Alexandra M Kasianova

We present a major update of the HOCOMOCO collection that provides DNA binding specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make this release, we performed motif discovery in peak sets that originated from 14 183 ChIP-Seq experiments and reads from 2554 HT-SELEX experiments yielding more than 400 thousand candidate motifs. The candidate motifs were annotated according to their similarity to known motifs and the hierarchy of DNA-binding domains of the respective transcription factors. Next, the motifs underwent human expert curation to stratify distinct motif subtypes and remove non-informative patterns and common artifacts. Finally, the curated subset of 100 thousand motifs was supplied to the automated benchmarking to select the best-performing motifs for each transcription factor. The resulting HOCOMOCO v12 core collection contains 1443 verified position weight matrices, including distinct subtypes of DNA binding motifs for particular transcription factors. In addition to the core collection, HOCOMOCO v12 provides motif sets optimized for the recognition of binding sites in vivo and in vitro, and for annotation of regulatory sequence variants. HOCOMOCO is available at https://hocomoco12.autosome.org and https://hocomoco.autosome.org.

We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification.

Abstract Advances in high-throughput sequencing have illuminated a complexity of transcriptome landscape in eukaryotes. An inherent part of this complexity is the presence of multiple isoforms generated by the alternative splicing and the use of alternative transcription start and polyadenylation sites. However, currently available tools have limited capacity to infer full-length isoforms. To address this problem, we developed a new pipeline, FLIC (Full-Length Isoform Constructor). FLIC is based on the long-read transcriptome data and integrates several key features: 1) utilizing biological replicate concordance to filter out noise and artifacts; 2) employing peak calling to precisely identify transcription start and polyadenylation sites; 3) enabling robust isoform reconstruction with minimal reliance on existing annotations. We evaluated FLIC using a dedicated set of real and simulated data of Arabidopsis thaliana cDNA sequencing. Results demonstrate that FLIC accurately reconstructs known and novel isoforms, outperforming existing tools, especially in the absence of reference annotations. A direct comparison with CAGE, currently regarded as golden standard for TSS identification shows that FLIC is equally accurate, while being much less time-consuming. Thus FLIC provides a valuable tool for comprehensive transcript characterization, particularly for non-model organisms or when dealing with incomplete or inaccurate annotations.

The genus Capsella serves as a model for understanding speciation, hybridization, and genome evolution in plants. Here, we present a chromosome-scale genome assembly of Capsella orientalis, the maternal progenitor of a cosmopolitan allotetraploid C. bursa-pastoris. Using nanopore sequencing and data on chromatin contacts (Hi-C), we assembled the genome into eight pseudo-chromosomes with high contiguity, evidenced by a benchmarking universal single-copy orthologs (BUSCO) completeness score of 99.3%. Comparative analysis with C. rubella and C. bursa-pastoris revealed overall synteny, except for 2 Mb inversion on chromosome 4 of C. rubella. Comparative genome analysis highlighted the conservation of gene content and structural integrity in the C. orientalis-derived subgenome of C. bursa-pastoris, with the exception of a 1.8 Mb region absent in O subgenome but present in C. orientalis. The genome annotation includes 27,675 protein-coding genes, with most exhibiting one-to-one orthology with Arabidopsis thaliana. Notably, 2,155 genes showed no similarity to A. thaliana ones. These results establish a robust genomic resource for C. orientalis, facilitating future studies on polyploid evolution, gene regulation, and species divergence within Capsella.