Identification and Characterization of Factors Required for Microtubule Growth and Nucleation in the Early C. elegans Embryo

AbstractAn essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

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Calcineurin, a Calcium/Calmodulin-dependent Protein Phosphatase, Is Involved in Movement, Fertility, Egg Laying, and Growth inCaenorhabditis elegans

Molecular Biology of the Cell ◽

10.1091/mbc.e02-01-0005 ◽

2002 ◽

Vol 13 (9) ◽

pp. 3281-3293 ◽

Cited By ~ 79

Author(s):

Jaya Bandyopadhyay ◽

Jiyeon Lee ◽

Jungsoo Lee ◽

Jin Il Lee ◽

Jae-Ran Yu ◽

...

Keyword(s):

Signaling Pathways ◽

Protein Phosphatase ◽

Body Wall ◽

Egg Laying ◽

Α Subunit ◽

C Elegans ◽

Calcium Calmodulin Dependent ◽

Dependent Protein ◽

Identification And Characterization

Calcineurin is a Ca2+-calmodulin–dependent serine/threonine protein phosphatase that has been implicated in various signaling pathways. Here we report the identification and characterization of calcineurin genes in Caenorhabditis elegans (cna-1 and cnb-1), which share high homology with Drosophila and mammalian calcineurin genes. C. elegans calcineurin binds calcium and functions as a heterodimeric protein phosphatase establishing its biochemical conservation in the nematode. Calcineurin is expressed in hypodermal seam cells, body-wall muscle, vulva muscle, neuronal cells, and in sperm and the spermatheca. cnb-1 mutants showed pleiotropic defects including lethargic movement and delayed egg-laying. Interestingly, these characteristic defects resembled phenotypes observed in gain-of-function mutants ofunc-43/Ca2+-calmodulin–dependent protein kinase II (CaMKII) and goa-1/Go-protein α-subunit. Double mutants of cnb-1 andunc-43(gf) displayed an apparent synergistic severity of movement and egg-laying defects, suggesting that calcineurin may have an antagonistic role in CaMKII-regulated phosphorylation signaling pathways in C. elegans.

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Identification and characterization of a putative C. elegans potassium channel gene (Ce-slo-2) distantly related to Ca2+-activated K+ channels

Gene ◽

10.1016/s0378-1119(99)00398-4 ◽

1999 ◽

Vol 240 (1) ◽

pp. 35-43 ◽

Cited By ~ 12

Author(s):

Hyun-Ho Lim ◽

Byung-Jae Park ◽

Hueng-Sik Choi ◽

Chul-Seung Park ◽

Soo Hyun Eom ◽

...

Keyword(s):

Potassium Channel ◽

K Channels ◽

C Elegans ◽

Channel Gene ◽

Identification And Characterization ◽

Potassium Channel Gene

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Identification and characterization of phosphatases that regulate TGFβ signaling in C. elegans

Developmental Biology ◽

10.1016/j.ydbio.2008.05.222 ◽

2008 ◽

Vol 319 (2) ◽

pp. 528

Author(s):

Sheng Xiong ◽

Cathy Savage-Dunn

Keyword(s):

Tgfβ Signaling ◽

C Elegans ◽

Identification And Characterization

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Neuronal KGB-1 JNK MAPK signaling regulates the dauer developmental decision in response to environmental stress in C. elegans

10.1101/2021.06.28.450206 ◽

2021 ◽

Author(s):

Deepshikha Dogra ◽

Warakorn Kulalert ◽

Frank Schroeder ◽

Dennis H Kim

Keyword(s):

Elevated Temperature ◽

Signaling Pathways ◽

Mapk Pathway ◽

Negative Regulator ◽

Loss Of Function ◽

C Elegans ◽

Metabolic Remodeling ◽

Dauer Formation ◽

Identification And Characterization

In response to stressful growth conditions of high population density, food scarcity and elevated temperature, young larvae of nematode Caenorhabditis elegans can enter a developmentally arrested stage called dauer that is characterized by dramatic anatomic and metabolic remodeling. Genetic analysis of dauer formation of C. elegans has served as an experimental paradigm for the identification and characterization of conserved neuroendocrine signaling pathways. Here, we report the identification and characterization of a conserved JNK-like mitogen-activated protein kinase (MAPK) pathway that is required for dauer formation in response to environmental stressors. We observed that loss-of-function mutations in the MLK-1-MEK-1-KGB-1 MAPK pathway suppress dauer entry. Loss-of-function mutation in the VHP-1 MAPK phosphatase, a known negative regulator of KGB-1 signaling, results in constitutive dauer formation which is dependent on the presence of dauer pheromone but independent of diminished food levels or elevated temperatures. Our data suggest that KGB-1 pathway acts in the sensory neurons, in parallel to established insulin and TGF-β signaling pathways, to transduce the dauer-inducing environmental cues of diminished food levels and elevated temperature.

