Diverse digital and fuzzy composite transcriptional elements are prevalent features of mammalian cis-regulomes

Mammalian transcriptional regulatory sequences are comprised of complex combinations of simple transcription factor (TF) motifs. Stereospecific juxta-positioning of simple TF motifs generates composite elements (CEs), that increase combinatorial and regulatory specificity of TF-DNA interactions. Although a small number of CEs and their cooperative or anti-cooperative modes of TF binding have been thoroughly characterized, a systematic analysis of CE diversity, prevalence and properties in cis-regulomes has not been undertaken. We developed a computational pipeline termed CEseek to discover >20,000 CEs in open chromatin regions of diverse immune cells and validated many using CAP-SELEX, ChIP-Seq and STARR-seq datasets. Strikingly, the CEs manifested a bimodal distribution of configurations, termed digital and fuzzy, based on their stringent or relaxed stereospecific constraints, respectively. Digital CEs mediate cooperative as well as anti-cooperative binding of structurally diverse TFs that likely reflect AND/OR genomic logic gates. In contrast, fuzzy CEs encompass a less diverse set of TF motif pairs that are selectively enriched in p300 associated, multi-genic enhancers. The annotated CEs greatly expand the regulatory DNA motif lexicon and the universe of TF-TF interactions that underlie combinatorial logic of gene regulation.

Defining the AHR regulated transcriptome in NK cells reveal gene expression program relevant to development and function

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates cellular processes in cancer and immunity, including innate immune cell development and effector function. However, the transcriptional repertoire through which AHR mediates these effects remains largely unexplored. To elucidate the transcriptional elements directly regulated by AHR in NK cells, we performed RNA- and ChIP-sequencing on NK cells exposed to AHR agonist or antagonist. We show that mature peripheral blood NK cells lack AHR, but its expression is induced by Stat3 during IL-21-driven activation and proliferation, coincident with increased NCAM1 (CD56) expression resulting in a CD56bright phenotype. Compared to control conditions, NK cells expanded in the presence of the AHR antagonist, StemRegenin-1, were unaffected in proliferation or cytotoxicity, had no increase in NCAM1 transcription and maintained the CD56dim phenotype. However, it showed altered expression of 1,004 genes including those strongly associated with signaling pathways. In contrast, NK cells expanded in the presence of the AHR agonist, kynurenine, showed decreased cytotoxicity and altered expression of 97 genes including those strongly associated with oxidative stress and cellular metabolism. By overlaying these differentially expressed genes with AHR chromatin binding we identified 160 genes directly regulated by AHR, including hallmark AHR targets AHRR and CYP1B1, and known regulators of phenotype, development, metabolism, and function such as NCAM1, KIT, NQO1, and TXN. In summary, we define the AHR transcriptome in NK cells, propose a model of AHR and Stat3 coregulation, and identify potential pathways that may be targeted to overcome AHR-mediated immune suppression.

LsaYAB7, A Homologous Gene of FILAMENTOUS FLOWER, Participating In The Regulation of Adaxial-Abaxial Polarity of Leaves In Lettuce

Background: The plant-specific YABBY transcription factor plays important roles in the development of lateral organs, the establishment of adaxial-abaxial polarity and abiotic stress response. However, the function of YABBY gene family in lettuce (Lactuca sativa), an important leaf vegetable is still unclear yet. Results: In this study, we analyzed the chromosomal distribution, gene structure and cis-transcriptional elements of the YABBY gene family in lettuce. Phylogenetic analysis of YABBY genes in lettuce, Arabidopsis, maize and rice classified them into five groups. In addition, the expression profile of YABBY genes in lettuce indicated that they may play distinct functions in different tissues and developmental processes. The subcellular localization analysis and transactivation assay showed that LsaYAB7 probably functions as a transcription factor in the nucleus. Furthermore, the ectopic expression of LsaYAB7 exhibited abaxially curled leaves, not only in Arabidopsis, but also in lettuce. Conclusion: Altogether, LsaYAB7 is a key functional gene in determining the adaxial-abaxial polarity of lettuce leaves. Our study laid foundation for the molecular research of functional genes in lettuce.

