category 'Lab Meeting'

Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning

Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning

Abstract: In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits....

Liu Guanqing
OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice

OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice

Abstract: Grains from cereals contribute an important source of protein to human food, and grain protein content (GPC) is an important determinant of nutritional quality in cereals. Here we show...

Tan Yan
H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction

H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction

Abstract: Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and...

Pan Kairui
Splicing-mediated activation of SHAGGY-like kinases underpinning carbon partitioning in Arabidopsis seeds

Splicing-mediated activation of SHAGGY-like kinases underpinning carbon partitioning in Arabidopsis seeds

Abstract: Glycogen synthase kinase 3 (GSK3) family members serve as signaling hubs for plant development and stress responses, yet the underlying mechanism of their transcriptional regulation remains a long-standing mystery....

Zhang Xin
Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa

Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa

Abstract: Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. How- ever, little is known about their cis- and trans-regulatory contributions in gene expression under salt...

Wu Wenwen
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

Abstract: Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of reg- ulatory elements is fundamental for annotating genomes and...

Ding Yu
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation

Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation

Abstract: High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to...

Bao Yu
DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development

DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development

Abstract: A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic...

Xin Xiaoyue
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

Abstract: Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understanding...

Liu Guanqing
A comprehensive catalog of predicted functional upstream open reading frames in humans

A comprehensive catalog of predicted functional upstream open reading frames in humans

Abstract: Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active...

Wu Yuechao
ALK, the Key Gene for Gelatinization Temperature, is a Modifier Gene for Gel Consistency in Rice

ALK, the Key Gene for Gelatinization Temperature, is a Modifier Gene for Gel Consistency in Rice

Abstract: Gelatinization temperature (GT) is an important parameter in evaluating the cooking and eating quality of rice. Indeed, the phenotype, biochemistry and inheritance of GT have been widely studied in...

Tan Yan
Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

Abstract: Background: Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function....

Pan Kairui
The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element

The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element

Abstract: Vernalization, a long-term cold-mediated acquisition of flowering competence, is critically regulated by VERNALIZATION INSENSITIVE 3 (VIN3), a gene induced by vernalization in Arabidopsis. Although the function of VIN3 has...

Zhang Xin
A quantitative genomics map of rice provides genetic insights and guides breeding

A quantitative genomics map of rice provides genetic insights and guides breeding

Abstract: Extensive allelic variation in agronomically important genes serves as the basis of rice breeding. Here, we present a comprehen- sive map of rice quantitative trait nucleotides (QTNs) and inferred...

Han Yangshuo
A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype

A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype

Abstract: AtHB1 is an Arabidopsis (Arabidopsis thaliana) homeodomain-leucine zipper transcription factor that participates in hypocotyl elongation under short-day conditions. Here, we show that its expression is posttranscriptionally regulated by an...

Ding Yu
Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20

Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20

Abstract: Grain number per panicle (GNP) is an important agronomic trait that contributes to rice grain yield. Despite its importance in rice breeding, the molecular mechanism underlying GNP regulation remains...

Xin Xiaoyue
Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Abstract: Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess...

Liu Guanqing
Quantitative regulation of Waxy expression by CRISPR/Cas9-based promoter and 5’UTR-intron editing improves grain quality in rice

Quantitative regulation of Waxy expression by CRISPR/Cas9-based promoter and 5’UTR-intron editing improves grain quality in rice

Abstract: In cereal crops, grain starches are composed of different proportions of amylose and amylopectin, which determine the cooking and eating qualities. The amylose synthesis is controlled by the Waxy...

Tan Yan
Nucleolar histone deacetylases HDT1, HDT2 and HDT3 regulate plant reproductive development

Nucleolar histone deacetylases HDT1, HDT2 and HDT3 regulate plant reproductive development

Abstract: Nucleolus is a membrane-less organelle where ribosomes are assembled and rRNAs transcribed and processed. The assembled ribosomes composed of ribosomal proteins and rRNAs synthesize proteins for cell survival. In...

Pan Kairui
Plastidic Pyruvate Dehydrogenase Complex E1 Component Subunit Alpha1 Is Involved in Galactolipid Biosynthesis Required for Amyloplast Development in Rice

Plastidic Pyruvate Dehydrogenase Complex E1 Component Subunit Alpha1 Is Involved in Galactolipid Biosynthesis Required for Amyloplast Development in Rice

Abstract: Starch accounts for over 80% of the total dry weight in cereal endosperm and determines the kernel texture and nutritional quality. Amyloplasts, terminally differentiated plastids, are responsible for starch...

Zhang Xin
Organization and regulation of gene transcription

Organization and regulation of gene transcription

Abstract: The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and...

Han Yangshuo
A photoregulatory mechanism of the circadian clock in Arabidopsis

A photoregulatory mechanism of the circadian clock in Arabidopsis

Abstract: Cryptochromes (CRYs) are photoreceptors that mediate light regulation of the circadian clock in plants and animals. Here we show that CRYs mediate blue-light regulation of N6-methyladenosine (m6A) modification of...

Liu Shuo
Report: MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

Report: MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

Abstract: MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5...

