METTL3 is a crucial mRNA methyltransferase in mammals,essential for the regulation of gene expression and various biological processes.Here,we demonstrate that Mettl3 knockout(KO)in mouse embryonic stem cells(mESCs)le...METTL3 is a crucial mRNA methyltransferase in mammals,essential for the regulation of gene expression and various biological processes.Here,we demonstrate that Mettl3 knockout(KO)in mouse embryonic stem cells(mESCs)leads to widespread upregulation of transposable elements(TEs)and 2-cell(2C)-like genes in a m^(6)A enzyme activitydependent manner,independent of culture conditions.Furthermore,embryo chimera experiments using a transient METTL3 degradation system(dTAG)revealed that METTL3-deficient mESCs can contribute to trophectoderm lineages at the blastocyst stage,indicative of expanded developmental potential.These findings highlight the role of METTL3-mediated m^(6)A modifications in regulating the transcriptional and developmental plasticity of mESCs and suggest a link between m^(6)A loss and the acquisition of a 2C-like state with features of extended potency.展开更多
Mammalian mitochondria have small genomes encoding very limited numbers of proteins.Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria.H...Mammalian mitochondria have small genomes encoding very limited numbers of proteins.Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria.Here,we report the identification of hundreds of circular RNAs(mecciRNAs)encoded by the mitochondrial genome.We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate the mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins.Known components involved in mitochondrial protein and RNA importation,such as TOM40 and PNPASE,interact with mecciRNAs and regulate protein entry.The expression of mecciRNAs is regulated,and these transcripts are critical for the adaption of mitochondria to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation.mecciRNAs and their associated physiological roles add categories and functions to the known eukaryotic circular RNAs and shed novel light on the communication between mitochondria and the nucleus.展开更多
Pluripotent stem cells(PSCs)can be expanded in vitro in different culture conditions,resulting in a spectrum of cell states with distinct properties.Understanding how PSCs transition from one state to another,ultimate...Pluripotent stem cells(PSCs)can be expanded in vitro in different culture conditions,resulting in a spectrum of cell states with distinct properties.Understanding how PSCs transition from one state to another,ultimately leading to lineage-specific differentiation,is important for developmental biology and regenerative medicine.Although there is significant information regarding gene expression changes controlling these transitions,less is known about post-translational modifications of proteins.Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group.Here,we employed affinity purification of crotonylated(LC–MS/MS)to systematically profile protein crotonylation in mouse PSCs in different states including ground,metastable,and primed states,as well as metastable PSCs undergoing early pluripotency exit.We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins.These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis,central carbon metabolism,and proteasome function.Moreover,we found that increasing the cellular levels of crotonyl-coenzyme A(crotonyl-CoA)through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation,consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency.Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.展开更多
The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions.This reorganization occurs in a multi-phased manner and involves a gradual rev...The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions.This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome.Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long noncoding RNAs(lncR NAs),a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function.Deeper understanding of lncR NAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts,such as development,aging,and cancer.In this review,we summarize the current progress made in profiling and analyzing the role of lncR NAs in various phases of somatic cell reprogramming,with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.展开更多
Oct4 is a key transcription factor essential for maintaining pluripotency and self-renewal in embryonic stem cells(ESCs),where it activates pluripotency-related genes and represses differentiation-associated genes.Whi...Oct4 is a key transcription factor essential for maintaining pluripotency and self-renewal in embryonic stem cells(ESCs),where it activates pluripotency-related genes and represses differentiation-associated genes.While previous studies have identified OCT4 target genes using methods such as chromatin immunoprecipitation sequencing(ChIP-seq)and RNA interference(RNAi),these approaches may not fully capture direct transcriptional regulation.The auxin-inducible degron(AID)system,which enables rapid and reversible protein degradation,combined with nascent RNA sequencing,provides a refined method for identifying direct transcriptional targets by detecting immediate transcriptional changes in both protein-coding genes and non-coding RNAs.In this study,we utilized mouse Oct4-mAID ESCs and nascent RNA sequencing with 5-ethynyl uridine(5-EU)labeling to systematically identify direct OCT4 targets.Our results uncovered novel potential OCT4 targets,providing a dataset for further research into the functions and regulatory networks of Oct4 and related transcription factors.展开更多
基金supported by the National Key Research and Development Program of China(2024YFA1107000,2024YFA1107901,2021YFA1102200 and 2024YFA1802300)the National Natural Science Foundation of China(32225012)+2 种基金Guangdong Basic and Applied Basic Research Foundation(2025A1515012713)partially supported by Science and Technology Planning Project of Guangdong Province,China(2023B1212060050,2023B1212120009)Health@InnoHK Program launched by Innovation Technology Commission of the Hong Kong SAR,China.
文摘METTL3 is a crucial mRNA methyltransferase in mammals,essential for the regulation of gene expression and various biological processes.Here,we demonstrate that Mettl3 knockout(KO)in mouse embryonic stem cells(mESCs)leads to widespread upregulation of transposable elements(TEs)and 2-cell(2C)-like genes in a m^(6)A enzyme activitydependent manner,independent of culture conditions.Furthermore,embryo chimera experiments using a transient METTL3 degradation system(dTAG)revealed that METTL3-deficient mESCs can contribute to trophectoderm lineages at the blastocyst stage,indicative of expanded developmental potential.These findings highlight the role of METTL3-mediated m^(6)A modifications in regulating the transcriptional and developmental plasticity of mESCs and suggest a link between m^(6)A loss and the acquisition of a 2C-like state with features of extended potency.
