4.8 Article

Robust regulatory architecture of pan-neuronal gene expression

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Temporal transitions in the post-mitotic nervous system of Caenorhabditis elegans

HaoSheng Sun et al.

Summary: This study using the model organism Caenorhabditis elegans reveals that post-mitotic nervous system undergoes distinct functional and molecular states across temporal transitions during post-embryonic development. The regulation of neuron-type-specific gene expression by the conserved miRNA LIN-4 and its target lin-14 plays a crucial role in promoting a mature neuronal transcriptional program. The findings provide insights into regulatory strategies controlling distinct behavioral states across temporal, sexual, and environmental dimensions during post-embryonic development.

NATURE (2021)

Article Cell Biology

Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation

Quirino Attilio Vassalli et al.

Summary: Photoreceptor cells have diversified during evolution, with the homeodomain transcription factor Onecut (Oc) playing a key role in their differentiation and functioning. Downstream genes of Oc are involved in functions such as exocytosis, calcium homeostasis, and neurotransmission in both tunicates and vertebrates.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Molecular topography of an entire nervous system

Seth R. Taylor et al.

Summary: The gene expression profiles of 302 neurons in the C. elegans nervous system show that individual neuron classes can be identified by the combinatorial expression of specific gene families, forming a complex and extensive signaling network. Computational approaches were used to identify cis-regulatory elements for neuron-specific gene expression and reveal adhesion proteins related to process placement and synaptic specificity. This neuron-specific gene expression directory is expected to drive investigations into the mechanisms that define anatomy, connectivity, and function in the C. elegans nervous system.
Review Neurosciences

Homeobox genes and the specification of neuronal identity

Oliver Hobert

Summary: This article discusses the significance of Homeobox genes in specifying neuronal identity in animal nervous systems, emphasizing the method of defining neuron types through cell-type-specific gene battery expression.

NATURE REVIEWS NEUROSCIENCE (2021)

Review Developmental Biology

Brn3/POU-IV-type POU homeobox genes-Paradigmatic regulators of neuronal identity across phylogeny

Eduardo Leyva-Diaz et al.

WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2020)

Article Multidisciplinary Sciences

Unique homeobox codes delineate all the neuron classes ofC. elegans

Molly B. Reilly et al.

NATURE (2020)

Review Neurosciences

The crux of Cux genes in neuronal function and plasticity

Linnea A. Weiss et al.

BRAIN RESEARCH (2019)

Article Biochemistry & Molecular Biology

ONECUT transcription factors induce neuronal characteristics and remodel chromatin accessibility

Jori van der Raadt et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Neurosciences

Neuronal identity control by terminal selectors in worms, flies, and chordates

Oliver Hobert et al.

CURRENT OPINION IN NEUROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

The Encyclopedia of DNA elements (ENCODE): data portal update

Carrie A. Davis et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Biochemistry & Molecular Biology

Homeodomain proteins: an update

Thomas R. Buerglin et al.

CHROMOSOMA (2016)

Article Biochemical Research Methods

Tissue enrichment analysis for C. elegans genomics

David Angeles-Albores et al.

BMC BIOINFORMATICS (2016)

Article Neurosciences

Regulatory Logic of Pan-Neuronal Gene Expression in C-elegans

Nikolaos Stefanakis et al.

NEURON (2015)

Article Biochemistry & Molecular Biology

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

Matthew T. Weirauch et al.

Article Biochemical Research Methods

CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion

Christophe Restif et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Modular Control of Glutamatergic Neuronal Identity in C. elegans by Distinct Homeodomain Proteins

Esther Serrano-Saiz et al.

Article Biochemistry & Molecular Biology

DNA-Binding Specificities of Human Transcription Factors

Arttu Jolma et al.

Article Developmental Biology

The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth

Hiroshi Kagoshima et al.

DEVELOPMENTAL BIOLOGY (2013)

Article Biochemical Research Methods

A database of Caenorhabditis elegans behavioral phenotypes

Eviatar Yemini et al.

NATURE METHODS (2013)

Article Biochemistry & Molecular Biology

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

Mihail Sarov et al.

Article Biochemistry & Molecular Biology

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

Florian A. Steiner et al.

GENOME RESEARCH (2012)

Article Biochemical Research Methods

NIH Image to ImageJ: 25 years of image analysis

Caroline A. Schneider et al.

NATURE METHODS (2012)

Review Biochemistry & Molecular Biology

The Role of EHD Proteins at the Neuronal Synapse

Maria S. Ioannou et al.

SCIENCE SIGNALING (2012)

Article Genetics & Heredity

Large-Scale Screening for Targeted Knockouts in the Caenorhabditis elegans Genome

Robert Barstead et al.

G3-GENES GENOMES GENETICS (2012)

Article Biochemical Research Methods

MEME-ChIP: motif analysis of large DNA datasets

Philip Machanick et al.

BIOINFORMATICS (2011)

Review Neurosciences

The molecular and gene regulatory signature of a neuron

Oliver Hobert et al.

TRENDS IN NEUROSCIENCES (2010)

Article Multidisciplinary Sciences

Genetic analysis of crawling and swimming locomotory patterns in C. elegans

Jonathan T. Pierce-Shimomura et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biotechnology & Applied Microbiology

Quantifying similarity between motifs

Shobhit Gupta et al.

GENOME BIOLOGY (2007)

Article Biochemical Research Methods

Analysis of synaptic transmission in Caenorhabditis elegans using an aldicarb-sensitivity assay

Timothy R. Mahoney et al.

NATURE PROTOCOLS (2006)

Article Biochemistry & Molecular Biology

Expression profiling of GABAergic motor neurons in Caenorhabditis elegans

H Cinar et al.

CURRENT BIOLOGY (2005)

Review Neurosciences

Proneural genes and the specification of neural cell types

N Bertrand et al.

NATURE REVIEWS NEUROSCIENCE (2002)

Article Cell Biology

Expression of multiple UNC-13 proteins in the Caenorhabditis elegans nervous system

RE Kohn et al.

MOLECULAR BIOLOGY OF THE CELL (2000)