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Measurement of the absolute branching fraction of the singly Cabibbo suppressed decay Λc⁺ → pη′
(2022)
The singly Cabibbo suppressed decay Λ+𝑐→𝑝𝜂′ is measured using 4.5 fb−1 of 𝑒+𝑒− collision data collected at center-of-mass energies between 4.600 and 4.699 GeV with the BESIII detector at BEPCII. Evidence for Λ+𝑐→𝑝𝜂′ with a statistical significance of 3.6𝜎 is reported with a double-tag approach. The Λ+𝑐→𝑝𝜂′ absolute branching fraction is determined to be (5.62+2.46−2.04±0.26)×10−4, where the first and second uncertainties are statistical and systematic, respectively. Our result is consistent with the branching fraction obtained by the Belle collaboration within the uncertainty of 1𝜎.
A search for a massless dark photon 𝛾′ is conducted using 4.5 fb−1 of 𝑒+𝑒− collision data collected at center-of-mass energies between 4.600 and 4.699 GeV with the BESIII detector at BEPCII. No significant signal is observed, and the upper limit on the branching fraction ℬ(Λ+𝑐→𝑝𝛾′) is determined to be 8.0×10−5 at 90% confidence level.
Measurement of the absolute branching fraction of the singly Cabibbo suppressed decay Λc⁺ → pη′
(2022)
The singly Cabibbo suppressed decay Λ+c→pη′ is measured using 4.5 fb−1 of e+e− collision data collected at center-of-mass energies between 4.600 and 4.699 GeV with the BESIII detector at BEPCII. Evidence for Λ+c→pη′ with a statistical significance of 3.6σ is reported with a double-tag approach. The Λ+c→pη′ absolute branching fraction is determined to be (5.62+2.46−2.04±0.26)×10−4, where the first and second uncertainties are statistical and systematic, respectively. Our result is consistent with the branching fraction obtained by the Belle collaboration within the uncertainty of 1σ.
Measurement of the absolute branching fraction of the singly Cabibbo suppressed decay Λc⁺ → pη′
(2022)
The singly Cabibbo suppressed decay Λ+c→pη′ is measured using 4.5 fb−1 of e+e− collision data collected at center-of-mass energies between 4.600 and 4.699 GeV with the BESIII detector at BEPCII. Evidence for Λ+c→pη′ with a statistical significance of 3.6σ is reported with a double-tag approach. The Λ+c→pη′ absolute branching fraction is determined to be (5.62+2.46−2.04±0.26)×10−4, where the first and second uncertainties are statistical and systematic, respectively. Our result is consistent with the branching fraction obtained by the Belle collaboration within the uncertainty of 1σ.
A search for a massless dark photon γ′ is conducted using 4.5 fb−1 of e+e− collision data collected at center-of-mass energies between 4.600 and 4.699 GeV with the BESIII detector at BEPCII. No significant signal is observed, and the upper limit on the branching fraction B(Λ+c→pγ′) is determined to be 8.0×10−5 at 90% confidence level.
A search for a massless dark photon γ′ is conducted using 4.5 fb−1 of e+e− collision data collected at center-of-mass energies between 4.600 and 4.699 GeV with the BESIII detector at BEPCII. No significant signal is observed, and the upper limit on the branching fraction B(Λ+c→pγ′) is determined to be 8.0×10−5 at 90% confidence level.
Using about 23 fb−1 of data collected with the BESIII detector operating at the BEPCII storage ring, a precise measurement of the e+e−→π+π−J/ψ Born cross section is performed at center-of-mass energies from 3.7730 to 4.7008 GeV. Two structures, identified as the Y(4220) and the Y(4320) states, are observed in the energy-dependent cross section with a significance larger than 10σ. The masses and widths of the two structures are determined to be (M,Γ) = (4221.4±1.5±2.0 MeV/c2, 41.8±2.9±2.7 MeV) and (M,Γ) = (4298±12±26 MeV/c2, 127±17±10 MeV), respectively. A small enhancement around 4.5 GeV with a significance about 3σ, compatible with the ψ(4415), might also indicate the presence of an additional resonance in the spectrum. The inclusion of this additional contribution in the fit to the cross section affects the resonance parameters of the Y(4320) state.
