Hi-C techniques: from genome assemblies to transcription regulation.

The invention of chromosome-conformation capture (3C) techniques, in particular the key method Hi-C providing genome-wide information about chromatin contacts, revolutionized the way we study the three-dimensional (3D) organization of the nuclear genome and how it impacts transcription, replication and DNA repair. Since the frequency of chromatin contacts between pairs of genomic segments predictably relates to the distance in the linear genome, the Hi-C information has also proved useful for scaffolding genomic sequences. Here, we review recent enhancements in experimental procedures of Hi-C and its various derivatives such as Micro-C, HiChIP, and Capture Hi-C. We assess advantages and limitations of the techniques, and present examples of their use in recent plant studies. We also report on progress in computational tools used in assembling genome sequences.

Core promoterome of barley embryo.

Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.