Chromatin accessibility is dynamically regulated across C. elegans development and ageing

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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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 cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

10.1101/683284 ◽

2019 ◽

Author(s):

Wei Fang ◽

Yi Wen ◽

Xiangyun Wei

Keyword(s):

Core Promoter ◽

Regulatory Elements ◽

Specific Gene ◽

Protein Coding ◽

Core Promoters ◽

Protein Coding Genes ◽

The Core ◽

Cell Type Specific ◽

Identification And Characterization

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.

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How to find genomic regions relevant for gene regulation

Medizinische Genetik ◽

10.1515/medgen-2021-2074 ◽

2021 ◽

Vol 33 (2) ◽

pp. 157-165

Author(s):

Xuanzong Guo ◽

Uwe Ohler ◽

Ferah Yildirim

Keyword(s):

Functional Characterization ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

High Throughput Analysis ◽

Protein Coding ◽

Coding Regions ◽

The Past ◽

Genomic Regions ◽

Regulatory Functions

Abstract Genetic variants associated with human diseases are often located outside the protein coding regions of the genome. Identification and functional characterization of the regulatory elements in the non-coding genome is therefore of crucial importance for understanding the consequences of genetic variation and the mechanisms of disease. The past decade has seen rapid progress in high-throughput analysis and mapping of chromatin accessibility, looping, structure, and occupancy by transcription factors, as well as epigenetic modifications, all of which contribute to the proper execution of regulatory functions in the non-coding genome. Here, we review the current technologies for the definition and functional validation of non-coding regulatory regions in the genome.

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Identification and Characterization of MYC Regulatory Elements: Links to Prostate Cancer

10.21236/ada574740 ◽

2012 ◽

Author(s):

Nora Wasserman ◽

Marcelo Nobrega

Keyword(s):

Prostate Cancer ◽

Regulatory Elements ◽

Identification And Characterization

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Identification and characterization of a new member of the gas3/PMP22 gene family in C. elegans

Gene ◽

10.1016/s0378-1119(99)00199-7 ◽

1999 ◽

Vol 234 (2) ◽

pp. 267-274 ◽

Cited By ~ 6

Author(s):

E. Agostoni ◽

S. Gobessi ◽

C. Brancolini ◽

C. Schneider

Keyword(s):

Gene Family ◽

Pmp22 Gene ◽

C Elegans ◽

Identification And Characterization

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Global identification and characterization of lncRNAs that control inflammation in malignant cholangiocytes

BMC Genomics ◽

10.1186/s12864-018-5133-8 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Bo-Wei Han ◽

Hua Ye ◽

Pan-Pan Wei ◽

Bo He ◽

Cai Han ◽

...

Keyword(s):

Global Identification ◽

Identification And Characterization

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Identification and characterization of protein coding genes in monsonia (Monsonia burkeana Planch. ex harv) using a combination of approaches

Genes & Genomics ◽

10.1007/s13258-016-0499-y ◽

2016 ◽

Vol 39 (3) ◽

pp. 245-259 ◽

Cited By ~ 2

Author(s):

Adugna A. Woldesemayat ◽

Khayalethu Ntushelo ◽

David M. Modise

Keyword(s):

Protein Coding ◽

Protein Coding Genes ◽

Identification And Characterization

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

Developmental Cell ◽

10.1016/j.devcel.2005.07.003 ◽

2005 ◽

Vol 9 (2) ◽

pp. 223-236 ◽

Cited By ~ 163

Author(s):

Martin Srayko ◽

Aynur Kaya ◽

Joanne Stamford ◽

Anthony A. Hyman

Keyword(s):

C Elegans ◽

Microtubule Growth ◽

Identification And Characterization

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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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