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Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation
Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and...
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Species-aware DNA language models capture regulatory elements and their evolution
BackgroundThe rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory...
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Map** the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
BackgroundDrug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease-associated...
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3D organization of regulatory elements for transcriptional regulation in Arabidopsis
BackgroundAlthough spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial...
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Novel lncRNA regulatory elements in milk somatic cells of Holstein dairy cows associated with mastitis
Despite regulatory elements such as long non - coding RNAs representing most of the transcriptome, the functional understanding of long non - coding...
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Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements...
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Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
The inability to scalably and precisely measure the activity of developmental cis -regulatory elements (CREs) in multicellular systems is a bottleneck...
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Targeting cis-regulatory elements of FOXO family is a novel therapeutic strategy for induction of leukemia cell differentiation
Differentiation therapy has been proposed as a promising therapeutic strategy for acute myeloid leukemia (AML); thus, the development of more...
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An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure
A deeper knowledge of the dynamic transcriptional activity of promoters and enhancers is needed to improve mechanistic understanding of the...
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H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence...
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Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C
BackgroundRegulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin...
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Development of dual reporter vector system for estimating translational activity of regulatory elements
BackgroundFor the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has...
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HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements
Hepatocyte nuclear factor 4A (HNF4A/NR2a1), a transcriptional regulator of hepatocyte identity, controls genes that are crucial for liver functions,...
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Genome-Wide Map** of Active Regulatory Elements Using ATAC-seq
Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property...
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Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits
BackgroundInsights into the genetic basis of complex traits and disease in both human and livestock species have been achieved over the past decade...
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H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells
BackgroundThe histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are...
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Regulatory Networks
This chapter elaborates on the overview presented in Chapter 3. Gene regulatory networks are complex systems that control the expression of genes in...
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Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes
BackgroundCell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs...
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Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
BackgroundThe gram-positive bacterium, Streptomyces avermitilis , holds industrial importance as the producer of avermectin, a widely used...