基金Supported by grants to G. S.: the National Key R&D Program of China (2019YFA0802600 and 2018YFC1004500)the National Natural Science Foundation of China (31725016, 31930019, and 91940303)and the Strategic Priority Research Program (Pilot Study) “Biological basis of aging and therapeutic strategies” of the Chinese Academy of Sciences (XDPB10).
文摘Mammalian mitochondria have small genomes encoding very limited numbers of proteins.Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria.Here,we report the identification of hundreds of circular RNAs(mecciRNAs)encoded by the mitochondrial genome.We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate the mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins.Known components involved in mitochondrial protein and RNA importation,such as TOM40 and PNPASE,interact with mecciRNAs and regulate protein entry.The expression of mecciRNAs is regulated,and these transcripts are critical for the adaption of mitochondria to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation.mecciRNAs and their associated physiological roles add categories and functions to the known eukaryotic circular RNAs and shed novel light on the communication between mitochondria and the nucleus.
基金supported by the National Key R&D Program of China(Grant Nos.2018YFA0106903,2016YFA0100102,and 2016YFA010070)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA16030502)+5 种基金the Natural Science Foundation of Guangdong Province,China(Grant No.2018B030306042)the Youth Innovation Promotion Association of the Chinese Academy of Sciences(Grant No.2015294)the Innovation Team Project grant from the Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory),China(Grant No.2018GZR110103001)the Science and Technology Planning Project of Guangdong Province,China(Grant No.2020B1212060052)supported by a Zhujiang Talent-Overseas Postdoctoral Funding Grant,Chinaa President’s International Fellowship Initiative grant from the Chinese Academy of Sciences
文摘Pluripotent stem cells(PSCs)can be expanded in vitro in different culture conditions,resulting in a spectrum of cell states with distinct properties.Understanding how PSCs transition from one state to another,ultimately leading to lineage-specific differentiation,is important for developmental biology and regenerative medicine.Although there is significant information regarding gene expression changes controlling these transitions,less is known about post-translational modifications of proteins.Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group.Here,we employed affinity purification of crotonylated(LC–MS/MS)to systematically profile protein crotonylation in mouse PSCs in different states including ground,metastable,and primed states,as well as metastable PSCs undergoing early pluripotency exit.We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins.These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis,central carbon metabolism,and proteasome function.Moreover,we found that increasing the cellular levels of crotonyl-coenzyme A(crotonyl-CoA)through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation,consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency.Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.
基金supported by the National Key R&D Program of China(Grant Nos.2016YFA0100701,2016YFA0100102,2018YFA0106903,and 2016YFA0100300)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA16030502)+8 种基金the Youth Innovation Promotion Association of the Chinese Academy of Sciences(Grant No.2015294)the National Natural Science Foundation of China(Grant Nos.31671537,31571524,and 31501192)the Natural Science Foundation of Guangdong Province(Grant No.2018B030306042)the Guangdong Province Science and Technology Program(Grant Nos.2014A030312001,2016A050503037,2016B030229007,and 2017B050506007)the Science and Technology Planning Project of Guangdong Province(Grant No.2017B030314056)the Pearl River Science and Technology Nova Program of Guangzhou(Grant No.201610010107)the Guangzhou Science and Technology Program(Grant No.201807010066),Chinasupported by a President’s International Fellowship Initiative program from the Chinese Academy of Sciencessupported by a Pearl River Overseas Young Talents Postdoctoral Fellowship
文摘The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions.This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome.Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long noncoding RNAs(lncR NAs),a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function.Deeper understanding of lncR NAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts,such as development,aging,and cancer.In this review,we summarize the current progress made in profiling and analyzing the role of lncR NAs in various phases of somatic cell reprogramming,with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.
基金supported by the National Key Research and Development Program of China(2024YFA1108201,2021YFA1100401 to X.B.)Jiangxi Province Ganpo Talent Program(GPYC202411 to W.Z.)+2 种基金the National Natural Science Foundation of China(32470842,32170797 to W.Z.)the National Natural Science Foundation of China(32170745 to X.B.)partially supported by Science and Technology Planning Project of Guangdong Province,China(2023B1212060050,2023B1212120009 to X.B.).
文摘Oct4 is a key transcription factor essential for maintaining pluripotency and self-renewal in embryonic stem cells(ESCs),where it activates pluripotency-related genes and represses differentiation-associated genes.While previous studies have identified OCT4 target genes using methods such as chromatin immunoprecipitation sequencing(ChIP-seq)and RNA interference(RNAi),these approaches may not fully capture direct transcriptional regulation.The auxin-inducible degron(AID)system,which enables rapid and reversible protein degradation,combined with nascent RNA sequencing,provides a refined method for identifying direct transcriptional targets by detecting immediate transcriptional changes in both protein-coding genes and non-coding RNAs.In this study,we utilized mouse Oct4-mAID ESCs and nascent RNA sequencing with 5-ethynyl uridine(5-EU)labeling to systematically identify direct OCT4 targets.Our results uncovered novel potential OCT4 targets,providing a dataset for further research into the functions and regulatory networks of Oct4 and related transcription factors.
