More Like this

1. Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

   https://doi.org/10.3389/fgene.2021.785934  

   Holm, Inge ; Nardini, Luisa ; Pain, Adrien ; Bischoff, Emmanuel ; Anderson, Cameron E. ; Zongo, Soumanaba ; Guelbeogo, Wamdaogo M. ; Sagnon, N’Fale ; Gohl, Daryl M. ; Nowling, Ronald J. ; et al ( January 2022 , Frontiers in Genetics)

   Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii , a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNAmore »of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences. Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii , will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.« less
2. Functional in vivo characterization of sox10 enhancers in neural crest and melanoma development

   https://doi.org/10.1038/s42003-021-02211-0  

   Cunningham, Rebecca L. ; Kramer, Eva T. ; DeGeorgia, Sophia K. ; Godoy, Paula M. ; Zarov, Anna P. ; Seneviratne, Shayana ; Grigura, Vadim ; Kaufman, Charles K. ( June 2021 , Communications Biology)

   The role of a neural crest developmental transcriptional program, which critically involves Sox10 upregulation, is a key conserved aspect of melanoma initiation in both humans and zebrafish, yet transcriptional regulation ofsox10expression is incompletely understood. Here we used ATAC-Seq analysis of multiple zebrafish melanoma tumors to identify recurrently open chromatin domains as putative melanoma-specificsox10enhancers. Screening in vivo with EGFP reporter constructs revealed 9 of 11 putativesox10enhancers with embryonic activity in zebrafish. Focusing on the most active enhancer region in melanoma, we identified a region 23 kilobases upstream ofsox10, termedpeak5, that drivesEGFPreporter expression in a subset of neural crest cells, Kolmer-Agduhrmore »neurons, and early melanoma patches and tumors with high specificity. A ~200 base pair region, conserved inCyprinidae, withinpeak5is required for transgenic reporter activity in neural crest and melanoma. This region contains dimeric SoxE/Sox10 dimeric binding sites essential forpeak5neural crest and melanoma activity. We show that deletion of the endogenouspeak5conserved genomic locus decreases embryonicsox10expression and disrupts adult stripe patterning in our melanoma model background. Our work demonstrates the power of linking developmental and cancer models to better understand neural crest identity in melanoma.

   « less
3. Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling

   https://doi.org/10.1101/gr.275684.121  

   Khor, Jian Ming ; Guerrero-Santoro, Jennifer ; Douglas, William ; Ettensohn, Charles A. ( September 2021 , Genome Research)

   We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus . We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expressionmore »tended to parallel those of nearby genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays was associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are available at Echinobase, the public database of information related to echinoderm genomics.« less
4. MrpC, a CRP/Fnr homolog, functions as a negative autoregulator during the Myxococcus xanthus multicellular developmental program

   https://doi.org/https://doi.org/10.1111/mmi.13982  

   McLaughlin, Patrick T ; Bhardwaj, Vidhi ; Feeley, Brooke E ; Higgs, Penelope I. ( May 2018 , Molecular microbiology)

   MrpC, a member of the CRP/Fnr superfamily of transcriptional regulators, plays a key role in coordination of the multicellular developmental program in Myxococcus xanthus. Previous reports suggest MrpC is subject to complex regulation including activation by an unusual LonD‐dependent proteolytic processing event that removes its unique N‐terminal peptide, producing the isoform MrpC2. MrpC2 is proposed to positively autoregulate and regulate transcription of hundreds of genes necessary for both the aggregation and sporulation phases of the developmental program. We demonstrate here that mrpC expression bifurcates corresponding to different cell populations within the developmental program. During our analysis of regulatory events controllingmore »this process, we demonstrate that MrpC2 is not an active isoform; rather, the N‐terminal peptide is instead essential for MrpC function in vivo. We also demonstrate that MrpC is instead a negative autoregulator and represses its own expression by specifically competing with its enhancer binding protein, MrpB. These results provide an additional rare example of CRP/EBP coordinated regulation, and significantly revise the model for control of the central developmental transcriptional activator of the M. xanthus developmental program.« less
5. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic

   https://doi.org/10.7554/eLife.59351  

   Waymack, Rachel ; Fletcher, Alvaro ; Enciso, German ; Wunderlich, Zeba ( August 2020 , eLife)

   In all higher organisms, life begins with a single cell. During the early stages of development, this single cell grows and divides multiple times to develop into the many different kinds of cells that make up an organism. This is a highly regulated process during which cells receive instructions telling them what kind of cell to become. These instructions are relayed via genes, and a particular combination of activated genes determines the cell’s fate. Specific pieces of DNA, known as enhancers, act as switches that control when and where genes are active, while so-called shadow enhancers are found in groupsmore »and work together to turn on the same gene in a similar way. Shadow enhancers are often active during the early stages of life to direct the formation of specialized cells in different parts of the body. But so far, it has been unclear why it is beneficial to the divide the role of activating genes across several shadow enhancers rather than a single one. Here, Waymack et al. examined shadow enhancers around a gene called Kruppel in embryos of the fruit fly Drosophila melanogaster . Manipulating the shadow enhancers showed that they help to make gene activity more resistant to changes. Factors such as fluctuations in temperature have different effects on each shadow enhancer. Having several shadow enhancers working together ensures that, whatever happens, the right genes still get activated. For genes like Kruppel , which are key for healthy development, the ability to withstand unexpected changes is a valuable evolutionary benefit. The study of Waymack et al. reveals why shadow enhancers are involved in the regulation of many genes, which may help to better understand developmental defects. Many conditions caused by such defects are influenced by both genetics and the environment. Genetic illnesses can vary in severity, which may be related to the roles of shadow enhancers. As such, studying shadow enhancers could lead to new approaches for treating genetic diseases.« less