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Chromatin accessibility dynamics across C. elegans development and ageing

eLife ◽

10.7554/elife.37344 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 22

Author(s):

Jürgen Jänes ◽

Yan Dong ◽

Michael Schoof ◽

Jacques Serizay ◽

Alex Appert ◽

...

Keyword(s):

Regulatory Mechanism ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Protein Coding ◽

C Elegans ◽

Transcription Profiles ◽

Physiological Processes ◽

Global Identification ◽

Identification And Characterization

An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here, we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one Caenorhabditis elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

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Identification and characterization of a putative basic helix-loop-helix (bHLH) transcription factor interacting with calcineurin in C. elegans

Molecules and Cells ◽

10.1007/s10059-009-0145-5 ◽

2009 ◽

Vol 28 (5) ◽

pp. 455-461 ◽

Cited By ~ 11

Author(s):

Soo-Ung Lee ◽

Hyun-Ok Song ◽

Wonhae Lee ◽

Gunasekaran Singaravelu ◽

Jae-Ran Yu ◽

...

Keyword(s):

Transcription Factor ◽

Bhlh Transcription Factor ◽

C Elegans ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Identification And Characterization

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Comprehensive identification and characterization of conserved small ORFs in animals

10.1101/017772 ◽

2015 ◽

Author(s):

Sebastian D Mackowiak ◽

Henrik Zauber ◽

Chris Bielow ◽

Denise Thiel ◽

Kamila Kutz ◽

...

Keyword(s):

Purifying Selection ◽

Fruit Fly ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Mass Spectrometry Data ◽

C Elegans ◽

Small Orfs ◽

Identification And Characterization

There is increasing evidence that non-annotated short open reading frames (sORFs) can encode functional micropeptides, but computational identification remains challenging. We expand our published method and predict conserved sORFs in human, mouse, zebrafish, fruit fly and the nematode C. elegans. Isolating specific conservation signatures indicative of purifying selection on encoded amino acid sequence, we identify about 2000 novel sORFs in the untranslated regions of canonical mRNAs or on transcripts annotated as non-coding. Predicted sORFs show stronger conservation signatures than those identified in previous studies and are sometimes conserved over large evolutionary distances. Encoded peptides have little homology to known proteins and are enriched in disordered regions and short interaction motifs. Published ribosome profiling data indicate translation for more than 100 of novel sORFs, and mass spectrometry data gives peptidomic evidence for more than 70 novel candidates. We thus provide a catalog of conserved micropeptides for functional validation in vivo.

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Neuronal KGB-1 JNK MAPK signaling regulates the dauer developmental decision in response to environmental stress in C. elegans

Genetics ◽

10.1093/genetics/iyab186 ◽

2021 ◽

Author(s):

Deepshikha Dogra ◽

Warakorn Kulalert ◽

Frank C Schroeder ◽

Dennis H Kim

Keyword(s):

Elevated Temperature ◽

Signaling Pathways ◽

Mapk Pathway ◽

Negative Regulator ◽

Loss Of Function ◽

C Elegans ◽

Metabolic Remodeling ◽

Dauer Formation ◽

Identification And Characterization

Abstract In response to stressful growth conditions of high population density, food scarcity and elevated temperature, young larvae of nematode Caenorhabditis elegans can enter a developmentally arrested stage called dauer that is characterized by dramatic anatomic and metabolic remodeling. Genetic analysis of dauer formation of C. elegans has served as an experimental paradigm for the identification and characterization of conserved neuroendocrine signaling pathways. Here, we report the identification and characterization of a conserved JNK-like mitogen-activated protein kinase (MAPK) pathway that is required for dauer formation in response to environmental stressors. We observed that loss-of-function mutations in the MLK-1-MEK-1-KGB-1 MAPK pathway suppress dauer entry. Loss-of-function mutation in the VHP-1 MAPK phosphatase, a known negative regulator of KGB-1 signaling, results in constitutive dauer formation which is dependent on the presence of dauer pheromone but independent of diminished food levels or elevated temperatures. Our data suggest that KGB-1 pathway acts in the sensory neurons, in parallel to established insulin and TGF-β signaling pathways, to transduce the dauer-inducing environmental cues of diminished food levels and elevated temperature.

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