Wu Wenwen
Report: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

Report: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

Abstract: Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood....

Ding Yu
Report: Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish

Report: Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish

Abstract: Sight depends on the tight cooperation between photoreceptors and pigmented cells, which derive from common progenitors through the bifurcation of a single gene regulatory network into the neural retina...

Bao Yu
Report: RGN1 controls grain number and shapes panicle architecture in rice

Report: RGN1 controls grain number and shapes panicle architecture in rice

Abstract: Yield in rice is determined mainly by panicle architecture. Using map-based cloning we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle...

Xin Xiaoyue
Report: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

Report: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

Abstract: Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We...

Pan Kairui
Report: PAM-less plant genome editing using a CRISPR–SpRY toolbox

Report: PAM-less plant genome editing using a CRISPR–SpRY toolbox

Abstract: The rapid development of the CRISPR–Cas9, –Cas12a and – Cas12b genome editing systems has greatly fuelled basic and translational plant research1–6. DNA targeting by these Cas nucleases is restricted...

Wu Yuechao
Report: The key role of terminators on the expression and post- transcriptional gene silencing of transgenes

Report: The key role of terminators on the expression and post- transcriptional gene silencing of transgenes

Abstract: Transgenes have become essential to modern biology, being an important tool in functional genomic studies and also in the development of biotechnological products. One of the major challenges in...

Pan Kairui
Report: KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

Report: KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

Abstract: Gene set enrichment (GSE) analysis plays an essen- tial role in extracting biological insight from genome- scale experiments. ORA (overrepresentation analy- sis), FCS (functional class scoring), and PT (path-...

Han Yangshuo
Report: Integrated global analysis reveals a vitamin E- vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence

Report: Integrated global analysis reveals a vitamin E- vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence

Abstract: Rice, a staple food with tropical/subtropical origination, is susceptible to cold stress, one of the major con- straints on its yield and distribution. Asian cultivated rice consists of two...

Zhang Xin
Report: The Taxus genome provides insights into paclitaxel biosynthesis

Report: The Taxus genome provides insights into paclitaxel biosynthesis

Abstract: The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We...

Liu Shuo
Report: In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

Report: In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

Abstract: Background: mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites,...

Wu Wenwen
Report: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

Report: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

Abstract: Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood....

Ding Yu
Report: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity

Report: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity

Abstract: Human dendritic cells (DCs) comprise subsets with distinct phenotypic and functional characteristics, but the transcriptional programs that dictate their identity remain elusive. Here, we analyze global chromatin acces- sibility...

Bao Yu
Report: Natural variations of SLG1 confer high-temperature tolerance in indica rice

Report: Natural variations of SLG1 confer high-temperature tolerance in indica rice

Abstract: With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living...

Xin Xiaoyue
Report: Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression

Report: Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression

Abstract: Pinpointing functional noncoding DNA sequences and defining their contributions to health-related traits is a major challenge for modern genetics. We developed a high-throughput framework to map noncoding DNA functions...

Liu Guanqing
Report: Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing

Report: Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing

Abstract: Genome editing has therapeutic potential for treating genetic diseases and cancer. However, the currently most practicable approaches rely on the generation of DNA double-strand breaks (DSBs), which can give...

Wu Yuechao
Report: Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

Report: Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

Abstract: Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in...

Han Yangshuo
Report: A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Report: A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Abstract: Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here,...

Liu Shuo
Report: Unidirectional movement of small RNAs from shoots to roots in interspecific heterograf

Report: Unidirectional movement of small RNAs from shoots to roots in interspecific heterograf

Abstract: Long-distance RNA movement is important for plant growth and environmental responses; however, the extent to which RNAs move between distant tissues, their relative magnitude and functional importance remain to...

Wu Wenwen
Report: G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice

Report: G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice

Abstract: The simultaneous improvement of grain quality and yield of cereal crops is a major challenge for modern agriculture. Here we show that a rice grain yield quantitative trait locus...

Ding Yu
Report: Molecular Networks of Seed Size Control in Plants

Report: Molecular Networks of Seed Size Control in Plants

Abstract: The size of seeds affects not only evolutionary fitness but also grain yield of crops. Understanding the mechanisms controlling seed size has become an important research field in plant...

Bao Yu
Report: Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves

Report: Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves

Abstract: Genetic engineering of cis-regulatory elements in crop plants is a promising strategy to ensure food security. However, such engineering is currently hindered by our limited knowledge of plant cis-regulatory...

Xin Xiaoyue
Report: Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

Report: Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

Abstract: Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions...

Liu Guanqing
Report: Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

Report: Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

Abstract: Plant somatic embryogenesis refers to a phenomenon where embryos develop from somatic cells in the absence of fertilization. Previous studies have revealed that the phytohormone auxin plays a crucial...

Wu Yuechao
Report: The relationship between genome structure and function

Report: The relationship between genome structure and function

Abstract: Precise patterns of gene expression in metazoans are controlled by three classes of regulatory elements: promoters, enhancers and boundary elements. During differentiation and development, these elements form specific interactions...

Han Yangshuo