Luminosities and energies of e⁺e⁻ collision data taken between √s=4.61 GeV and 4.95 GeV at BESIII
(2022)
From December 2019 to June 2021, the BESIII experiment collected about 5.85 fb−1 of data at center-of-mass energies between 4.61 GeV and 4.95 GeV. This is the highest collision energy BEPCII has reached so far. The accumulated e+e− annihilation data samples are useful for studying charmonium(-like) states and charmed-hadron decays. By adopting a novel method of analyzing the production of Λ+cΛ¯−c pairs in e+e− annihilation, the center-of-mass energies are measured with a precision of ∼0.6 MeV. Integrated luminosities are measured with a precision of better than 1\% by analyzing the events of large-angle Bhabha scattering. These measurements provide important inputs to the analyses based on these data samples.
The radiative hyperon decay Λ→nγ is studied using (10087±44)×106 J/ψ events collected with the BESIII detector operating at BEPCII. The absolute branching fraction of the decay Λ→nγ is determined with a significance of 5.6σ to be [0.832±0.038(stat.)±0.054(syst.)]×10−3, which lies significantly below the current PDG value. By analyzing the joint angular distribution of the decay products, the first determination of the decay asymmetry αγ is reported with a value of −0.16±0.10(stat.)±0.05(syst.).
Using (10087±44)×106 J/ψ events collected with the BESIII detector, numerous Ξ− and Λ decay asymmetry parameters are simultaneously determined from the process J/ψ→Ξ−Ξ¯+→Λ(pπ−)π−Λ¯(n¯π0)π+ and its charge-conjugate channel. The precisions of α0 for Λ→nπ0 and α¯0 for Λ¯→n¯π0 compared to world averages are improved by factors of 4 and 1.7, respectively. The ratio of decay asymmetry parameters of Λ→nπ0 to that of Λ→pπ−, ⟨α0⟩/⟨αΛ−⟩, is determined to be 0.873±0.012+0.011−0.010, where the first and the second uncertainties are statistical and systematic, respectively. The ratio is smaller than unity more than 5σ, which signifies the existence of the ΔI=3/2 transition in Λ for the first time. Beside, we test for CP violation in Ξ−→Λπ− and in Λ→nπ0 with the best precision to date.
Observation of ηc(2S) → 3(π⁺π⁻) and measurements of χcJ → 3(π⁺π⁻) in ψ(3686) radiative transitions
(2022)
The hadronic decay 𝜂𝑐(2𝑆)→3(𝜋+𝜋−) is observed with a statistical significance of 9.3 standard deviations using (448.1±2.9)×106 𝜓(3686) events collected by the BESIII detector at the BEPCII collider. The measured mass and width of 𝜂𝑐(2𝑆) are (3643.4±2.3 (stat)±4.4 (syst)) MeV/𝑐2 and (19.8±3.9 (stat)±3.1 (syst)) MeV, respectively, which are consistent with the world average values within two standard deviations. The product branching fraction ℬ[𝜓(3686)→𝛾𝜂𝑐(2𝑆)]×ℬ[𝜂𝑐(2𝑆)→3(𝜋+𝜋−)] is measured to be (9.2±1.0 (stat)±1.2 (syst))×10−6. Using ℬ[𝜓(3686)→𝛾𝜂𝑐(2𝑆)]=(7.0+3.4−2.5)×10−4, we obtain ℬ[𝜂𝑐(2𝑆)→3(𝜋+𝜋−)]=(1.31±0.15 (stat)±0.17 (syst) (+0.64−0.47) (extr))×10−2, where the third uncertainty is from ℬ[𝜓(3686)→𝛾𝜂𝑐(2𝑆)]. We also measure the 𝜒𝑐𝐽→3(𝜋+𝜋−) (𝐽=0, 1, 2) decays via 𝜓′→𝛾𝜒𝑐𝐽 transitions. The branching fractions are ℬ[𝜒𝑐0→3(𝜋+𝜋−)]=(2.080±0.006 (stat)±0.068 (syst))×10−2, ℬ[𝜒𝑐1→3(𝜋+𝜋−)]=(1.092±0.004 (stat)±0.035 (syst))×10−2, and ℬ[𝜒𝑐2→3(𝜋+𝜋−)]=(1.565±0.005 (stat)±0.048 (syst))×10−2.
