scholarly journals Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction

2021 ◽  
Author(s):  
Jingyao Wang ◽  
Shihe Zhang ◽  
Hongfang Lu ◽  
Heng Xu
Keyword(s):  
Single Molecule ◽  
Target Gene ◽  
Expression Patterns ◽  
Differential Regulation ◽  
Alternative Promoters ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene ◽  
Eukaryotic Gene Regulation ◽  
Kinetics Of ◽  
Promoter Interaction

Abstract Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the dynamics of complex eukaryotic gene regulation.

scholarly journals Differential Bcd activation of two hunchback promoters emerges from unified kinetics of enhancer-promoter interaction

2021 ◽  
Author(s):  
Jingyao Wang ◽  
Shihe Zhang ◽  
Hongfang Lu ◽  
Heng Xu
Keyword(s):  
Single Molecule ◽  
Target Gene ◽  
Expression Patterns ◽  
Alternative Promoters ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene ◽  
Eukaryotic Gene Regulation ◽  
Kinetics Of ◽  
Drosophila Embryos ◽  
Promoter Interaction

Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the dynamics of complex eukaryotic gene regulation.

scholarly journals A Simplified Method for Obtaining cDNA of Low-Copy and Silent Eukaryotic Genes Using Human Renalase as an the Example

2019 ◽  
Vol 2 (2) ◽  
pp. e00101 ◽  
Author(s):  
V.I. Fedchenko ◽  
A.A. Kaloshin
Keyword(s):  
Genomic Dna ◽  
Expression Vector ◽  
Target Gene ◽  
Direct Synthesis ◽  
Terminal Sequence ◽  
Initial Sequence ◽  
Eukaryotic Genes ◽  
Restriction Sites ◽  
Simplified Method ◽  
Eukaryotic Gene

A simplified «exon» method was developed for producing cDNA of low-copy and silent eukaryotic genes. It is based on assembly of the target gene from genomic DNA by direct synthesis of its exons, followed by their PCR-based joining without further purification of the amplicons. During the synthesis of exons, direct primers were used; these included about ~ 20 nucleotides of the 3`-terminal sequence previous (from the amplified) exon and ~ 20 nucleotides of the 5`-initial sequence of the amplified exon. Reverse primers included ~ 20 nucleotides complementary to the terminal sequence of the amplified exon. Forward and reverse primers flanking the gene to be assembled included the restriction sites necessary for insertion into the expression vector. Using this approach it is possible to assemble almost any eukaryotic gene with a known nucleotide sequence of genomic DNA available in the database.

scholarly journals Roles of the INO80 and SWR1 Chromatin Remodeling Complexes in Plants

2019 ◽  
Vol 20 (18) ◽  
pp. 4591 ◽  
Author(s):  
Jianhao Wang ◽  
Sujuan Gao ◽  
Xiuling Peng ◽  
Keqiang Wu ◽  
Songguang Yang
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Gene Regulation ◽  
Dna Replication ◽  
Chromatin Remodeling ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene ◽  
Chromatin Remodeling Complexes ◽  
Eukaryotic Gene Regulation ◽  
Environmental Responses

Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and recombination. The INO80 and SWR1 chromatin remodeling complexes (INO80-c and SWR1-c) are ATP-dependent complexes that modulate the incorporation of the histone variant H2A.Z into nucleosomes, which is a critical step in eukaryotic gene regulation. Although SWR1-c has been identified in plants, plant INO80-c has not been successfully isolated and characterized. In this review, we will focus on the functions of the SWR1-c and putative INO80-c (SWR1/INO80-c) multi-subunits and multifunctional complexes in Arabidopsis thaliana. We will describe the subunit compositions of the SWR1/INO80-c and the recent findings from the standpoint of each subunit and discuss their involvement in regulating development and environmental responses in Arabidopsis.

scholarly journals Response to Nodal morphogen gradient is determined by the kinetics of target gene induction

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Julien Dubrulle ◽  
Benjamin M Jordan ◽  
Laila Akhmetova ◽  
Jeffrey A Farrell ◽  
Seok-Hyung Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Target Genes ◽  
Expression Patterns ◽  
Gene Induction ◽  
Morphogen Gradient ◽  
Morphogen Gradients ◽  
Zebrafish Embryogenesis ◽  
Target Gene Induction ◽  
Kinetics Of

