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The spatial organization of the genome is essential for the precise control of gene expression. Recent advances in sequencing and imaging technologies allow us to explore the 3D genome and its relationship to gene regulation at an unprecedented scale. In this review, we provide an overview of lessons learned from studying the chromatin structure and their implications in communications between gene promoters and distal cis-regulatory elements, such as enhancers. We first review the current knowledge of general genome organization, followed by the importance of chromatin folding in gene regulation. Next, we proceed to a brief survey of the recently developed chromosome conformation capture technologies, as well as most widely adopted read-outs from such data. We then introduce two emerging models that offer explanations regarding how distal enhancers achieve transcriptional control of target genes in the 3D genome. Last, we discuss the promising prospects of leveraging knowledge in chromatin spatial organization for studying complex diseases and traits.
This article was published in the following journal.
Name: Human molecular genetics
Nearly half of the human genome is made up of transposable elements (TEs), and there is evidence that TEs are involved in gene regulation. In this study, we have integrated publicly available genomic,...
Our understanding of gene regulation is constantly evolving. It is now clear that the majority of cellular transcripts are non-coding RNAs. The spectrum of non-coding RNAs is diverse and includes shor...
Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/o...
The 3D structure of chromatin in the nucleus is important for the regulation of gene expression and the correct deployment of developmental programs. The differentiation of germ cells and early embryo...
A cohesin-loading factor (NIPBL) is one of important regulatory factors in the maintenance of 3D genome organization and function, by interacting with a large number of factors, e.g. cohesion, CCCTC-b...
To reveal the genetic determinants of the treatment outcome of escitalopram in depressed patients (by using candidate gene approach and whole genome scanning).
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Multiple biomarker development through validation of useful markers generated by next generation bio-data based genome research and cohort study
A left-handed double helix of DNA. Its name derives from its narrow zigzag structure that is the least twisted and thinnest form of DNA. Z-DNA forming regions within the GENOME may play an important role in GENE EXPRESSION REGULATION.
ATP-dependent DNA helicase that contains two N-terminal ZINC FINGERS and C-terminal ATP-binding and helicase domains. It functions in the regulation of gene transcription and CHROMATIN REMODELING. ATRX undergoes cell-cycle dependent phosphorylation, which causes it to translocate from the NUCLEAR MATRIX to CHROMATIN; thus, it may change its role from gene regulation during INTERPHASE to ensuring proper chromosome segregation at MITOSIS. Mutations in the ATRX gene are associated with cases of X-LINKED MENTAL RETARDATION co-morbid with ALPHA-THALASSEMIA (ATRX syndrome).
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
The process of gene expression is used by eukaryotes, prokaryotes, and viruses to generate the macromolecular machinery for life. Steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-tran...