The cross sections of e+e−→K+K−J/ψ at center-of-mass energies from 4.127 to 4.600~GeV are measured based on 15.6 fb−1 data collected with the BESIII detector operating at the BEPCII storage ring. Two resonant structures are observed in the line shape of the cross sections. The mass and width of the first structure are measured to be (4225.3±2.3±21.5) MeV and (72.9±6.1±30.8)~MeV, respectively. They are consistent with those of the established Y(4230). The second structure is observed for the first time with a statistical significance greater than 8σ, denoted as Y(4500). Its mass and width are determined to be (4484.7±13.3±24.1) MeV and (111.1±30.1±15.2) MeV, respectively. The first presented uncertainties are statistical and the second ones are systematic. The product of the electronic partial width with the decay branching fraction Γ(Y(4230)→e+e−)B(Y(4230)→K+K−J/ψ) is reported.
Observation of ηc(2S) → 3(π⁺π⁻) and measurements of χcJ → 3(π⁺π⁻) in ψ(3686) radiative transitions
(2022)
The hadronic decay ηc(2S)→3(π+π−) is observed with a statistical significance of 9.3 standard deviations using (448.1±2.9)×106 ψ(3686) events collected by the BESIII detector at the BEPCII collider. The measured mass and width of ηc(2S) are (3643.4±2.3(stat.)±4.4(syst.)) MeV/c2 and (19.8±3.9(stat.)±3.1(syst.)) MeV, respectively, which are consistent with the world average values within two standard deviations. The product branching fraction B[ψ(3686) → γηc(2S)]×B[ηc(2S)→3(π+π−)] is measured to be (9.2±1.0(stat.)±0.9(syst.))×10−6. Using B[ψ(3686)→γηc(2S)]=(7.0+3.4−2.5)×10−4, we obtain B[ηc(2S)→3(π+π−)]=(1.31±0.15(stat.)±0.13(syst.)(+0.64−0.47)(extr))×10−2, where the third uncertainty is from B[ψ(3686)→γηc(2S)]. We also measure the χcJ→3(π+π−) (J=0,1,2) decays via ψ(3686)→γχcJ transitions. The branching fractions are B[χc0→3(π+π−)]=(2.080±0.006(stat.)±0.068(syst.))×10−2, B[χc1→3(π+π−)]=(1.092±0.004(stat.)±0.035(syst.))×10−2, and B[χc2→3(π+π−)]=(1.565±0.005(stat.)±0.048(syst.))×10−2.
Utilizing the data set corresponding to an integrated luminosity of 3.19 fb−1 collected by the BESIII detector at a center-of-mass energy of 4.178 GeV, we perform an amplitude analysis of the D+s→π+π−π+ decay. The sample contains 13,797 candidate events with a signal purity of ∼80%. We use a quasi-model-independent approach to measure the magnitude and phase of the D+s→π+π−π+ decay, where the P and D waves are parameterized by a sum of three Breit-Wigner amplitudes ρ(770)0, ρ(1450)0, and f2(1270). The fit fractions of different decay channels are also reported.
