scholarly journals Identification and characterization of the hypoxia response regulatory elements in the accessible genome

2020 ◽  
Author(s):  
Xi Lu ◽  
Xingqi Chen
Keyword(s):  
Solid Tumor ◽  
Regulatory Elements ◽  
Hypoxia Response ◽  
Genomic Features ◽  
Structure Response ◽  
Precision Therapy ◽  
Identification And Characterization ◽  
Epigenetic Feature ◽  
Hypoxia Treatment

AbstractHypoxia is commonly observed in the solid tumor and contributes to the drug resistance in cancer therapy. Deciphering the epigenetic feature under the hypoxia condition in the solid tumor is critical for us to understand the tumorigenesis and design the precision therapy. Using the time series of ATAC-seq data under the hypoxia treatment from the epithelia cells, we identified the hypoxia response regulatory elements (HRREs) in the accessible genome. We found that these different HRREs have unique genomic features and are enriched with different transcriptional factors (TFs). Our study provides insights into the chromatin structure response to the hypoxia treatment and identifies useful genomic features for a better understanding of the hypoxia biology in the solid tumor.

scholarly journals Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

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.

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

2018 ◽  
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

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.

scholarly journals Identification and characterization of regulatory elements of the human prostatic acid phosphatase promoter

Oncogene ◽  
2002 ◽  
Vol 21 (23) ◽  
pp. 3696-3705 ◽  
Author(s):  
Stanislav Zelivianski ◽  
Tsukasa Igawa ◽  
Stephen Lim ◽  
Rodney Taylor ◽  
Ming-Fong Lin
Keyword(s):  
Acid Phosphatase ◽  
Prostatic Acid Phosphatase ◽  
Regulatory Elements ◽  
Identification And Characterization

scholarly journals Chromatin accessibility dynamics across C. elegans development and ageing

eLife ◽  
2018 ◽  
Vol 7 ◽  
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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