synthase (NOS), cyclooxygenase-1 (COX-1), and protein kinase C-α (PKC-α) levels were determined by Western blotting. RESULTS: EA significantly reduced portal pressure and serum TNF-α, NOx and 6-keto-PGF1α levels compared to the untreated BDL group, enhanced maximum contractile responses in the aorta, up-regulated PKC-α, and down-regulated iNOS and COX-1 levels. In addition, EA decreased the aortic angiogenesis signaling cascade, reflected by down-regulation of vascular endothelial growth factor (VEGF) abundance and transforming growth factor ß receptor (TGFßR)I/II expression, as assessed by immunostaining. CONCLUSION: EA attenuates TNF-α, NO and 6-keto-PGF1α overproduction, modulates the vascular levels of constitutive NOS and PKC-α, blunts the development of the angiogenesis cascade, and enhances vascular contractile force in PHT rats.

Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment.

Human cardiac regeneration is limited by low cardiomyocyte replicative rates and progressive polyploidization by unclear mechanisms. To study this process, we engineer a human cardiomyocyte model to track replication and polyploidization using fluorescently tagged cyclin B1 and cardiac troponin T. Using time-lapse imaging, in vitro cardiomyocyte replication patterns recapitulate the progressive mononuclear polyploidization and replicative arrest observed in vivo. Single-cell transcriptomics and chromatin state analyses reveal that polyploidization is preceded by sarcomere assembly, enhanced oxidative metabolism, a DNA damage response, and p53 activation. CRISPR knockout screening reveals p53 as a driver of cell-cycle arrest and polyploidization. Inhibiting sarcomere function, or scavenging ROS, inhibits cell-cycle arrest and polyploidization. Finally, we show that cardiomyocyte engraftment in infarcted rat hearts is enhanced 4-fold by the increased proliferation of troponin-knockout cardiomyocytes. Thus, the sarcomere inhibits cell division through a DNA damage response that can be targeted to improve cardiomyocyte replacement strategies.

Dynamic transcriptomic m5 C and its regulatory role in RNA processing.

RNA 5-methylcytosine (m5 C) is a prevalent RNA modification in multiple RNA species, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and noncoding RNAs (ncRNAs), and broadly distributed from archaea, prokaryotes to eukaryotes. The multiple detecting techniques of m5 C have been developed, such as m5 C-RIP-seq, miCLIP-seq, AZA-IP-seq, RNA-BisSeq, TAWO-seq, and Nanopore sequencing. These high-throughput techniques, combined with corresponding analysis pipeline, provide a precise m5 C landscape contributing to the deciphering of its biological functions. The m5 C modification is distributed along with mRNA and enriched around 5'UTR and 3'UTR, and conserved in tRNAs and rRNAs. It is dynamically regulated by its related enzymes, including methyltransferases (NSUN, DNMT, and TRDMT family members), demethylases (TET families and ALKBH1), and binding proteins (ALYREF and YBX1). So far, accumulative studies have revealed that m5 C participates in a variety of RNA metabolism, including mRNA export, RNA stability, and translation. Depletion of m5 C modification in the organism could cause dysfunction of mitochondria, drawback of stress response, frustration of gametogenesis and embryogenesis, abnormality of neuro and brain development, and has been implicated in cell migration and tumorigenesis. In this review, we provide a comprehensive summary of dynamic regulatory elements of RNA m5 C, including methyltransferases (writers), demethylases (erasers), and binding proteins (readers). We also summarized the related detecting technologies and biological functions of the RNA 5-methylcytosine, and provided future perspectives in m5 C research. This article is categorized under: RNA Processing > RNA Editing and Modification.

Role of mesenteric component in Crohn's disease: A friend or foe?

