scholarly journals A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

Cell Reports ◽  
2014 ◽  
Vol 8 (2) ◽  
pp. 622-632 ◽  
Author(s):  
Jose L. Pruneda-Paz ◽  
Ghislain Breton ◽  
Dawn H. Nagel ◽  
S. Earl Kang ◽  
Katia Bonaldi ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Functional Characterization ◽  
A Genome ◽  
Genome Scale

scholarly journals Protocol: Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening

2016 ◽  
Author(s):  
Julia Joung ◽  
Silvana Konermann ◽  
Jonathan S. Gootenberg ◽  
Omar O. Abudayyeh ◽  
Randall J. Platt ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Functional Characterization ◽  
Library Design ◽  
Genetic Screens ◽  
Guide Rna ◽  
A Genome ◽  
Forward Genetic Screens ◽  
Genome Scale ◽  
Indel Rate

Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial immune system CRISPR (clustered regularly interspaced short palindromic repeats) has been adapted for genome-scale screening by combining Cas9 with guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom-or ready-made guide RNA libraries are constructed and packaged into lentivirus for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified from the screen, we further describe strategies for confirming the screening phenotype as well as genetic perturbation through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 6-10 weeks followed by 3-4 weeks of validation.

Functional characterization of two bZIP transcription factors in Verticillium dahliae

Gene ◽  
2017 ◽  
Vol 626 ◽  
pp. 386-394 ◽  
Author(s):  
Yulin Fang ◽  
Dianguang Xiong ◽  
Longyan Tian ◽  
Chen Tang ◽  
Yonglin Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Verticillium Dahliae ◽  
Functional Characterization ◽  
Bzip Transcription Factors

scholarly journals Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent

2019 ◽  
Author(s):  
Sonia Balyan ◽  
Sombir Rao ◽  
Sarita Jha ◽  
Chandni Bansal ◽  
Jaishri Rubina Das ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Heat Stress ◽  
Functional Characterization ◽  
Transcriptome Profiling ◽  
Negative Regulator ◽  
Comparative Transcriptome ◽  
Regulatory Pathways ◽  
Cool Region ◽  
Promoter Swapping

AbstractThe footprint of tomato cultivation, a cool region crop that exhibits heat stress (HS) sensitivity, is increasing in the tropics/sub-tropics. Knowledge of novel regulatory hot-spots from varieties growing in the Indian sub-continent climatic zones could be vital for developing HS-resilient crops. Comparative transcriptome-wide signatures of a tolerant (CLN1621L) and sensitive (CA4) cultivar-pair short-listed from a pool of varieties exhibiting variable thermo-sensitivity using physiological, survival and yield-related traits revealed redundant to cultivar-specific HS-regulation with more up-regulated genes for CLN1621L than CA4. The anatgonisiticly-expressing genes include enzymes; have roles in plant defense and response to different abiotic stresses. Functional characterization of three antagonistic genes by overexpression and TRV-VIGS silencing established Solyc09g014280 (Acylsugar acyltransferase) and Solyc07g056570 (Notabilis), that are up-regulated in tolerant cultivar, as positive regulators of HS-tolerance and Solyc03g020030 (Pin-II proteinase inhibitor), that is down-regulated in CLN1621L, as negative regulator of thermotolerance. Transcriptional assessment of promoters of these genes by SNPs in stress-responsive cis-elements and promoter swapping experiments in opposite cultivar background showed inherent cultivar-specific orchestration of transcription factors in regulating transcription. Moreover, overexpression of three ethylene response transcription factors (ERF.C1/F4/F5) also improved HS-tolerance in tomato. This study identifies several novel HS-tolerance genes and provides proof of their utility in tomato-thermotolerance.HighlightNovel heat stress regulatory pathways uncovered by comparative transcriptome profiling between contrasting tomato cultivars from Indian sub-continent for improving thermotolerance. (20/30)

Transcription factors–DNA interactions in rice: identification and verification

2019 ◽  
Vol 21 (3) ◽  
pp. 946-956 ◽  
Author(s):  
Zijie Shen ◽  
Yuan Lin ◽  
Quan Zou
Keyword(s):  
Transcription Factors ◽  
Functional Characterization ◽  
Rice Genome ◽  
Research Strategies ◽  
Promoter Regions ◽  
Rice Varieties ◽  
Rice Genome Sequence ◽  
Advantages And Disadvantages ◽  
Genomics Research

Abstract The completion of the rice genome sequence paved the way for rice functional genomics research. Additionally, the functional characterization of transcription factors is currently a popular and crucial objective among researchers. Transcription factors are one of the groups of proteins that bind to either enhancer or promoter regions of genes to regulate expression. On the basis of several typical examples of transcription factor analyses, we herein summarize selected research strategies and methods and introduce their advantages and disadvantages. This review may provide some theoretical and technical guidelines for future investigations of transcription factors, which may be helpful to develop new rice varieties with ideal traits.

scholarly journals Genome-Wide Identification and Analysis of VQ Motif-containing Gene Family in Brassica napus and Functional Characterization of BnMKS1 in Response to Leptosphaeria maculans

2020 ◽  
Author(s):  
Zhongwei Zou ◽  
Fei Liu ◽  
Shuanglong Huang ◽  
DILANTHA GERARD FERNANDO
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Characterization ◽  
Leptosphaeria Maculans ◽  
Defense Responses ◽  
Marker Genes ◽  
Blackleg Disease ◽  
Genome Wide ◽  
A Genome

