Autism Spectrum Disorders(ASDs)are reported as a group of neurodevelopmental disorders.The structural changes of brain regions including the hippocampus were widely reported in autistic patients and mouse models with ...Autism Spectrum Disorders(ASDs)are reported as a group of neurodevelopmental disorders.The structural changes of brain regions including the hippocampus were widely reported in autistic patients and mouse models with dysfunction of ASD risk genes,but the underlying mechanisms are not fully understood.Here,we report that deletion of Trio,a high-susceptibility gene of ASDs,causes a postnatal dentate gyrus(DG)hypoplasia with a zigzagged suprapyramidal blade,and the Trio-defcient mice display autism-like behaviors.The impaired morphogenesis of DG is mainly caused by disturbing the postnatal distribution of postmitotic granule cells(GCs),which further results in a migration defcit of neural progenitors.Furthermore,we reveal that Trio plays diferent roles in various excitatory neural cells by spatial transcriptomic sequencing,especially the role of regulating the migration of postmitotic GCs.In summary,our fndings provide evidence of cellular mechanisms that Trio is involved in postnatal DG morphogenesis.展开更多
Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is esse...Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change.An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ developmentrelated genes and thereby help us to understand organ developmental processes.Here,we constructed a comprehensive,integrated transcriptomic atlas for soybeans,integrating bulk RNA sequencing(RNAseq)datasets from 314 samples across the soybean life cycle,along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs:root,nodule,shoot apex,leaf,and stem.Investigating genes related to organ specificity,blade development,and nodule formation,we demonstrate that the atlas has robust power for exploring key genes involved in organ formation.In addition,we developed a user-friendly panoramic database for the transcriptomic atlas,enabling easy access and queries,which will serve as a valuable resource to significantly advance future soybean functional studies.展开更多
The development of spatial transcriptomics(ST)technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and...The development of spatial transcriptomics(ST)technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and function of various cell subsets in different environments and organs.The large-scale data generated by these ST technologies,which contain spatial gene expression information,have elicited the need for spatially resolved approaches to meet the requirements of computational and biological data interpretation.These requirements include dealing with the explosive growth of data to determine the cell-level and gene-level expression,correcting the inner batch effect and loss of expression to improve the data quality,conducting efficient interpretation and in-depth knowledge mining both at the single-cell and tissue-wide levels,and conducting multi-omics integration analysis to provide an extensible framework toward the in-depth understanding of biological processes.However,algorithms designed specifically for ST technologies to meet these requirements are still in their infancy.Here,we review computational approaches to these problems in light of corresponding issues and challenges,and present forward-looking insights into algorithm development.展开更多
The year 2021 marks the 20th anniversary of the official publication of the first draft of a human genome sequence generated by the Human Genome Project(HGP)consortium[1].The whole world has further acknowledged the ...The year 2021 marks the 20th anniversary of the official publication of the first draft of a human genome sequence generated by the Human Genome Project(HGP)consortium[1].The whole world has further acknowledged the HGP’s contributions to both life sciences and humanity amid combating the COVID-19 coronavirus.展开更多
基金supported by grants from the Key Realm R&D Program of Guangdong Province(2019B030335001)the National Natural Science Foundation of China(82071541,81971283,82271576,and 82101570)the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(2023-PT320-08).
文摘Autism Spectrum Disorders(ASDs)are reported as a group of neurodevelopmental disorders.The structural changes of brain regions including the hippocampus were widely reported in autistic patients and mouse models with dysfunction of ASD risk genes,but the underlying mechanisms are not fully understood.Here,we report that deletion of Trio,a high-susceptibility gene of ASDs,causes a postnatal dentate gyrus(DG)hypoplasia with a zigzagged suprapyramidal blade,and the Trio-defcient mice display autism-like behaviors.The impaired morphogenesis of DG is mainly caused by disturbing the postnatal distribution of postmitotic granule cells(GCs),which further results in a migration defcit of neural progenitors.Furthermore,we reveal that Trio plays diferent roles in various excitatory neural cells by spatial transcriptomic sequencing,especially the role of regulating the migration of postmitotic GCs.In summary,our fndings provide evidence of cellular mechanisms that Trio is involved in postnatal DG morphogenesis.
基金supported by the National Natural Science Foundation of China(grant no.32388201)the National Key Research and Development Program of China(2022YFF1003301,and 2023YFF1000101)+1 种基金the Taishan Scholars Programthe Xplorer Prize.
文摘Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change.An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ developmentrelated genes and thereby help us to understand organ developmental processes.Here,we constructed a comprehensive,integrated transcriptomic atlas for soybeans,integrating bulk RNA sequencing(RNAseq)datasets from 314 samples across the soybean life cycle,along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs:root,nodule,shoot apex,leaf,and stem.Investigating genes related to organ specificity,blade development,and nodule formation,we demonstrate that the atlas has robust power for exploring key genes involved in organ formation.In addition,we developed a user-friendly panoramic database for the transcriptomic atlas,enabling easy access and queries,which will serve as a valuable resource to significantly advance future soybean functional studies.
基金We thank Ying Zhang,Chao Liu,and Ping Qiu for their assistance for the manuscript.
文摘The development of spatial transcriptomics(ST)technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and function of various cell subsets in different environments and organs.The large-scale data generated by these ST technologies,which contain spatial gene expression information,have elicited the need for spatially resolved approaches to meet the requirements of computational and biological data interpretation.These requirements include dealing with the explosive growth of data to determine the cell-level and gene-level expression,correcting the inner batch effect and loss of expression to improve the data quality,conducting efficient interpretation and in-depth knowledge mining both at the single-cell and tissue-wide levels,and conducting multi-omics integration analysis to provide an extensible framework toward the in-depth understanding of biological processes.However,algorithms designed specifically for ST technologies to meet these requirements are still in their infancy.Here,we review computational approaches to these problems in light of corresponding issues and challenges,and present forward-looking insights into algorithm development.
文摘The year 2021 marks the 20th anniversary of the official publication of the first draft of a human genome sequence generated by the Human Genome Project(HGP)consortium[1].The whole world has further acknowledged the HGP’s contributions to both life sciences and humanity amid combating the COVID-19 coronavirus.
