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Background: Pressure on carotid artery by hyoid bone may influence plaque formation. We studied CTA-based hyoid-carotid anatomical interaction and its relationship with carotid stenosis degree and stenosis-related stroke., Methods: We retrospectively analysed pre-operative CTA of 205 consecutive adults having undergone carotid endarterectomy (CEA) for asymptomatic or symptomatic stenosis. Radiological measurements were: degree stenosis, hyoid-carotid distance, carotid position in regard to hyoid, and hyoid morphology., Results: In total, 410 carotids (including 114 symptomatic and 296 asymptomatic stenotic and non-stenotic carotids) from 205 CEA patients (median age 74, 72% men) were analysed. Median carotid stenosis was 61% (70% for symptomatic and 51% for asymptomatic carotids, p<0.0001; 70% for CEA and 30.5% for non-CEA carotids, p<0.0001). None of the other radiological parameters differed between asymptomatic/symptomatic carotids, between non-CEA/CEA carotids, or between asymptomatic/symptomatic patients. Median hyoid-carotid distance was 4.3mm, with 82% of carotids in posterolateral quadrant position in regard to the hyoid. There was no correlation between stenosis degree and hyoid-carotid distance (rho=-0.039), hyoid width (rho=-0.079), length (rho=0.007) or circumferential length (rho=-0.005), and stenosis degree was comparable between different carotid position quadrants (p=0.51)., Conclusions: Hyoid-carotid distance, hyoid position and morphology are not correlated with the degree of carotid stenosis or symptomatic carotid stenosis., Clinical Trial Registration-Url: http://www., Clinicaltrials: gov: Unique identifier: NCT05349526., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

Background: Periventricular white matter hyperintensities (PVWMHs) in cerebral amyloid angiopathy (CAA) have been reported posterior predominant using semiautomated segmentation method and logarithmic transformation. We aimed to compare PVWMH extent and posterior/anterior distribution between patients with CAA and patients with hypertensive arteriopathy with radiological tools available in daily practice., Methods: We retrospectively analyzed confluent PVWMH directly adjacent to lateral ventricles on axial FLAIR (fluid-attenuated inversion recovery) from 108 patients with CAA and 99 patients with hypertensive arteriopathy presenting with hemorrhage-related symptoms consecutively recruited in our stroke database (Nîmes University Hospital, France) between January 2015 and March 2022. For each of the left (L), right (R), anterior (A), and posterior (P) horns of lateral ventricles, the maximal distance between the outer PVWMH border and ventricle border was measured. The sum of anterior left PVWMH and anterior right PVWMH, and posterior left PVWMH and posterior right PVWMH resulted in anterior and posterior extent, respectively., Results: Compared with hypertensive arteriopathy, patients with CAA were older (median, 77 versus 71; P =0.0010) and less frequently male (46% versus 64%; P =0.012) and had less frequent hypertension (45% versus 63%; P =0.013) and more chronic hemorrhages ( P <0.0001). CAA showed slightly more extensive anterior right PVWMH (median, 6.50 versus 5.90 mm; P =0.034), far more extensive (all P <0.0001) posterior left PVWMH (median, 13.95 versus 6.95 mm), posterior right PVWMH (median, 14.15 versus 5.45 mm), posterior (median, 27.95 versus 13.00 mm), and total (median, 39.60 versus 24.65 mm) PVWMH, and higher posterior/anterior ratios (median, 1.82 versus 1.01). Age-/sex-adjusted model predicting CAA incorporating total PVWMH extent and posterior/anterior ratios for the given score (-4.3683+0.0268×PVWMH-T+0.3749×posterior/anterior PVWMH ratio+0.0394×age+0.3046 when female) showed highest area under the curve (0.76 [0.70-0.83]), with a 72% [62.50-80.99] sensitivity and 76% [67.18-84.12] specificity. Values above the optimal threshold of 0.22 for the score showed a crude relative risk of 2.75 (2.26-2.37; P <0.0001)., Conclusions: Severe posterior PVWMH and high posterior/anterior PVWMH ratio assessed by radiological tools used in daily practice are associated with probable CAA versus hypertensive arteriopathy., Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT05486897., Competing Interests: None.