Mapping origins of variation in neural trajectories of human pluripotent stem cells

SUMMARYVariability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. We identify differences in the spontaneous self-organization of individual hPSC lines during self-renewal that lie along a fundamental axis of in vivo development. Distinct stable and dynamic transcriptional elements were revealed by decomposition of RNA-seq data in pluripotency and early lineage emergence. Stable differences within pluripotency predicted regional bias in the dynamics of neural differentiation that were also observed in large collections of hPSC lines. Using replicate human induced PSC (hiPSC) lines and paired adult tissue, we demonstrate that cells from individual humans expressed unique transcriptional signatures that were maintained throughout life. In addition, replicate hiPSC lines from one donor showed divergent expression phenotypes driven by distinct chromatin states. These stable transcriptional states are under both genetic and epigenetic control and predict bias in subsequent forebrain and hindbrain neural trajectories. These results define mechanisms controlling transcription in pluripotency to first establish human neural diversity. Data availability: GSE164055;https://nemoanalytics.org/p?l=KimEtAL2021&g=GBX2.Abstract Figure

Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community

SummaryMicrobial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behavior. This aspect of microbiome function has not been well characterized in natural high-salt environments. To address this knowledge gap, and to build a general framework of relating the genomic and transcriptomic components in a microbiome, we performed a meta-omic survey of extremophile communities inhabiting halite (salt) nodules in the Atacama Desert. We found that the major phyla of this halophilic community have very different levels of total transcriptional activity and that different metabolic pathways were activated in their transcriptomes. We report that a novel Dolichomastix alga – the only eukaryote found in this system – was by far the most active community member. It produced the vast majority of the community’s photosynthetic transcripts despite being outnumbered by members of the Cyanobacteria. The divergence in the transcriptional landscapes of these segregated communities, compared to the relatively stable metagenomic functional potential, suggests that microbiomes in each salt nodule undergo unique transcriptional adjustments to adapt to local conditions. We also report the characterization of several previously unknown halophilic viruses, many of which exhibit transcriptional activity indicative of host infection.Originality-Significance StatementWhile the metagenomics of hypersaline environments have already led to many discoveries, the transcriptional adaptations and functions of halophilic microbial communities in natural environments remains understudied. We perform the first robust meta-omic investigation of a hypersaline desert ecosystem, linking the genomic and transcriptional elements of the community. Our analysis unexpectedly revealed that Eukaryotes may be the main primary producers in this extreme environment, despite halophilic Archaea and Bacteria dominating the biomass. We also expand on the existing known diversity of halophilic viruses and demonstrate abundance (copies per million reads) and metatranscriptomic activity (transcripts per million reads); putative hosts are shown on the right.

Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci

Background Bacterial symbiosis is widespread in arthropods, especially in insects. Some of the symbionts undergo a long-term co-evolution with the host, resulting in massive genome decay. One particular consequence of genome decay is thought to be the elimination of transcriptional elements within both the coding region and intergenic sequences. In the whitefly Bemisia tabaci species complex, the obligate symbiont Candidatus Portiera aleyrodidarum is of vital importance in nutrient provision, and yet little is known about the regulatory capacities of it. Methods Portiera genomes of two whitefly species in China were sequenced and assembled. Gene content of these two Portiera genomes was predicted, and then subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis. Together with two other Portiera genomes from whitefly species available previously, four Portiera genomes were utilized to investigate regulatory capacities of Portiera, focusing on transcriptional elements, including genes related with transcription and functional elements within the intergenic spacers. Results Comparative analyses of the four Portiera genomes of whitefly B. tabaci indicate that the obligate symbionts Portiera is similar in different species of whiteflies, in terms of general genome features and possible functions in the biosynthesis of essential amino acids. The screening of transcriptional factors suggests compromised ability of Portiera to regulate the essential amino acid biosynthesis pathways. Meanwhile, thermal tolerance ability of Portiera is indicated with the detection of a σ32 factor, as well as two predicted σ32 binding sites. Within intergenic spacers, functional elements are predicted, including 37 Shine-Dalgarno sequences and 34 putative small RNAs.

Biolistic transformation of Haematococcus pluvialis with constructs based on the flanking sequences of its endogenous alpha tubulin gene

The complete sequence information of the alpha tubulin (tub) genes was obtained from both Haematococcus pluvialis NIES144 and SCCAP K0084., Putative transcriptional elements and polyadenylation signals were identified respectively in their 5’ and 3’ flanking regions. Three selection cassettes of tub/aadA, tub/hyr and tub/ble with 3 different antibiotic-resistant genes fused between the 5’ and 3’ flanking sequences of the tub gene were constructed and utilized for biolistic transformation of H.pluvialis. Antibiotic resistant transformants were obtained in the bombardments with the tub/aadA cassette in 2 strains. It was found that, the foreign tub/aadA DNA could be completely transferred and inherited in their genome through non-homologous recombination. Moreover, transcripts of the insert and spectinomycin resistance were identified. Transformation efficiencies up to 3×10-5 per μg DNA could be obtained in H.pluvialis NIES144 or SCCAP K0084 through utilization of a culture with a high percentage of flagellate cells and by optimizing bombarding protocol. The presented selection marker and optimized transforming procedures in this report should strengthen the platform technology for genetical manipulation and modification of H.pluvialis.