Proteins containing Valine-glutamine (VQ) motifs play important roles in plant growth and development, as well as in defense responses to both abiotic and biotic stresses. Blackleg disease, which is caused by Leptosphaeria maculans, is the most important disease in canola (Brassica napus L.) worldwide. H; however, the identification of B. napus VQs and their functions in response to blackleg disease have not yet been reported. In this study, we conducted a genome genome-wide identification and characterization of the VQ gene family in B. napus, including chromosome location, phylogenetic relations, gene structure, motif domain, synteny analysis, and cis-elements categorization of their promoter regions. To understand B. napus VQ gene function in response to blackleg disease, we overexpressed BnVQ7 (BnaA01g36880D, also known as the mitogen-activated protein kinase4 substrate1 (MKS1) gene) in a blackleg-susceptible canola variety Westar. Overexpression The overexpression of BnMKS1 in canola did not improve its resistance to blackleg disease at the seedling stage. H; however, transgenic canola plants overexpressing BnMKS1 displayed an enhanced resistance to L. maculans infection at the adult plant stage. Expression levels of downstream and defense marker genes in cotyledons increased significantly at the necrotrophic stage of L. maculans infection in the overexpression line of BnMKS1, suggesting that the SA salicylic acid (SA)- and jasmonic acid (JA )-mediated signaling pathways were both involved in the defense responses. Together, these results suggest that BnMKS1 might play an important role in the defense against L. maculans.

scholarly journals Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha

2019 ◽  
Vol 36 (12) ◽  
pp. 2805-2812
Author(s):  
Aaron Hardin ◽  
Kimberly A Nevonen ◽  
Walter L Eckalbar ◽  
Lucia Carbone ◽  
Nadav Ahituv
Keyword(s):  
Functional Characterization ◽  
Mammary Glands ◽  
Comparative Genomic ◽  
Lassa Virus ◽  
Enhancer Activity ◽  
A Genome ◽  
Genomic Tool ◽  
Mastomys Coucha ◽  
Comparative Genomic Tool

Abstract Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.

scholarly journals Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN

Science ◽  
2018 ◽  
Vol 362 (6414) ◽  
pp. eaat0572 ◽  
Author(s):  
Quinlan L. Sievers ◽  
Georg Petzold ◽  
Richard D. Bunker ◽  
Aline Renneville ◽  
Mikołaj Słabicki ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Small Molecules ◽  
Zinc Finger ◽  
Ubiquitin Ligase ◽  
Biochemical Analysis ◽  
Zinc Fingers ◽  
Functional Characterization ◽  
C2h2 Zinc Finger

The small molecules thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) by recruiting a Cys2-His2 (C2H2) zinc finger domain to Cereblon (CRBN), the substrate receptor of the CRL4CRBN E3 ubiquitin ligase. We screened the human C2H2 zinc finger proteome for degradation in the presence of thalidomide analogs, identifying 11 zinc finger degrons. Structural and functional characterization of the C2H2 zinc finger degrons demonstrates how diverse zinc finger domains bind the permissive drug-CRBN interface. Computational zinc finger docking and biochemical analysis predict that more than 150 zinc fingers bind the drug-CRBN complex in vitro, and we show that selective zinc finger degradation can be achieved through compound modifications. Our results provide a rationale for therapeutically targeting transcription factors that were previously considered undruggable.

scholarly journals Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis

2020 ◽  
Author(s):  
Amir Banaei-Esfahani ◽  
Andrej Trauner ◽  
Sonia Borrell ◽  
Sebastian M. Gygli ◽  
Tige R. Rustad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitric Oxide ◽  
Mycobacterium Tuberculosis ◽  
Transcription Factors ◽  
List Type ◽  
Phylogenetic Distance ◽  
Clinical Strains ◽  
A Genome ◽  
L1 And L2 ◽  
Genome Scale

SummaryThe Mycobacterium tuberculosis (Mtb) complex comprises seven phylogenetically distinct human-adapted lineages exhibiting different geographical distribution and degrees of pathogenicity. Among these, Lineage 1 (L1) has been associated with low virulence whereas Lineage 2 (L2) has been linked to hyper-virulence, enhanced transmission and drug resistance. Here, we conducted multi-layer comparative analyses using whole genome sequencing data combined with quantitative transcriptomic and proteomic profiling of a set of L1 and L2 clinical strains, each grown under two different conditions in vitro. Our data revealed different degrees of correlation between transcript and protein abundances across clinical strains and functional gene categories, indicating variable levels of post-transcriptional regulation in the tested lineages. Contrasting genomic and gene expression data showed that the magnitude of the transcriptional and translational changes was proportional to the phylogenetic distance between strains, with one out of three single nucleotide polymorphisms leading to a transcriptional and/or translational change on average. We devised a new genome-scale transcriptional regulatory model and identified several master transcription factors, strongly linked to the sigma factor network, whose targets were differentially regulated between the two lineages. These differences resulted in a higher basal expression of DosR proteins and a stronger response to nitric oxide (NO) exposure in L2 compared to L1. These patterns are most likely responsible for the shorter NO-induced growth arrest in L2 observed. Given the limited genetic variation between strains, it appears that phenotypic differences in Mtb are substantially driven by differences in the regulation of biochemical networks through master transcriptional regulators.HighlightsProteomic and transcriptomic characterization of fully sequenced diverse L1 and L2 clinical isolates of Mtb.Post-transcriptional control mechanisms for regulatory and virulence genes are mitigated in Mtb L2.By applying a genome-scale transcriptional framework, DosR, Rv1985c, Lsr2 and Rv0691c are identified as master transcription factors responsible for differential target gene expression in L2 strains compared to L1.L1 and L2 DosR proteins respond differently to nitric oxide stress, thus determining a relevant phenotype.

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