Background and Objectives: The aim of this study was to identify novel biomarkers for multiple sclerosis (MS) diagnosis and prognosis, addressing the critical need for specific and prognostically valuable markers in the field., Methods: We conducted an extensive proteomic investigation, combining analysis of (1) CSF proteome from symptomatic controls, fast and slow converters after clinically isolated syndromes, and patients with relapsing-remitting MS (n = 10 per group) using label-free quantitative proteomics and (2) oligodendrocyte secretome changes under proinflammatory or proapoptotic conditions using stable isotope labeling by amino acids in cell culture. Proteins exhibiting differential abundance in both proteomic analyses were combined with other putative MS biomarkers, yielding a comprehensive list of 87 proteins that underwent quantification through parallel reaction monitoring (PRM) in a novel cohort, comprising symptomatic controls, inflammatory neurologic disease controls, and patients with MS at various disease stages (n = 10 per group). The 11 proteins that passed this qualification step were subjected to a new PRM assay within an expanded cohort comprising 158 patients with either MS at different disease stages or other inflammatory or noninflammatory neurologic disease controls., Results: This study unveiled a promising biomarker signature for MS, including previously established candidates, such as chitinase 3-like protein 1, chitinase 3-like protein 2, chitotriosidase, immunoglobulin kappa chain region C, neutrophil gelatinase-associated lipocalin, and CD27. In addition, we identified novel markers, namely cat eye syndrome critical region protein 1 (adenosine deaminase 2, a therapeutic target in multiple sclerosis) and syndecan-1, a proteoglycan, also known as plasma cell surface marker CD138 and acting as chitinase 3-like protein 1 receptor implicated in inflammation and cancer signaling. CD138 exhibited good diagnostic accuracy in distinguishing MS from inflammatory neurologic disorders (area under the curve [AUC] = 0.85, CI 0.75-0.95). CD138 immunostaining was also observed in the brains of patients with MS and cultured oligodendrocyte precursor cells but was absent in astrocytes., Discussion: These findings identify CD138 as a specific CSF biomarker for MS and suggest the selective activation of the chitinase 3-like protein 1/CD138 pathway within the oligodendrocyte lineage in MS. They offer promising prospects for improving MS diagnosis and prognosis by providing much-needed specificity and clinical utility., Classification of Evidence: This study provides Class II evidence that CD138 distinguishes multiple sclerosis from other inflammatory neurologic disorders with an AUC of 0.85 (95% CI 0.75-0.95).

Objectives: Primary acute convexity subarachnoid hemorrhage (cSAH) in older patients can be observed in cerebral amyloid angiopathy (CAA) or idiopathic (with cSAH as potential initial manifestation of suspected CAA). We aimed to analyze baseline, clinical and MRI (including quantitative cSAH surface analysis and topographical probabilistic cSAH mapping) characteristics in elderly cSAH patients with CAA., Materials and Methods: Baseline/clinical/MRI characteristics of 50 consecutive primary acute cSAH patients ≥ 55 years with suspected/possible/probable CAA were retrospectively analyzed., Results: Median age was 74, with 26% of patients showing suspected, 22% possible and 52% probable CAA. Transient focal neurological episode (TFNE) was observed in 78%, with spreading symptoms in 79% (median spreading speed five minutes), a median of two episodes before cSAH diagnosis, and similar symptoms in 91% when multiple TFNE, with a median duration of 15 min. Motor/sensory/speech/visual symptoms were observed in 85%/69%/46%/8%, respectively, and brachiofacial/brachial was the most frequent distribution for sensory-motor symptoms. Positive clinical-radiological correlation was observed in 84%, headache in 22%, and antiepileptics started in 78%. MRI showed chronic intracerebral hemorrhage in 10%, cortical superficial siderosis in 68%, cerebral microbleeds in 48%, median total Fazekas score of 3, lacunes in 6% and DWI lesion (all unique/cortical/ < 10 mm) in 6%. cSAH involved a median of 1 sulcus, with central sulcus as most frequently (47.5%) involved followed by precentral sulcus (17%). Median cSAH surface was 2170 mm 2 . No baseline, clinical or MRI characteristics were associated with cSAH surface extent in multivariate analysis., Conclusions: Baseline, clinical, or MRI features seem not to influence CAA-related cSAH extent., Clinical Trial Registration-Url: http://www., Clinicaltrials: gov . Unique identifier: NCT04825808., (© 2022. The Author(s) under exclusive licence to Belgian Neurological Society.)