Crohn's disease (CD) is a complex and relapsing gastrointestinal disease with mesenteric alterations. The mesenteric neural, vascular, and endocrine systems actively take part in the gut dysbiosis-adaptive immunity-mesentery-body axis, and this axis has been proven to be bidirectional. The abnormalities of morphology and function of the mesenteric component are associated with intestinal inflammation and disease progress of CD via responses to afferent signals, neuropeptides, lymphatic drainage, adipokines, and functional cytokines. The hypertrophy of mesenteric adipose tissue plays important roles in the pathogenesis of CD by secreting large amounts of adipokines and representing a rich source of proinflammatory or profibrotic cytokines. The vascular alteration, including angiogenesis and lymphangiogenesis, is concomitant in the disease course of CD. Of note, the enlarged and obstructed lymphatic vessels, which have been described in CD patients, are likely related to the early onset submucosa edema and being a cause of CD. The function of mesenteric lymphatics is influenced by endocrine of mesenteric nerves and adipocytes. Meanwhile, the structure of the mesenteric lymphatic vessels in hypertrophic mesenteric adipose tissue is mispatterned and ruptured, which can lead to lymph leakage. Leaky lymph factors can in turn stimulate adipose tissue to proliferate and effectively elicit an immune response. The identification of the role of mesentery and the crosstalk between mesenteric tissues in intestinal inflammation may shed light on understanding the underlying mechanism of CD and help explore new therapeutic targets.

Probing CRISPR-Cas12a Nuclease Activity Using Double-Stranded DNA-Templated Fluorescent Substrates.

The CRISPR-Cas12a nuclease shreds short single-stranded DNA (ssDNA) substrates indiscriminately through trans-cleavage upon activation with a specific target DNA. This shredding activity offered the potential for development of ssDNA-templated probes with fluorescent dye (F) and quencher (Q) labels. However, the formulations of double-stranded DNA (dsDNA)-templated fluorescent probes have not been reported possibly due to unknown (or limited) activity of Cas12a against short dsDNAs. The ssDNA probes have been shown to be powerful for diagnostic applications; however, limiting the probe selections to short ssDNAs could be restrictive from an application and probe diversification standpoint. Here, we report a dsDNA substrate (probe-full) for probing Cas12a trans-cleavage activity upon target detection. A diverse set of Cas12a substrates with alternating dsDNA character were designed and studied using fluorescence spectroscopy. We have observed that probe-full without any nick displayed trans-cleavage performance that was better than that of the form that contains a nick. Different experimental conditions of salt concentration, target concentration, and mismatch tolerance were examined to evaluate the probe performance. The activity of Cas12a was programmed for a dsDNA frame copied from a tobacco curly shoot virus (TCSV) or hepatitis B virus (HepBV) genome by using crRNA against TCSV or HepBV, respectively. While on-target activity offered detection of as little as 10 pM dsDNA target, off-target activity was not observed even at 1 nM control DNAs. This study demonstrates that trans-cleavage of Cas12a is not limited to ssDNA substrates, and Cas12a-based diagnostics can be extended to dsDNA substrates.

Author Correction: Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer featured with high intra-tumoral heterogeneity and poor prognosis. To comprehensively delineate the PDAC intra-tumoral heterogeneity and the underlying mechanism for PDAC progression, we employed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomic atlas of 57,530 individual pancreatic cells from primary PDAC tumors and control pancreases, and identified diverse malignant and stromal cell types, including two ductal subtypes with abnormal and malignant gene expression profiles respectively, in PDAC. We found that the heterogenous malignant subtype was composed of several subpopulations with differential proliferative and migratory potentials. Cell trajectory analysis revealed that components of multiple tumor-related pathways and transcription factors (TFs) were differentially expressed along PDAC progression. Furthermore, we found a subset of ductal cells with unique proliferative features were associated with an inactivation state in tumor-infiltrating T cells, providing novel markers for the prediction of antitumor immune response. Together, our findings provide a valuable resource for deciphering the intra-tumoral heterogeneity in PDAC and uncover a connection between tumor intrinsic transcriptional state and T cell activation, suggesting potential biomarkers for anticancer treatment such as targeted therapy and immunotherapy.

5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs.