By analyzing an electron-positron collision data sample corresponding to an integrated luminosity of 2.93 fb−1 taken at the center-of-mass energy of 3.773 GeV with the BESIII detector, we obtain for the first time the absolute branching fractions for seven 𝐷0 and 𝐷+ hadronic decay modes and search for the hadronic decay 𝐷0→𝐾0𝑆𝐾0𝑆𝜋0 with much improved sensitivity. The results are ℬ(𝐷0→𝐾0𝑆𝜋0𝜋0𝜋0)=(7.64±0.30±0.29)×10−3, (𝐷0→𝐾−𝜋+𝜋0𝜋0𝜋0)=9.54±0.30±0.31)×10−3, ℬ(𝐷0→𝐾0𝑆𝜋+𝜋−𝜋0𝜋0)=(12.66±0.45±0.43)×10−3, ℬ(𝐷+→𝐾0𝑆𝜋+𝜋0𝜋0)=(29.04±0.62±0.87)×10−3, ℬ(𝐷+→𝐾0𝑆𝜋+𝜋+𝜋−𝜋0)=(15.28±0.57±0.60)×10−3, ℬ(𝐷+→𝐾0𝑆𝜋+𝜋0𝜋0𝜋0)=(5.54±0.44±0.32)×10−3, ℬ(𝐷+→𝐾−𝜋+𝜋+𝜋0𝜋0)=(4.95±0.26±0.19)×10−3, and ℬ(𝐷0→𝐾0𝑆𝐾0𝑆𝜋0)<1.45×10−4 at the 90% confidence level. Here, the first uncertainties are statistical, and the second ones are systematic. The newly studied decays greatly enrich the knowledge of the 𝐷→¯𝐾𝜋𝜋𝜋 and 𝐷→¯𝐾𝜋𝜋𝜋𝜋 hadronic decays and open a bridge to access more two-body hadronic 𝐷 decays containing scalar, vector, axial, and tensor mesons in the charm sector.
We report a search for a heavier partner of the recently observed Zcs(3985)− state, denoted as Z′−cs, in the process e+e−→K+D∗−sD∗0+c.c., based on e+e− collision data collected at the center-of-mass energies of s√=4.661, 4.682 and 4.699 GeV with the BESIII detector. The Z′−cs is of interest as it is expected to be a candidate for a hidden-charm and open-strange tetraquark. A partial-reconstruction technique is used to isolate K+ recoil-mass spectra, which are probed for a potential contribution from Z′−cs→D∗−sD∗0 (c.c.). We find an excess of Z′−cs→D∗−sD∗0 (c.c.) candidates with a significance of 2.1σ, after considering systematic uncertainties, at a mass of (4123.5±0.7stat.±4.7syst.) MeV/c2. As the data set is limited in size, the upper limits are evaluated at the 90\% confidence level on the product of the Born cross sections (σBorn) and the branching fraction (B) of Z′−cs→D∗−sD∗0, under different assumptions of the Z′−cs mass from 4.120 to 4.140 MeV and of the width from 10 to 50 MeV at the three center-of-mass energies. The upper limits of σBorn⋅B are found to be at the level of O(1) pb at each energy. Larger data samples are needed to confirm the Z′−cs state and clarify its nature in the coming years.
Utilizing the data set corresponding to an integrated luminosity of 3.19 fb−1 collected by the BESIII detector at a center-of-mass energy of 4.178 GeV, we perform an amplitude analysis of the 𝐷+
𝑠→𝜋+𝜋−𝜋+ decay. The sample contains 13,797 candidates with a signal purity of ∼80%. The amplitude and phase of the contributing 𝜋𝜋 𝒮 wave are measured based on a quasi-model-independent approach, along with the amplitudes and phases of the 𝒫 and 𝒟 waves parametrized by Breit-Wigner models. The fit fractions of different intermediate decay channels are also reported.
By analyzing e+e− annihilation data with an integrated luminosity of 2.93 fb−1 collected at the center-of-mass energy s√= 3.773 GeV with the BESIII detector, we present the first absolute measurements of the branching fractions of twenty Cabibbo-suppressed hadronic D0(+) decays involving multiple pions. The largest four branching fractions obtained are B(D0→π+π−π0) = >(1.343±0.013stat±0.016syst)%, B(D0→π+π−2π0) = (0.998±0.019stat±0.024syst)%, B(D+→2π+π−π0)
(1.174±0.021stat±0.021syst)%, and B(D+→2π+π−2π0) = (1.074±0.040stat±0.030syst)%. The CP asymmetries for the six decays with highest event yields are also determined.
