Gene Regulatory Elements

2012 ◽  
pp. 1-17 ◽  
Author(s):  
Nadav Ahituv
Keyword(s):  
Regulatory Elements ◽  
Gene Regulatory Elements ◽  
Gene Regulatory

Development of Integrative Map of MicroRNA Gene Regulatory Elements

MicroRNA ◽  
2016 ◽  
Vol 4 (3) ◽  
pp. 205-208 ◽  
Author(s):  
Minja Zorc ◽  
Tanja Kunej
Keyword(s):  
Regulatory Elements ◽  
Microrna Gene ◽  
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

scholarly journals Temporal autoregulation during human PU.1 locus SubTAD formation

Blood ◽  
2018 ◽  
Vol 132 (25) ◽  
pp. 2643-2655 ◽  
Author(s):  
Daniel Schuetzmann ◽  
Carolin Walter ◽  
Boet van Riel ◽  
Sabrina Kruse ◽  
Thorsten König ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Adaptor Protein ◽  
Regulatory Elements ◽  
Genomic Region ◽  
Spatial Interactions ◽  
Lim Domain ◽  
Control Of Gene Expression ◽  
Gene Regulatory Elements ◽  
Hit And Run ◽  
Gene Regulatory

Abstract Epigenetic control of gene expression occurs within discrete spatial chromosomal units called topologically associating domains (TADs), but the exact spatial requirements of most genes are unknown; this is of particular interest for genes involved in cancer. We therefore applied high-resolution chromosomal conformation capture sequencing to map the three-dimensional (3D) organization of the human locus encoding the key myeloid transcription factor PU.1 in healthy monocytes and acute myeloid leukemia (AML) cells. We identified a dynamic ∼75-kb unit (SubTAD) as the genomic region in which spatial interactions between PU.1 gene regulatory elements occur during myeloid differentiation and are interrupted in AML. Within this SubTAD, proper initiation of the spatial chromosomal interactions requires PU.1 autoregulation and recruitment of the chromatin-adaptor protein LDB1 (LIM domain–binding protein 1). However, once these spatial interactions have occurred, LDB1 stabilizes them independently of PU.1 autoregulation. Thus, our data support that PU.1 autoregulates its expression in a “hit-and-run” manner by initiating stable chromosomal loops that result in a transcriptionally active chromatin architecture.

Discovering Gene Regulatory Elements Using Coverage-Based Heuristics

2018 ◽  
Vol 15 (4) ◽  
pp. 1290-1300 ◽  
Author(s):  
Rami Al-Ouran ◽  
Robert Schmidt ◽  
Ashwini Naik ◽  
Jeffrey Jones ◽  
Frank Drews ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Gene Regulatory Elements ◽  
Gene Regulatory
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