Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse

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Unraveling gene function in agricultural species using gene co-expression networks

Co-expression networks have been shown to be a powerful tool for inferring a gene's function when little is known about it. With the advent of next generation sequencing technologies, the construction and analysis of co-expression networks is now possible in non-model species, including those with agricultural importance. Here, we review fundamental concepts in the construction and application of co-expression networks with a focus on agricultural crops. We survey past and current applications of co-expression network analysis in several agricultural species and provide perspective on important considerations that arise when analyzing network relationships. We conclude with a perspective on future directions and potential challenges of utilizing this powerful approach in crops. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.     

Complex regulation of the immunoglobulin mu heavy-chain gene enhancer: microB, a new determinant of enhancer function.

The B-lymphocyte-specific activity of the immunoglobulin mu heavy-chain gene enhancer has been attributed to the octamer motif (ATTTGCAT) present within the enhancer that binds a B-cell-specific factor designated NF-A2/OTF-2. However, significant residual enhancer activity even after deletion of this element has suggested the presence of a second critical functional determinant. We have used deletion and mutational analyses to define an element, microB (TTTGGGGAA), that is essential for B-cell-specific enhancer activity in S194 myeloma cells in the absence of the octamer. Transfection analysis in a panel of lymphoid cell lines suggests that the presence of either microB or octamer leads to considerable enhancer activity in cell lines representing later stages of B-cell differentiation, whereas both elements are needed for function in cell lines representing earlier stages. Furthermore, in contrast to the results in pre-B-cell lines, both microB and octamer elements function independently in certain T-cell lines in which the mu enhancer is active.     

CFTR and TNR-CFTR expression and function in the kidney

The cystic fibrosis transmembrane conductance regulator (CFTR) is abundantly expressed in the kidney. CFTR mRNA is detected in all nephron segments of rats and humans and its expression is higher in the renal cortex and outer medulla than in the inner medulla. CFTR protein is detected at the apical surface of both proximal and distal tubules of rat kidney but not in the outer medullary collecting ducts. The localization of CFTR in the proximal tubules is compatible with that of endosomes, suggesting that CFTR might regulate pH in endocytic vesicles by equilibrating H⁺ accumulation due to H⁺-ATPase activity. Many studies have also demonstrated that CFTR also regulates channel pore opening and the transport of sodium, chloride and potassium. The kidneys also express a CFTR splicing variant, called TNR-CFTR, in a tissue-specific manner, primarily in the renal medulla. This splicing variant conserves the functional characteristics of wild-type CFTR. The functional significance of TNR-CFTR remains to be elucidated, but our group proposes that TNR-CFTR may have a basic function in intracellular organelles, rather than in the plasma membrane. Also, this splicing variant is able to partially substitute CFTR functions in the renal medulla of Cftr^-/- mice and CF patients. In this review we discuss the major functions that have been proposed for CFTR and TNR-CFTR in the kidney.     

From gene regulation to gene function: regulatory networks in bacillus subtilis

Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis and gene regulation programmes, together with an extensive understanding of its biochemistry and physiology, makes this micro-organism a prime candidate in which to model regulatory networks in silico. In this paper we discuss combined molecular biological and bioinformatical approaches that are being developed to model this organism's responses to changes in its environment.     

Molecular mechanisms controlling CFTR gene expression in the airway

The low levels of CFTR gene expression and paucity of CFTR protein in human airway epithelial cells are not easily reconciled with the pivotal role of the lung in cystic fibrosis pathology. Previous data suggested that the regulatory mechanisms controlling CFTR gene expression might be different in airway epithelium in comparison to intestinal epithelium where CFTR mRNA and protein is much more abundant. Here we examine chromatin structure and modification across the CFTR locus in primary human tracheal (HTE) and bronchial (NHBE) epithelial cells and airway cell lines including 16HBE14o- and Calu3. We identify regions of open chromatin that appear selective for primary airway epithelial cells and show that several of these are enriched for a histone modification (H3K4me1) that is characteristic of enhancers. Consistent with these observations, three of these sites encompass elements that have cooperative enhancer function in reporter gene assays in 16HBE14o- cells. Finally, we use chromosome conformation capture (3C) to examine the three-dimensional structure of nearly 800 kb of chromosome 7 encompassing CFTR and observe long-range interactions between the CFTR promoter and regions far outside the locus in cell types that express high levels of CFTR.