Based on (10087±44)×106 𝐽/𝜓 events collected with the BESIII detector at BEPCII, the double Dalitz decay 𝜂′→𝑒+𝑒−𝑒+𝑒− is observed for the first time via the 𝐽/𝜓→𝛾𝜂′ decay process. The significance is found to be 5.7𝜎 with systematic uncertainties taken into consideration. Its branching fraction is determined to be ℬ(𝜂′→𝑒+𝑒−𝑒+𝑒−)=(4.5±1.0(stat)±0.5(sys))×10−6.
Utilizing the data set corresponding to an integrated luminosity of 3.19 fb−1 collected by the BESIII detector at a center-of-mass energy of 4.178 GeV, we perform an amplitude analysis of the D+s→π+π−π+ decay. The sample contains 13,797 candidates with a signal purity of ∼80%. The amplitude and phase of the contributing ππ S wave are measured based on a quasi-model-independent approach, along with the amplitudes and phases of the P and D waves parametrized by Breit-Wigner models. The fit fractions of different intermediate decay channels are also reported.
Using a data sample of (1.0087±0.0044)×1010 J/ψ decay events collected with the BESIII detector at the center-of-mass energy of s√=3.097 GeV, we present a search for the hyperon semileptonic decay Ξ0→Σ−e+νe which violates the ΔS=ΔQ rule. No significant signal is observed, and the upper limit on the branching fraction B(Ξ0→Σ−e+νe) is determined to be 1.6×10−4 at the 90% confidence level. This result improves the previous upper limit result by about one order of magnitude.
Using a data sample of (1.0087±0.0044)×1010 J/ψ decay events collected with the BESIII detector at the center-of-mass energy of s√=3.097 GeV, we present a search for the hyperon semileptonic decay Ξ0→Σ−e+νe which violates the ΔS=ΔQ rule. No significant signal is observed, and the upper limit on the branching fraction B(Ξ0→Σ−e+νe) is determined to be 1.6×10−4 at the 90% confidence level. This result improves the previous upper limit result by about one order of magnitude.
Using inclusive decays of the J/ψ, a precise determination of the number of J/ψ events collected with the BESIII detector is performed. For the two data sets taken in 2009 and 2012, the numbers of J/ψ events are recalculated to be (224.0±1.3)×106 and (1088.5±4.4)×106 respectively, which are in good agreement with the previous measurements. For the J/ψ sample taken in 2017--2019, the number of events is determined to be (8774.0±39.4)×106. The total number of J/ψ events collected with the BESIII detector is determined to be (10087±44)×106, where the uncertainty is dominated by systematic effects and the statistical uncertainty is negligible.
Using (10.087±0.044)×109 𝐽/𝜓 events collected by the Beijing Spectrum III (BESIII) detector at the Beijing Electron Positron Collider II (BEPCII) collider, we search for the hyperon semileptonic decay Ξ−→Ξ0𝑒−¯𝜈𝑒. No significant signal is observed and the upper limit on the branching fraction ℬ(Ξ−→Ξ0𝑒−¯𝜈𝑒) is set to be 2.59×10−4 at 90% confidence level. This result is one order of magnitude more strict than the previous best limit.
The integrated luminosities of data samples collected in the BESIII experiment in 2016–2017 at center-of-mass energies between 4.19 and 4.28 GeV are measured with a precision better than 1% by analyzing large-angle Bhabha scattering events. The integrated luminosities of old datasets collected in 2010–2014 are updated by considering corrections related to detector performance, offsetting the effect of newly discovered readout errors in the electromagnetic calorimeter, which can haphazardly occur.