Background and Objectives: In stroke patients treated with intravenous thrombolysis (IVT), presence and high number of strictly lobar cerebral microbleeds (compatible with cerebral amyloid angiopathy, CAA) seems to be associated with increased risk of hemorrhagic transformation, symptomatic hemorrhagic transformation, remote hemorrhage, and poor functional outcome. Some of these CAA patients with cerebral microbleeds also have chronic lobar intracerebral hemorrhage. Few data are available on IVT-treated CAA patients showing cortical superficial siderosis. There are no reports studying factors associated with brain hemorrhagic complication or functional outcome in IVT-treated CAA patients. We present a case series study of IVT-treated stroke patients with CAA features on pre-IVT MRI in whom we have evaluated brain hemorrhagic complications on 24 h-CT and functional outcome after IVT., Material and Methods: In our stroke center, IVT decision in patients with CAA MRI features is at the physician's discretion. We retrospectively screened our stroke database between January 2015 and July 2022 for pre-IVT imaging of 959 consecutive IVT-treated stroke patients without ongoing anticoagulation therapy for probable CAA MRI features defined by modified Boston criteria. After exclusion of 119 patients with missing MRI (n = 47), MRI showing motion artefacts (n = 49) or with alternative chronic brain hemorrhage cause on MRI (n = 23), 15 IVT-treated patients with probable CAA on pre-IVT MRI were identified. In these 15 patients, clinical, biological and MRI characteristics were compared between patients with vs. without post-IVT hemorrhage and between patients with poor (MRS 3-6) vs. good (MRS 0-2) functional outcome at discharge., Results: Two patients showed brain hemorrhage on 24 h-CT and both died after 40 and 31 days respectively. The remaining patients had no brain hemorrhage and showed very good outcome except one. Atrial fibrillation (p = 0.029) and Fazekas scale (p = 0.029) were associated with brain hemorrhage whereas atrial fibrillation (p = 0.0022), NIHSS (p = 0.027), blood glucose level (p = 0.024), CRP (p = 0.022) and DWI ASPECT (p = 0.016) were associated with poor outcome., Discussion: Consequences of IVT in CAA patients can be dramatic. Larger studies are needed to compare IVT risks and outcome between CAA and non-CAA patients, also including CAA patients with chronic intracerebral hemorrhage or cortical superficial siderosis. In addition, future studies should try to identify clinical, biological and radiological features at high risk for brain hemorrhage and poor outcome in order to assess the risk-benefit ratio for IVT in CAA., Clinical Trial Registration-Url: http://www., Clinicaltrials: gov. Unique identifier: NCT05565144., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background and Aims: Multiple sclerosis (MS) is associated with osteoporosis, possibly due to neurological disability and decreased calcium intake. The objective of this study was to evaluate the efficacy of a personalized nutritional advice program by a dietitian compared to the delivery of a standard advice form to optimize dietary calcium intake in outpatients with MS., Methods: We performed a randomized, controlled, parallel trial comparing the efficacy of a personalized dietary advice (PDA) program to standard advice form (SAF) to increase daily calcium intake in MS patients. The study population was composed by patients with relapsing-remitting MS aged 18-69 years old. PDA program consisted in dietary advice delivered by a dietitian at baseline, 1 month, and 3 months. Calcium and nutrient intake in patients from both groups was evaluated at baseline and 6 months using a dietary survey., Results: Of the 194 patients screened for inclusion, 182 patients were included (79% female, median age of 42 years, and median EDSS of 2.0), and randomized to SAF ( n = 92) or PDA ( n = 90). At 6 months, median calcium intake increased by 241 mg/day in the PDA group and decreased by 120 mg/day in the SAF group ( p < 0.0001). However, the median calcium intake was 947 mg/day in the SAF group and 778 mg/day in the PDA group at baseline ( p = 0.0077), potentially favoring the effect of dietary advice. Complementary analyses focusing on patients with insufficient calcium intakes at baseline revealed comparable values in both groups ( p = 0.69). Of those, patients included in the PDA group obtained significantly higher calcium intakes at 6 months than patients from the SAF group ( p = 0.0086) independently of EDSS, PASAT, HADS and EQ-5D scores., Conclusion: This work shows the efficacy of dietary management based on personalized advice program over 3 months to durably increase calcium consumption in MS patients with insufficient calcium intake., Clinical Trial Registration: clinicaltrials.gov, identifier NCT02664623., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Fiorella, Agherbi, El Houjeiry, Castelnovo, Renard, Privat, Santamaria, Vallayer, Alonso, Chevallier, Bancal, Laurent-Chabalier and Thouvenot.)

