scholarly journals DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells

2010 ◽  
Vol 2010 (2) ◽  
pp. pdb.prot5384-pdb.prot5384 ◽  
Author(s):  
L. Song ◽  
G. E. Crawford
Keyword(s):  
High Resolution ◽  
Mammalian Cells ◽  
Regulatory Elements ◽  
Active Gene ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
High Resolution Technique

scholarly journals RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells

2017 ◽  
Vol 65 (2) ◽  
pp. 272-284 ◽  
Author(s):  
Honglian Zhang ◽  
Haiyun Gan ◽  
Zhiquan Wang ◽  
Jeong-Heon Lee ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Regulatory Elements ◽  
Gene Regulatory Elements ◽  
Gene Regulatory

scholarly journals Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 729-742 ◽  
Author(s):  
Lena Annika Street ◽  
Ana Karina Morao ◽  
Lara Heermans Winterkorn ◽  
Chen-Yu Jiao ◽  
Sarah Elizabeth Albritton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Protein Complexes ◽  
Regulatory Elements ◽  
Evolutionarily Conserved ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Regulatory Sites

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

scholarly journals Identification and Computational Analysis of Gene Regulatory Elements

2015 ◽  
Vol 2015 (1) ◽  
pp. pdb.top083642 ◽  
Author(s):  
Leila Taher ◽  
Leelavati Narlikar ◽  
Ivan Ovcharenko
Keyword(s):  
Computational Analysis ◽  
Regulatory Elements ◽  
Gene Regulatory Elements ◽  
Gene Regulatory

Gene-regulatory elements may change the amount, timing, or location of gene expression, cis-Regulation therapy platforms might become a gene therapy to treat many genetic diseases

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Gene Expression ◽  
Genetic Diseases ◽  
Regulatory Elements ◽  
Tissue Type ◽  
Gene Promoters ◽  
Expression Levels ◽  
Cis Regulation ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Gene Expression Levels

Changes in gene expression levels above or below a particular threshold may have a dramatic impact on phenotypes, leading to a wide spectrum of human illnesses. Gene-regulatory elements, also known as cis-regulatory elements (CREs), may change the amount, timing, or location (cell/tissue type) of gene expression, whereas mutations in a gene's coding sequence may result in lower or higher gene expression levels resulting in protein loss or gain. Loss-of-function mutations in both genes produce recessive human illness, while haploinsufficient mutations in 65 genes are also known to be deleterious due to function gain, according to the ClinVar1 and ClinGen3 databases. CREs are promoters living near to a gene's transcription start site and switching it on at predefined times, places, and levels. Other distal CREs, like enhancers and silencers, are temporal and tissue-specific control promoters. Enhancers activate promoters, commonly referred to as "promoters," whereas silencers turn them off. Insulators also restrict promiscuous interactions between enhancers and gene promoters. Systematic genomic approaches can help understand the cis-regulatory circuitry of gene expression by highly detecting and functionally defining these CREs. This includes the new use of CRISPR–CRISPR-associated protein 9 (CRISPR–Cas9) and other editing approaches to discover CREs. Cis-Regulation therapy (CRT) provides many promises to heal human ailments. CRT may be used to upregulate or downregulate disease-causing genes due to lower or higher levels of expression, and it may also be used to precisely adjust the expression of genes that assist in alleviating disease features. CRT may employ proteins that generate epigenetic modifications like methylation, histone modification, or gene expression regulation looping. Weighing CRT's advantages and downsides against alternative treatment methods is crucial. CRT platforms might become a practical technique to treat many genetic diseases that now lack treatment alternatives if academics, patient communities, clinicians, regulators and industry work together.

scholarly journals Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens

PLoS ONE ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. e0198463
Author(s):  
Bhaven B. Patel ◽  
Andres M. Lebensohn ◽  
Ganesh V. Pusapati ◽  
Jan E. Carette ◽  
Julia Salzman ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Regulatory Elements ◽  
Genetic Screens ◽  
Gene Regulatory Elements ◽  
Gene Regulatory
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