Using inclusive decays of the J/ψ, a precise determination of the number of J/ψ events collected with the BESIII detector is performed. For the two data sets taken in 2009 and 2012, the numbers of J/ψ events are recalculated to be (224.0±1.3)×106 and (1088.5±4.4)×106 respectively, which are in good agreement with the previous measurements. For the J/ψ sample taken in 2017--2019, the number of events is determined to be (8774.0±39.4)×106. The total number of J/ψ events collected with the BESIII detector is determined to be (10087±44)×106, where the uncertainty is dominated by systematic effects and the statistical uncertainty is negligible.
A revision of the wild species in the genus Malus Mill. (Rosaceae) is presented based on numerical analyses and specimens from herbaria around the world, while cultivated species such as Malus domestica (Suckow) Borkh. are not included because of their complicated domestication history. Infra- and interspecific morphological variation and species delimitation are clarified based on Principal Component Analyses (PCA) and Cluster Analyses (UPGMA). We found that several morphological characters traditionally used to distinguish species have limited taxonomic value because of high phenotypic variation or plasticity. There is a substantial conflict between traditional morphological and genetic taxonomic concepts, and as a result species lineages are often morphologically indistinguishable. None of the analyses supports the recognition of infraspecific categories in Malus transitoria (Batalin) C.K.Schneid. and interspecific categories between Malus doumeri (Bois) A.Chev. and Malus leiocalyca S.Z.Huang. Based on our analyses, we recognize 26 wild species in the genus, and propose seven new synonymies.
Aims: Carotid intima media thickness (CIMT) predicts cardiovascular (CVD) events, but the predictive value of CIMT change is debated. We assessed the relation between CIMT change and events in individuals at high cardiovascular risk.
Methods and results: From 31 cohorts with two CIMT scans (total n = 89070) on average 3.6 years apart and clinical follow-up, subcohorts were drawn: (A) individuals with at least 3 cardiovascular risk factors without previous CVD events, (B) individuals with carotid plaques without previous CVD events, and (C) individuals with previous CVD events. Cox regression models were fit to estimate the hazard ratio (HR) of the combined endpoint (myocardial infarction, stroke or vascular death) per standard deviation (SD) of CIMT change, adjusted for CVD risk factors. These HRs were pooled across studies.
In groups A, B and C we observed 3483, 2845 and 1165 endpoint events, respectively. Average common CIMT was 0.79mm (SD 0.16mm), and annual common CIMT change was 0.01mm (SD 0.07mm), both in group A. The pooled HR per SD of annual common CIMT change (0.02 to 0.43mm) was 0.99 (95% confidence interval: 0.95–1.02) in group A, 0.98 (0.93–1.04) in group B, and 0.95 (0.89–1.04) in group C. The HR per SD of common CIMT (average of the first and the second CIMT scan, 0.09 to 0.75mm) was 1.15 (1.07–1.23) in group A, 1.13 (1.05–1.22) in group B, and 1.12 (1.05–1.20) in group C.
Conclusions: We confirm that common CIMT is associated with future CVD events in individuals at high risk. CIMT change does not relate to future event risk in high-risk individuals.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI’s capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The expanding field of epitranscriptomics might rival the epigenome in the diversity of the biological processes impacted. However, the identification of modifications in individual RNA molecules remains challenging. We present CHEUI, a new method that detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) at single-nucleotide and single-molecule resolution from Nanopore signals. CHEUI predicts methylation in Nanopore reads and transcriptomic sites in a single condition, and differential m6A and m5C methylation between any two conditions. Using extensive benchmarking with Nanopore data derived from synthetic and natural RNA, CHEUI showed higher accuracy than other existing methods in detecting m6A and m5C sites and quantifying the site stoichiometry levels, while maintaining a lower proportion of false positives. CHEUI provides a new capability to detect RNA modifications with high accuracy and resolution that can be cost-effectively expanded to other modifications to unveil the full span of the epitranscriptome in normal and disease conditions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions, using signals from nanopore direct RNA sequencing. CHEUI processes observed and expected signals with convolutional neural networks to achieve high single-molecule accuracy and outperform other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.