scholarly journals Probing connectivity between transcriptional and post-transcriptional gene networks

2011 ◽  
Vol 32 (4) ◽  
pp. 166
Author(s):  
Sarah E Boyd ◽  
Johnathon M Keith ◽  
Ana Traven ◽  
Traude Beilharz
Keyword(s):  
Complete Genome ◽  
Cell Biology ◽  
Gene Networks ◽  
Eukaryotic Cell ◽  
Current Understanding ◽  
Multidimensional Datasets ◽  
Growth Requirements ◽  
Genome Wide ◽  
Simple Growth

The foundation for much of our current understanding of eukaryotic cell biology stems from studies exploiting the combined power of this yeast?s genetic tractability and its simple growth requirements. Furthermore, access to an early complete genome in 1996 allowed yeast researchers to spearhead the move toward genome-wide studies that underpin our thinking about systems-level biology today. Indeed, the last decade has been so rich in these studies that it has become close to impossible for most biologists to interrogate the data in an unbiased fashion. The challenge for the next decade is to generate the informational tools to sort the multidimensional datasets for underlying networks.

scholarly journals Genome-wide mapping of DNA double-strand breaks from eukaryotic cell cultures using Break-seq

2021 ◽  
Vol 2 (2) ◽  
pp. 100554
Author(s):  
Ishita Joshi ◽  
Jenna DeRycke ◽  
Megan Palmowski ◽  
Robert LeSuer ◽  
Wenyi Feng
Keyword(s):  
Cell Cultures ◽  
Eukaryotic Cell ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Genome Wide

scholarly journals PAK and other Rho-associated kinases – effectors with surprisingly diverse mechanisms of regulation

2005 ◽  
Vol 386 (2) ◽  
pp. 201-214 ◽  
Author(s):  
Zhou-shen ZHAO ◽  
Ed MANSER
Keyword(s):  
Rho Gtpases ◽  
Cell Biology ◽  
Rho Gtpase ◽  
Rho Kinase ◽  
Molecular Switches ◽  
Eukaryotic Cell ◽  
Effector Proteins ◽  
Downstream Effector ◽  
P21 Activated Kinase ◽  
Do So

The Rho GTPases are a family of molecular switches that are critical regulators of signal transduction pathways in eukaryotic cells. They are known principally for their role in regulating the cytoskeleton, and do so by recruiting a variety of downstream effector proteins. Kinases form an important class of Rho effector, and part of the biological complexity brought about by switching on a single GTPase results from downstream phosphorylation cascades. Here we focus on our current understanding of the way in which different Rho-associated serine/threonine kinases, denoted PAK (p21-activated kinase), MLK (mixed-lineage kinase), ROK (Rho-kinase), MRCK (myotonin-related Cdc42-binding kinase), CRIK (citron kinase) and PKN (protein kinase novel), interact with and are regulated by their partner GTPases. All of these kinases have in common an ability to dimerize, and in most cases interact with a variety of other proteins that are important for their function. A diversity of known structures underpin the Rho GTPase–kinase interaction, but only in the case of PAK do we have a good molecular understanding of kinase regulation. The ability of Rho GTPases to co-ordinate spatial and temporal phosphorylation events explains in part their prominent role in eukaryotic cell biology.

scholarly journals Mitochondrial DNA: an advance in eukaryotic cell biology in the 1960s

2005 ◽  
Vol 97 (9) ◽  
pp. 743-748 ◽  
Author(s):  
Jean-Claude Mounolou ◽  
François Lacroute
Keyword(s):  
Mitochondrial Dna ◽  
Cell Biology ◽  
Eukaryotic Cell ◽  
The 1960S

scholarly journals Regulatory links between imprinted genes: evolutionary predictions and consequences

2016 ◽  
Vol 283 (1824) ◽  
pp. 20152760 ◽  
Author(s):  
Manus M. Patten ◽  
Michael Cowley ◽  
Rebecca J. Oakey ◽  
Robert Feil
Keyword(s):  
Gene Networks ◽  
Cellular Proliferation ◽  
Point Of View ◽  
Imprinted Genes ◽  
Imprinted Gene ◽  
Genome Wide ◽  
Proliferation And Differentiation ◽  
Evolutionary View ◽  
In Trans ◽  
Regulatory Effects

Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis -acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans -regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.

scholarly journals Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles

BMC Genomics ◽  
2015 ◽  
Vol 16 (Suppl 5) ◽  
pp. S3 ◽  
Author(s):  
Sara Aibar ◽  
Celia Fontanillo ◽  
Conrad Droste ◽  
Beatriz Roson-Burgo ◽  
Francisco J Campos-Laborie ◽  
...  
Keyword(s):  
Gene Networks ◽  
Expression Profiles ◽  
Genome Wide ◽  
Disease Subtypes ◽  
Genome Wide Expression

scholarly journals Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Maria Victoria Gomez Roldan ◽  
Farhaj Izhaq ◽  
Marion Verdenaud ◽  
John Eleblu ◽  
Aimen Haraghi ◽  
...  
Keyword(s):  
Gene Networks ◽  
Growth Arrest ◽  
Reproductive Organs ◽  
Stress Signaling ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Inhibition Of Growth ◽  
Genome Wide ◽  
Male Flowers

AbstractIn cucurbits, CmWIP1 is a master gene controlling sex determination. To bring new insight in the function of CmWIP1, we investigated two Arabidopsis WIP transcription factors, AtWIP1/TT1 and AtWIP2/NTT. Using an inducible system we showed that WIPs are powerful inhibitor of growth and inducer of cell death. Using ChIP-seq and RNA-seq we revealed that most of the up-regulated genes bound by WIPs display a W-box motif, associated with stress signaling. In contrast, the down-regulated genes contain a GAGA motif, a known target of polycomb repressive complex. To validate the role of WIP proteins in inhibition of growth, we expressed AtWIP1/TT1 in carpel primordia and obtained male flowers, mimicking CmWIP1 function in melon. Using other promoters, we further demonstrated that WIPs can trigger growth arrest of both vegetative and reproductive organs. Our data supports an evolutionary conserved role of WIPs in recruiting gene networks controlling growth and adaptation to stress.

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