Engineering topics

Dickel, Diane

Publications and source records attributed to Dickel, Diane.

4 records

DOE OSTI2023

A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2

A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

First Plant Cell Atlas symposium report

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Plant Single-Cell Solutions for Energy and the Environment (Second Workshop Report)

Plants are important sources of energy and materials, and they collectively represent a critical component of Earth’s ecosystem. With increasing environmental stresses due to climate change and intensive agricultural practices, the need for resilient plants is greater than ever before. To secure plant resources for bioenergy, biomaterials, food, and ecosystem adaptation, a deeper understanding of the fundamental biology of plants at a cellular level is urgently needed. Plants contain a multitude of specialized cell types that compose tissues and organs. Pathogens often target specific cell types within plants, and the response of one cell to a particular stimulus is likely to be distinct from its neighbor because of underlying molecular and contextual differences. Understanding how these responses are distributed among cells, the main goal of single-cell approaches, will substantially enhance our ability to use targeted engineering for improving plant productivity and resilience. Furthermore, single-cell approaches are necessary to understand the interactions between plants and other ecosystem members such as fungi, bacteria, and archaea. Unlocking these gene-response mechanisms at a cellular level can improve our ability to adapt plants to environmental stresses, increasing their utility as feedstocks for biomaterials and bioenergy. Recent advances in high-throughput sequencing, mass spectrometry, microfluidics and miniaturization, artificial intelligence and machine learning, and bioinformatics have greatly improved our ability to detect and understand processes at a cellular level. In mammalian systems, single-cell transcriptomics has already led to many advances, such as newly identified cell types and cell-targeted treatment of diseases, and mass spectrometry-based single-cell proteomics has recently been demonstrated as a promising emerging technology. However, plant single-cell omics has lagged behind mammalian approaches due to the high cost of the technologies relative to available resources and to the innate biological features of plants, including the complexity of the cell wall and polyploidy. To better understand how single-cell methods could enable plant science, Lawrence Berkeley National Laboratory (Berkeley Lab) hosted a workshop on April 29, 2021, that brought together a diverse group of leaders in plant and/or single-cell biology. Attendees represented federal research programs and domestic and international academic institutions. During the workshop, three presenters described the current state of research in both experimental and computational approaches. While the focus of the workshop was on factors preventing plant biology researchers from fully adopting single-cell methodologies, workshop participants agreed that most barriers could be overcome with focused, strategic investment and coordinated efforts among institutions leading to significant scientific discoveries that would be difficult to obtain using more conventional technologies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

Topologically associating domain (TAD) boundaries are thought to partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotype, but the overall extent to which this occurs remains unknown. Here we show that TAD boundary deletions commonly disrupt normal genome function in vivo . We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80kb in size) from the genome in mice. All deletions examined resulted in at least one detectable molecular or organismal phenotype, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. For 5 of 8 (62%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and suggest that noncoding deletions affecting TAD boundaries should be carefully considered for potential pathogenicity in clinical genetics screening.

Rajderkar, Sudha↗