Morphogen gradients expose cells to different signal concentrations and induce target genes with different ranges of expression. To determine how the Nodal morphogen gradient induces distinct gene expression patterns during zebrafish embryogenesis, we measured the activation dynamics of the signal transducer Smad2 and the expression kinetics of long- and short-range target genes. We found that threshold models based on ligand concentration are insufficient to predict the response of target genes. Instead, morphogen interpretation is shaped by the kinetics of target gene induction: the higher the rate of transcription and the earlier the onset of induction, the greater the spatial range of expression. Thus, the timing and magnitude of target gene expression can be used to modulate the range of expression and diversify the response to morphogen gradients.

scholarly journals Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Wang ◽  
Lei Wang ◽  
Ling Wang ◽  
Meilian Tan ◽  
Collins O. Ogutu ◽  
...  
Keyword(s):  
Dna Repair ◽  
Drought Tolerance ◽  
Single Molecule ◽  
Linum Usitatissimum ◽  
Expression Patterns ◽  
Transcriptional Response ◽  
Enrichment Analysis ◽  
Resistant Variety ◽  
Proline Biosynthesis ◽  
Interacting Protein

Abstract Background Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known about how linseed coordinates the expression of drought resistance gene in response to different level of drought stress (DS) on the genome-wide level. Results To explore the linseed transcriptional response of DS and repeated drought (RD) stress, we determined the drought tolerance of different linseed varieties. Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) and reduce and visualize GO (REVIGO) enrichment analysis showed that upregulated genes of Z141 were enriched in more functional pathways related to plant drought tolerance than those of NY-17 were under DS. In addition, 4436 linseed transcription factors were identified, and 1190 were responsive to stress treatments. Moreover, protein-protein interaction (PPI) network analysis showed that the proline biosynthesis pathway interacts with stress response genes through RAD50 (DNA repair protein 50) interacting protein 1 (RIN-1). Finally, proline biosynthesis and DNA repair structural gene expression patterns were verified by RT- PCR. Conclusions The drought tolerance of Z141 may be related to its upregulation of drought tolerance genes under DS. Proline may play an important role in linseed drought tolerance by maintaining cell osmotic and protecting DNA from ROS damage. In summary, this study provides a new perspective to understand the drought adaptability of linseed.

Mapping the dynamic transfer functions of eukaryotic gene regulation

Cell Systems ◽  
2021 ◽  
Author(s):  
Jessica B. Lee ◽  
Leandra M. Caywood ◽  
Jennifer Y. Lo ◽  
Nicholas Levering ◽  
Albert J. Keung
Keyword(s):  
Gene Regulation ◽  
Transfer Functions ◽  
Eukaryotic Gene ◽  
Eukaryotic Gene Regulation

scholarly journals Evidence for Histone Eviction in trans upon Induction of the Yeast PHO5 Promoter

2004 ◽  
Vol 24 (24) ◽  
pp. 10965-10974 ◽  
Author(s):  
Philipp Korber ◽  
Tim Luckenbach ◽  
Dorothea Blaschke ◽  
Wolfram Hörz
Keyword(s):  
Hypersensitive Site ◽  
Chromosomal Locus ◽  
Small Plasmid ◽  
Sliding Mechanism ◽  
Eukaryotic Gene ◽  
In Trans ◽  
Dnase I Hypersensitive Site ◽  
Eukaryotic Gene Regulation ◽  
Nucleosome Sliding

ABSTRACT The yeast PHO5 promoter is a model system for the role of chromatin in eukaryotic gene regulation. Four positioned nucleosomes in the repressed state give way to an extended DNase I hypersensitive site upon induction. Recently this hypersensitive site was shown to be devoid of histone DNA contacts. This raises the mechanistic question of how histones are removed from the promoter. A displacement in trans or movement in cis, the latter according to the well established nucleosome sliding mechanism, are the major alternatives. In this study, we embedded the PHO5 promoter into the context of a small plasmid which severely restricts the space for nucleosome sliding along the DNA in cis. Such a construct would either preclude the chromatin transition upon induction altogether, were it to occur in cis, or gross changes in chromatin around the plasmid would be the consequence. We observed neither. Instead, promoter opening on the plasmid was indistinguishable from opening at the native chromosomal locus. This makes a sliding mechanism for the chromatin transition at the PHO5 promoter highly unlikely and points to histone eviction in trans.

