Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells.

Cell fate can be reprogrammed by ectopic expression of lineage-specific transcription factors (TFs). However, the exact cell state transitions during transdifferentiation are still poorly understood. Here, we have generated pancreatic exocrine cells of ductal epithelial identity from human fibroblasts using a set of six TFs. We mapped the molecular determinants of lineage dynamics using a factor-indexing method based on single-nuclei multiome sequencing (FI-snMultiome-seq) that enables dissecting the role of each individual TF and pool of TFs in cell fate conversion. We show that transition from mesenchymal fibroblast identity to epithelial pancreatic exocrine fate involves two deterministic steps: an endodermal progenitor state defined by activation of HHEX with FOXA2 and SOX17 and a temporal GATA4 activation essential for the maintenance of pancreatic cell fate program. Collectively, our data suggest that transdifferentiation-although being considered a direct cell fate conversion method-occurs through transient progenitor states orchestrated by stepwise activation of distinct TFs.

Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes.

Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.

Molecular and expression analysis indicate the role of CBL interacting protein kinases (CIPKs) in abiotic stress signaling and development in chickpea.

Calcineurin B-like proteins (CBL)-interacting protein kinases (CIPKs) regulate the developmental processes, hormone signal transduction and stress responses in plants. Although the genome sequence of chickpea is available, information related to the CIPK gene family is missing in this important crop plant. Here, a total of 22 CIPK genes were identified and characterized in chickpea. We found a high degree of structural and evolutionary conservation in the chickpea CIPK family. Our analysis showed that chickpea CIPKs have evolved with dicots such as Arabidopsis and soybean, and extensive gene duplication events have played an important role in the evolution and expansion of the CIPK gene family in chickpea. The three-dimensional structure of chickpea CIPKs was described by protein homology modelling. Most CIPK proteins are localized in the cytoplasm and nucleus, as predicted by subcellular localization analysis. Promoter analysis revealed various cis-regulatory elements related to plant development, hormone signaling, and abiotic stresses. RNA-seq expression analysis indicated that CIPKs are significantly expressed through a spectrum of developmental stages, tissue/organs that hinted at their important role in plant development. The qRT-PCR analysis revealed that several CaCIPK genes had specific and overlapping expressions in different abiotic stresses like drought, salt, and ABA, suggesting the important role of this gene family in abiotic stress signaling in chickpea. Thus, this study provides an avenue for detailed functional characterization of the CIPK gene family in chickpea and other legume crops.

Molecular Characterization Reveals the Involvement of Calcium Dependent Protein Kinases in Abiotic Stress Signaling and Development in Chickpea (Cicer arietinum).

Calcium-dependent protein kinases (CDPKs) are a major group of calcium (Ca2+) sensors in plants. CDPKs play a dual function of "Ca2+ sensor and responder." These sensors decode the "Ca2+ signatures" generated in response to adverse growth conditions such as drought, salinity, and cold and developmental processes. However, knowledge of the CDPK family in the legume crop chickpea is missing. Here, we have identified a total of 22 CDPK genes in the chickpea genome. The phylogenetic analysis of the chickpea CDPK family with other plants revealed their evolutionary conservation. Protein homology modeling described the three-dimensional structure of chickpea CDPKs. Defined arrangements of α-helix, ß-strands, and transmembrane-helix represent important structures like kinase domain, inhibitory junction domain, N and C-lobes of EF-hand motifs. Subcellular localization analysis revealed that CaCDPK proteins are localized mainly at the cytoplasm and in the nucleus. Most of the CaCDPK promoters had abiotic stress and development-related cis-regulatory elements, suggesting the functional role of CaCDPKs in abiotic stress and development-related signaling. RNA sequencing (RNA-seq) expression analysis indicated the role of the CaCDPK family in various developmental stages, including vegetative, reproductive development, senescence stages, and during seed stages of early embryogenesis, late embryogenesis, mid and late seed maturity. The real-time quantitative PCR (qRT-PCR) analysis revealed that several CaCDPK genes are specifically as well as commonly induced by drought, salt, and Abscisic acid (ABA). Overall, these findings indicate that the CDPK family is probably involved in abiotic stress responses and development in chickpeas. This study provides crucial information on the CDPK family that will be utilized in generating abiotic stress-tolerant and high-yielding chickpea varieties.

Transfer RNA-derived non-coding RNAs (tncRNAs): Hidden regulation of plants' transcriptional regulatory circuits.

The emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic gene regulatory networks. Amongst them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands exploration in the plant kingdom. We have designed a methodology to uncover the entire perspective of tncRNAome in plants. Using this pipeline, we have identified diverse tncRNAs with a size ranging from 14 to 50 nucleotides (nt) by utilizing 2448 small RNA-seq samples from six angiosperms, and studied their various features, including length, codon-usage, cleavage pattern, and modified tRNA nucleosides. Codon-dependent generation of tncRNAs suggests that the tRNA cleavage is highly specific rather than random tRNA degradation. The nucleotide composition analysis of tncRNA cleavage positions indicates that they are generated through precise endoribonucleolytic cleavage machinery. Certain nucleoside modifications detected on tncRNAs were found to be conserved across the plants, and hence may influence tRNA cleavage, as well as tncRNA functions. Pathway enrichment analysis revealed that common tncRNA targets are majorly enriched during metabolic and developmental processes. Further distinct tissue-specific tncRNA clusters highlight their role in plant development. Significant number of tncRNAs differentially expressed under abiotic and biotic stresses highlights their potential role in stress resistance. In summary, this study has developed a platform that will help in the understanding of tncRNAs and their involvement in growth, development, and response to various stresses. The workflow, software package, and results are freely available at http://nipgr.ac.in/tncRNA.

The gene arrangement and phylogeny using mitochondrial genomes in spiders (Arachnida: Araneae).

The complete mitochondrial genome (mitogenome) of Cheiracanthium triviale was sequenced for the first time. The 14,595 bp C. triviale mitogenome contained 37 genes (13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs) and one control region. The mitogenome of Dysdera silvatica which was available at NCBI GenBank was annotated. The mitogenome of C. triviale was compared with 43 previously sequenced spider species to observe the gene arrangements, control region and phylogeny. TreeREx analysis identified 19 mitochondrial gene rearrangements (11 transposition, 6 inversion, 2 inverse transposition) in spiders as compared with the putative ancestral gene order and lead to form new gene boundaries: trnQ-trnA, trnA-trnM for Loxosceles similis; nad3-trnS1, trnE-trnL2, trnL2-trnA, trnN-trnF for Agelena silvatica; trnN-trnE, trnE-trnA, trnR-trnF, nad4L-trnW, trnW-trnP for Carrhotus xanthogramma; trnQ-trnW, trnW-trnG, trnG-trnM for Tetragnatha nitens. Our study revealed that the gene rearrangement in spiders with putative ancestor is accelerated in Araneomorphae as compared to Mygalomorphae. Phylogenetic analysis of spiders using mitochondrial sequence data supports the monophyly of two infraorders, and sister relationship of Cheiracanthiidae with Selenopidae and Salticidae. The systematic position of the Cheiracanthium species always a controversial issue as this taxa was placed in different families by different authors.