scholarly journals Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

2020 ◽  
Author(s):  
Xizhi Li ◽  
Min Li ◽  
Beibei Zhou ◽  
Jinlin Bao ◽  
Liang Zhu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Leaf Development ◽  
Regulatory Network ◽  
Leaf Rolling ◽  
Knock Out ◽  
Genome Wide ◽  
Leaf Transcriptome ◽  
Dna Insertion ◽  
Gene Regulatory ◽  
Cuticle Development

Abstract Background SRL1 (SEMI-ROLLED LEAF 1) also named as CLD1 (CURLED LEAF AND DWARF 1), encoding a putative glyphopholipidininol-anchored membrane protein, has been characterized as a gene involved in the regulation of leaf morphology in rice. Mutants of srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit defects in leaf development resulting in a phenotype with adaxially rolled leaves. Results To explore the gene regulatory network of leaf development that controlled by SRL1 in rice, we created a homozygous SRL1 knock out (KO) line by CRISPR/Cas9, which showed defects in leaf development with adaxially rolling. By comparing the leaf transcriptome of a homozygous SRL1 KO line (srl1-KO) with the control, a total number of 3,178 genes were identified as differentially expressed genes, of which 1,216 genes were significantly up regulated, while 1,962 genes were down regulated. Further analyses indicated that, a group of known leaf rolling related genes, which involved in bulliform cells and cuticle development such as OsZHD1, OsLBD3-7, RFS, ACL1, CFL1, SND1, OsCESA5 and OsCESA6 were up or down regulated in the srl1-KO. Conclusions SRL1 might control leaf rolling by regulating a couple of genes that affecting cytological architecture of leaf cells such as bulliforms and cuticle of leaves.

Abstract MP208: A Shared Fog2 / Tbx5-dependent Gene Regulatory Network Identified By Transcription Factor-dependent Non-coding RNA Profiling Modulates Cardiac Rhythm

2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Linsin A Smith ◽  
Carlos Perez-Cervantes ◽  
Michael Broman ◽  
Rangarajan Nadadur ◽  
Jeff Steimle ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Cardiac Rhythm ◽  
Association Studies ◽  
Genome Wide Association ◽  
Calcium Handling ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Gene Regulatory ◽  
Atrial Rhythm

Atrial fibrillation (AF) is the most common cardiac arrhythmia, affecting over 33 million individuals throughout the world. AF is highly heritable and recent genome-wide association studies (GWAS) have cumulatively identified over 100 loci associated with AF risk. Genome-wide association studies (GWAS) often identify transcription factor (TF) loci in association with complex human diseases, implying that a significant transcriptional component underlies human disease risk and etiology. The transcription factors ZFPM2 (FOG2), GATA4, and TBX5 have all been implicated in human AF risk by genetic studies. We hypothesized that FOG2, GATA4, and TBX5 functionally interact to regulate a gene regulatory network essential for atrial rhythm control. We generated a novel mouse model of spontaneous AF based on FOG2 overexpression. FOG2 ChIP-seq identified FOG2 genomic localization at loci co-occupied by GATA4, a known FOG2 binding partner. However, we found that FOG2 OE caused gene expression alterations that correlated more highly with TBX5-dependent rather than GATA4-dependent gene expression, including a module of calcium handling genes required for atrial rhythm homeostasis. We applied TF-dependent non-coding transcriptional profiling to examine the FOG2 dependent atrial GRN, which identified 805 candidate regulatory regions with accessible chromatin and FOG2 dependent ncRNAs. TBX5 removal and FOG2 OE caused highly correlated dysregulation of ncRNA expression at open chromatin regions genome-wide, suggesting a functional interaction between TBX5 and FOG2. Furthermore, FOG2 OE only affected enhancer activity by altered ncRNA abundance at locations of TBX5 co-binding. The shared TBX5/FOG2 genomic interaction predicted a potential genetic interaction, and we found that cardiac rhythm abnormalities caused by Tbx5 haploinsufficiency were rescued by Fog2 haploinsufficiency. Taken together, TF-dependent ncRNA-profiling revealed an interconnected cardiac rhythm gene regulatory network (GRN) between FOG2, TBX5 and GATA4. These data nominate a specific model in which FOG2 is recruited by GATA4 to modulate a co-bound TBX5-dependent atrial gene regulatory network for calcium handling and atrial rhythm homeostasis.

scholarly journals A novel method of gene regulatory network structure inference from gene knock-out expression data

2019 ◽  
Vol 24 (4) ◽  
pp. 446-455 ◽  
Author(s):  
Xiang Chen ◽  
Min Li ◽  
Ruiqing Zheng ◽  
Siyu Zhao ◽  
Fang-Xiang Wu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Network Structure ◽  
Regulatory Network ◽  
Expression Data ◽  
Knock Out ◽  
Novel Method ◽  
Gene Regulatory

scholarly journals Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

Development ◽  
2014 ◽  
Vol 141 (12) ◽  
pp. 2542-2542 ◽  
Author(s):  
K. Rafiq ◽  
T. Shashikant ◽  
C. J. McManus ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

Development ◽  
2014 ◽  
Vol 141 (4) ◽  
pp. 950-961 ◽  
Author(s):  
K. Rafiq ◽  
T. Shashikant ◽  
C. J. McManus ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals MicroRNA319-mediated gene regulatory network impacts leaf development and morphogenesis in poplar

2021 ◽  
Vol 1 (1) ◽  
pp. 1-10
Author(s):  
Yanxia Cheng ◽  
◽  
Lihu Wang ◽  
Manzar Abbas ◽  
Xiong Huang ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Leaf Development ◽  
Regulatory Network ◽  
Gene Regulatory

scholarly journals Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation

2018 ◽  
Vol 98 (2) ◽  
pp. 209-217 ◽  
Author(s):  
D.G. Michael ◽  
T.J.F. Pranzatelli ◽  
B.M. Warner ◽  
H. Yin ◽  
J.A. Chiorini
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Salivary Gland ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Factors Associated ◽  
Genome Wide ◽  
Gene Regulatory ◽  
Cis And Trans ◽  
Genomic Footprinting

Significant effort has been applied to identify the genome-wide gene expression profiles associated with salivary gland development and pathophysiology. However, relatively little is known about the regulators that control salivary gland gene expression. We integrated data from DNase1 digital genomic footprinting, RNA-seq, and gene expression microarrays to comprehensively characterize the cis- and trans-regulatory components controlling gene expression of the healthy submandibular salivary gland. Analysis of 32 human tissues and 87 mouse tissues was performed to identify the highly expressed and tissue-enriched transcription factors driving salivary gland gene expression. Following RNA analysis, protein expression levels and subcellular localization of 39 salivary transcription factors were confirmed by immunohistochemistry. These expression analyses revealed that the salivary gland highly expresses transcription factors associated with endoplasmic reticulum stress, human T-cell lymphotrophic virus 1 expression, and Epstein-Barr virus reactivation. DNase1 digital genomic footprinting to a depth of 333,426,353 reads was performed and utilized to generate a salivary gland gene regulatory network describing the genome-wide chromatin accessibility and transcription factor binding of the salivary gland at a single-nucleotide resolution. Analysis of the DNase1 gene regulatory network identified dense interconnectivity among PLAG1, MYB, and 13 other transcription factors associated with balanced chromosomal translocations and salivary gland tumors. Collectively, these analyses provide a comprehensive atlas of the cis- and trans-regulators of the salivary gland and highlight known aberrantly regulated pathways of diseases affecting the salivary glands.

Sign in / Sign up

Export Citation Format

Share Document