Background and Objectives: Kappa free light chains (KFLC) seem to efficiently diagnose MS. However, extensive cohort studies are lacking to establish consensus cut-offs, notably to rule out non-MS autoimmune CNS disorders. Our objectives were to (1) determine diagnostic performances of CSF KFLC, KFLC index, and KFLC intrathecal fraction (IF) threshold values that allow us to separate MS from different CNS disorder control populations and compare them with oligoclonal bands' (OCB) performances and (2) to identify independent factors associated with KFLC quantification in MS., Methods: We conducted a retrospective multicenter study involving 13 French MS centers. Patients were included if they had a noninfectious and nontumoral CNS disorder, eligible data concerning CSF and serum KFLC, albumin, and OCB. Patients were classified into 4 groups according to their diagnosis: MS, clinically isolated syndrome (CIS), other inflammatory CNS disorders (OIND), and noninflammatory CNS disorder controls (NINDC)., Results: One thousand six hundred twenty-one patients were analyzed (675 MS, 90 CIS, 297 OIND, and 559 NINDC). KFLC index and KFLC IF had similar performances in diagnosing MS from nonselected controls and OIND ( p = 0.123 and p = 0.991 for area under the curve [AUC] comparisons) and performed better than CSF KFLC ( p < 0.001 for all AUC comparisons). A KFLC index of 8.92 best separated MS/CIS from the entire nonselected control population, with better performances than OCB ( p < 0.001 for AUC comparison). A KFLC index of 11.56 best separated MS from OIND, with similar performances than OCB ( p = 0.065). In the multivariate analysis model, female gender ( p = 0.003), young age ( p = 0.013), and evidence of disease activity ( p < 0.001) were independent factors associated with high KFLC index values in patients with MS, whereas MS phenotype, immune-modifying treatment use at sampling, and the FLC analyzer type did not influence KFLC index., Discussion: KFLC biomarkers are efficient tools to separate patients with MS from controls, even when compared with other patients with CNS autoimmune disorder. Given these results, we suggest using KFLC index or KFLC IF as a criterion to diagnose MS., Classification of Evidence: This study provides Class III evidence that KFLC index or IF can be used to differentiate patients with MS from nonselected controls and from patients with other autoimmune CNS disorders., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.)

Background and Objectives: To evaluate the predictive value of serum neurofilament light chain (sNfL) and CSF NfL (cNfL) in patients with radiologically isolated syndrome (RIS) for evidence of disease activity (EDA) and clinical conversion (CC)., Methods: sNfL and cNfL were measured at RIS diagnosis by single-molecule array (Simoa). The risk of EDA and CC according to sNfL and cNfL was evaluated using the Kaplan-Meier analysis and multivariate Cox regression models including age, spinal cord (SC) or infratentorial lesions, oligoclonal bands, CSF chitinase 3-like protein 1, and CSF white blood cells., Results: Sixty-one patients with RIS were included. At diagnosis, sNfL and cNfL were correlated (Spearman r = 0.78, p < 0.001). During follow-up, 47 patients with RIS showed EDA and 36 patients showed CC (median time 12.6 months, 1-86). When compared with low levels, medium and high cNfL (>260 pg/mL) and sNfL (>5.0 pg/mL) levels were predictive of EDA (log rank, p < 0.01 and p = 0.02, respectively). Medium-high cNfL levels were predictive of CC (log rank, p < 0.01). In Cox regression models, cNfL and sNfL were independent factors of EDA, while SC lesions, cNfL, and sNfL were independent factors of CC., Discussion: cNfL >260 pg/mL and sNfL >5.0 pg/mL at diagnosis are independent predictive factors of EDA and CC in RIS. Although cNfL predicts disease activity better, sNfL is more accessible than cNfL and can be considered when a lumbar puncture is not performed., Classification of Evidence: This study provides Class II evidence that in people with radiologic isolated syndrome (RIS), initial serum and CSF NfL levels are associated with subsequent evidence of disease activity or clinical conversion., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.)