Although 5-methylcytosine (m5C) is a widespread modification in RNAs, its regulation and biological role in pathological conditions (such as cancer) remain unknown. Here, we provide the single-nucleotide resolution landscape of messenger RNA m5C modifications in human urothelial carcinoma of the bladder (UCB). We identify numerous oncogene RNAs with hypermethylated m5C sites causally linked to their upregulation in UCBs and further demonstrate YBX1 as an m5C 'reader' recognizing m5C-modified mRNAs through the indole ring of W65 in its cold-shock domain. YBX1 maintains the stability of its target mRNA by recruiting ELAVL1. Moreover, NSUN2 and YBX1 are demonstrated to drive UCB pathogenesis by targeting the m5C methylation site in the HDGF 3' untranslated region. Clinically, a high coexpression of NUSN2, YBX1 and HDGF predicts the poorest survival. Our findings reveal an unprecedented mechanism of RNA m5C-regulated oncogene activation, providing a potential therapeutic strategy for UCB.

Ursodeoxycholic Acid Regulates Hepatic Energy Homeostasis and White Adipose Tissue Macrophages Polarization in Leptin-Deficiency Obese Mice.

Obesity has been shown to play a role in the pathogenesis of several forms of metabolic syndrome, including non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes. Ursodeoxycholic acid (UDCA) has been shown to possess antioxidant and anti-inflammatory properties and prevents mitochondrial dysfunction in the progression of obesity-associated diseases. The aim of the study was to evaluate the mechanisms of UDCA during obesity-linked hepatic mitochondrial dysfunction and obesity-associated adipose tissue macrophage-induced inflammation in obese mice. UDCA significantly decreased lipid droplets, reduced free fatty acids (FFA) and triglycerides (TG), improved mitochondrial function, and enhanced white adipose tissue browning in ob/ob mice. This is associated with increased hepatic energy expenditure, mitochondria biogenesis, and incorporation of bile acid metabolism (Abca1, Abcg1 mRNA and BSEP, FGFR4, and TGR5 protein). In addition, UDCA downregulated NF-κB and STAT3 phosphorylation by negative regulation of the expression of SOCS1 and SOCS3 signaling. These changes were accompanied by decreased angiogenesis, as shown by the downregulation of VEGF, VCAM, and TGF-ßRII expression. Importantly, UDCA is equally effective in reducing whole body adiposity. This is associated with decreased adipose tissue expression of macrophage infiltration (CD11b, CD163, and CD206) and lipogenic capacity markers (lipofuscin, SREBP-1, and CD36). Furthermore, UDCA significantly upregulated adipose browning in association with upregulation of SIRT-1-PGC1-α signaling in epididymis adipose tissue (EWAT). These results suggest that multi-targeted therapies modulate glucose and lipid biosynthesis fluxes, inflammatory response, angiogenesis, and macrophage differentiation. Therefore, it may be suggested that UDCA treatment may be a novel therapeutic agent for obesity.

Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome.

RNA-binding proteins (RBPs) play pivotal roles in directing RNA fate and function. Yet the current annotation of RBPs is largely limited to proteins carrying known RNA-binding domains. To systematically reveal dynamic RNA-protein interactions, we surveyed the human proteome by a protein array-based approach and identified 671 proteins with RNA-binding activity. Among these proteins, 525 lack annotated RNA-binding domains and are enriched in transcriptional and epigenetic regulators, metabolic enzymes, and small GTPases. Using an improved CLIP (crosslinking and immunoprecipitation) method, we performed genome-wide target profiling of isocitrate dehydrogenase 1 (IDH1), a novel RBP. IDH1 binds to thousands of RNA transcripts with enriched functions in transcription and chromatin regulation, cell cycle and RNA processing. Purified IDH1, but not an oncogenic mutant, binds directly to GA- or AU-rich RNA that are also enriched in IDH1 CLIP targets. Our study provides useful resources of unconventional RBPs and IDH1-bound transcriptome, and convincingly illustrates, for the first time, the in vivo and in vitro RNA targets and binding preferences of IDH1, revealing an unanticipated complexity of RNA regulation in diverse cellular processes.