Reduction in gene expression noise by targeted increase in accessibility at gene loci

2021 ◽  
Vol 118 (42) ◽  
pp. e2018640118
Author(s):  
LaTasha C. R. Fraser ◽  
Ryan J. Dikdan ◽  
Supravat Dey ◽  
Abhyudai Singh ◽  
Sanjay Tyagi
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Molecule ◽  
Single Cells ◽  
Global Changes ◽  
Messenger Rnas ◽  
Histone Acetyl Transferase ◽  
Gene Expression Noise ◽  
Expression Noise ◽  
Eukaryotic Genes

Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by periods of quiescence. Here, we show that the intermittent access of the promoters to transcription factors through relatively impervious chromatin contributes to this “noisy” transcription. We tethered a nuclease-deficient Cas9 fused to a histone acetyl transferase at the promoters of two endogenous genes in HeLa cells. An assay for transposase-accessible chromatin using sequencing showed that the activity of the histone acetyl transferase altered the chromatin architecture locally without introducing global changes in the nucleus and rendered the targeted promoters constitutively accessible. We measured the gene expression variability from the gene loci by performing single-molecule fluorescence in situ hybridization against mature messenger RNAs (mRNAs) and by imaging nascent mRNA molecules present at active gene loci in single cells. Because of the increased accessibility of the promoter to transcription factors, the transcription from two genes became less noisy, even when the average levels of expression did not change. In addition to providing evidence for chromatin accessibility as a determinant of the noise in gene expression, our study offers a mechanism for controlling gene expression noise which is otherwise unavoidable.

Single-Molecule Force-Clamp Experiments Reveal Kinetics of Mechanically Activated Silyl Ester Hydrolysis

ACS Nano ◽  
2012 ◽  
Vol 6 (2) ◽  
pp. 1314-1321 ◽  
Author(s):  
Sebastian W. Schmidt ◽  
Pavel Filippov ◽  
Alfred Kersch ◽  
Martin K. Beyer ◽  
Hauke Clausen-Schaumann
Keyword(s):  
Single Molecule ◽  
Ester Hydrolysis ◽  
Silyl Ester ◽  
Force Clamp ◽  
Kinetics Of

scholarly journals Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimer's pathology

2021 ◽  
Author(s):  
Shuo Chen ◽  
Yuzhou Chang ◽  
Liangping Li ◽  
Diana Acosta ◽  
Cody Morrison ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Brain Region ◽  
Expression Patterns ◽  
Middle Temporal Gyrus ◽  
Marker Genes ◽  
Gene Signatures ◽  
Unique Gene ◽  
Spatially Resolved ◽  
And Gender

Alzheimer's disease (AD) is pathologically characterized by amyloid beta (Aβ) plaques, neurofibrillary tangles (tau aggregates), and alterations in microglia, astrocytes and oligodendrocytes. The mesial temporal lobe is a vulnerable brain region in early AD; however, little is known about the transcriptome-scale gene expression in this region and its relation to AD pathology. Here we use the 10x Genomics Visium platform in combination with co-immunofluorescence staining of AD-associated pathological markers to define the spatial topography of gene expression in the middle temporal gyrus (MTG) from both early AD and age- and gender-matched control cases. We identify unique marker genes for six cortical layers and the adjacent white matter as well as gene expression patterns and alterations that showcase unique gene signatures and pathways associated with a range of AD pathology. Also, gene co-expression analyses of differentially expressed genes (DEGs) between AD and controls reveal four unique gene modules, which significantly change their co-expression patterns in the presence of variations of AD pathology. Furthermore, we validate the changes of key representative DEGs that are associated with AD pathology in neurons, microglia, astrocytes and oligodendrocytes using single-molecule fluorescent in situ hybridization. In summary, we provide a rich resource for the spatial transcriptomic profile of the human MTG, which will contribute to our understanding of the complex architecture and AD pathology of this vulnerable brain region.

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