Background and Purpose: Intraplaque hemorrhage is a key feature of vulnerable carotid atherosclerotic plaque (CAP), associated with low densities (<25 Hounsfield units [HU]) on computed tomographic angiography (CTA). This study aimed to analyze CAP on routine CTA performed in patients with symptomatic and asymptomatic carotid stenosis undergoing carotid endarterectomy (CEA) by assessing HU of the CAP area showing the lowest density (CAPALD) using radiological tools available in daily clinical practice, and to compare CAPALD values between symptomatic and asymptomatic carotids., Methods: We retrospectively screened preoperative CTA scans of 206 consecutive adult patients undergoing CEA for symptomatic or asymptomatic stenosis. CAPALD values were compared between symptomatic and asymptomatic carotids. Asymptomatic carotids included arteries contralateral to the symptomatic CEA artery, and asymptomatic stenotic arteries undergoing CEA and their contralateral arteries. Carotids were excluded when there was <30% stenosis, or when CAP could not be identified or CAPALD could not be measured., Results: In total, 95 symptomatic and 112 asymptomatic carotids (derived from 174 patients) were analyzed. In multivariate analysis, symptomatic arteries showed more severe stenosis (median 70% vs. 67%, p = 0.0228) and lower CAPALD values (median 17 vs. 25 HU, p = 0.049), whereas degree of stenosis and CAPALD values were not correlated (rho = -0.02, p = 0.77). HU values of <25 were more frequent in symptomatic than asymptomatic carotids (68% vs. 47%, p = 0.0022)., Conclusions: On CTA, symptomatic carotids are associated with CAP areas with low densities. CTA analysis of CAP may be interesting to help identify vulnerable plaques at risk for future stroke, especially in patients lacking strict indications for CEA based on the current guidelines., (© 2021 European Academy of Neurology.)

We compared Simoa TM and Ella TM immunoassays to assess serum neurofilament-light chain levels in 203 multiple sclerosis patients from the OFSEP HD study. There was a strong correlation (ρ = 0.86, p < 0.0001) between both platforms. The Ella TM instrument overestimated values by 17%, but as the data were linear (p = 0.57), it was possible to apply a correction factor to Ella TM results. As for Simoa TM , serum neurofilament-light chain levels measured by Ella TM were correlated with age and EDSS and were significantly higher in active multiple sclerosis, suggesting that these assays are equivalent and can be used in routine clinical practice., (© 2021 The Authors. Annals of Clinical and Translational Neurology published by Wiley Periodicals LLC on behalf of American Neurological Association.)

Introduction: 3,4-Dihydroxy-6-[ 18 F]-fluoro-L-phenylalanine (FDOPA) positron emission tomography (PET) is sensitive for identifying primary brain tumors. However, increased FDOPA uptake has been reported in pseudotumoral brain lesions. Our aim was to analyse FDOPA-PET in patients with pseudotumoral brain lesions and to compare them with patients with brain tumors., Methods: We retrospectively analysed consecutively recruited patients with suspected primary brain tumor (based on clinical and magnetic resonance imaging findings) referred for FDOPA-PET in our centre between November 2013 and June 2019 (n = 74). FDOPA-PET parameters (maximum and mean lesion standardised uptake values [SUV] and ratios comparing lesion with different background uptake SUV) and thresholds were evaluated to determine which offered optimal discrimination between pseudotumoral and tumoral lesions., Results: Overlapping PET values were observed between pseudotumoral (n = 26) and tumoral (n = 48) lesion, particularly for low-grade tumors. Based on receiver operating characteristic (ROC) analyses, the optimal PET parameters to discriminate pseudotumoral from tumoral lesions were SUV max lesion/basal ganglia, SUV max lesion/grey matter, SUV mean lesion/grey matter, and SUV max lesion/mirror area in contralateral hemisphere (all ratios showing area under the curve [AUC] 0.85, 95% CI). The narrowest 95% sensitivity-95% specificity window was observed for SUV max lesion/basal ganglia ratio, with ratio values of 0.79 and 1.35 corresponding to 95% sensitivity and 95% specificity, respectively., Conclusion: FDOPA-PET uptake should be interpreted with caution in patients with suspected primary brain tumor, especially in patients showing low or intermediate SUV values and ratios. CLINICAL TRIAL REGISTRATION-URL: https://www.clinicaltrials.gov . Unique identifier: NCT04306484.

Background: Acute infarction patterns have been described in cardioembolic stroke, mainly with atrial fibrillation (AF) or patent foramen ovale. We aimed to analyse acute infarction magnetic resonance imaging (MRI) characteristics in stroke patients with intracardiac thrombus (ICT) compared with stroke patients with AF., Methods: We performed a retrospective study analysing brain MRI scans of consecutive acute symptomatic cardioembolic infarction patients associated with ICT or AF who were recruited and registered in the stroke database between June 2018 and November 2019. Diffusion-weighted imaging performed within 1 week after symptom onset, intra-/extracranial vessel imaging, echocardiography, and ≥24-h ECG monitoring were required for inclusion. Baseline, biological, and echocardiography characteristics were assessed. Analysed MRI characteristics were infarction location (anterior/middle/posterior cerebral artery territory; anterior/posterior/mixed anterior-posterior circulation; multiterritorial infarction; brainstem; cerebellum; small cortical cerebellar infarctions [SCCIs] or non-SCCI; cortical/subcortical/cortico-subcortical), lesion number, subcortical lesion size (> or <15 mm), and total infarction volume., Results: We included 28 ICT and 94 AF patients presenting with acute stroke. ICT patients were younger (median age 66 vs. 81 years, p < 0.001), more frequently male (79 vs. 47%, p = 0.003), and smokers (39 vs. 17%, p = 0.013), had more frequent history of diabetes (36 vs. 18%, p = 0.049) and ischaemic heart disease (57 vs. 21%, p < 0.001), and had lower HDL cholesterol levels (0.39 vs. 0.53 g/L, p < 0.001). On MRI, SCCI was more frequent in the ICT group (25 vs. 5%, p = 0.006) in the absence of other differences in infarction localisation, number, size, or volume on MRI. On multivariate analysis, younger age (p < 0.001), history of ischaemic heart disease (p < 0.001), and low HDL cholesterol levels (p = 0.01) were significantly associated with ICT. Results approaching statistical significance were observed for SCCI (more frequent in the ICT group, p = 0.053) and non-SCCI (more frequent in the AF group, p = 0.053) on MRI., Conclusions: ICT-related stroke is associated with acute SCCI presence on MRI. Clinical Trial Registration-URL: http://www.clinicaltrials.gov. Unique identifier: NCT04456309., (© 2021 S. Karger AG, Basel.)

Activating mutations in NOTCH1, an essential regulator of T cell development, are frequently found in human T cell acute lymphoblastic leukemia (T-ALL). Despite important advances in our understanding of Notch signal transduction, the regulation of Notch functions in the nucleus remains unclear. Using immunoaffinity purification, we identified NOTCH1 nuclear partners in T-ALL cells and showed that, beyond the well-characterized core activation complex (ICN1-CSL-MAML1), NOTCH1 assembles a multifunctional complex containing the transcription coactivator AF4p12, the PBAF nucleosome remodeling complex, and the histone demethylases LSD1 and PHF8 acting through their demethylase activity to promote epigenetic modifications at Notch-target genes. Remarkably, LSD1 functions as a corepressor when associated with CSL-repressor complex and as a NOTCH1 coactivator upon Notch activation. Our work provides new insights into the molecular mechanisms that govern Notch transcriptional activity and represents glimpse into NOTCH1 interaction landscape, which will help in deciphering mechanisms of NOTCH1 functions and regulation., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Transcription elongation is increasingly recognized as an important mechanism of gene regulation. Here, we show that microprocessor controls gene expression in an RNAi-independent manner. Microprocessor orchestrates the recruitment of termination factors Setx and Xrn2, and the 3'-5' exoribonuclease, Rrp6, to initiate RNAPII pausing and premature termination at the HIV-1 promoter through cleavage of the stem-loop RNA, TAR. Rrp6 further processes the cleavage product, which generates a small RNA that is required to mediate potent transcriptional repression and chromatin remodeling at the HIV-1 promoter. Using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq), we identified cellular gene targets whose transcription is modulated by microprocessor. Our study reveals RNAPII pausing and premature termination mediated by the co-operative activity of ribonucleases, Drosha/Dgcr8, Xrn2, and Rrp6, as a regulatory mechanism of RNAPII-dependent transcription elongation., (Copyright © 2012 Elsevier Inc. All rights reserved.)

In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A overrepresentation at the 5' and 3' of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.

The idea that stem cells of adult tissues with high turnover are protected from DNA replication-induced mutations by maintaining the same 'immortal' template DNA strands together through successive divisions has been tested in several tissues. In the epithelium of the small intestine, the provided evidence was based on the assumption that stem cells are located above Paneth cells. The results of genetic lineage-tracing experiments point instead to crypt base columnar cells intercalated between Paneth cells as bona fide stem cells. Here we show that these cells segregate most, if not all, of their chromosomes randomly, both in the intact and in the regenerating epithelium. Therefore, the 'immortal' template DNA strand hypothesis does not apply to intestinal epithelial stem cells, which must rely on other strategies to avoid accumulating mutations.