Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping

Abstract

Abstract:The availability of complete human and other metazoan genome sequences has greatly facilitated positioning and analysis of various genomic functional elements, with initial emphasis on coding sequences. However, complete functional maps of sequenced eukaryotic genomes should include also positions of all non-coding regulatory elements. Unfortunately, experimental data on genomic positions of a multitude of regulatory sequences, such as enhancers, silencers, insulators, transcription terminators, and replication origins are very limited, especially at the whole genome level. Since most genomic regulatory elements (e.g. enhancers) are generally gene-, tissue-, or cell-specific, the prediction of these elements by computational methods is difficult and often ambiguous. Therefore, the development of high-throughput experimental approaches for identifying and mapping genomic functional elements is highly desirable. At the same time, the creation of whole-genome map of hundreds of thousands of regulatory elements in several hundreds of tissue/cell types is presently far beyond our capabilities. A possible alternative for the whole genome approach is to concentrate efforts on individual genomic segments and then to integrate the data obtained into a whole genome functional map. Moreover, the maps of polygenic fragments with functional cis-regulatory elements would provide valuable data on complex regulatory systems, including their variability and evolution. Here, we reviewed experimental approaches to the realization of these ideas, including our own developments of experimental techniques for selection of cis-acting functionally active DNA fragments from large (megabase-sized) segments of mammalian genomes.

Integrated bioinformatics analysis of the transcription factor-mediated gene regulatory networks in the formation of spermatogonial stem cells

“…The identified peaks can be used to predict motifs generally recognized by TFs, and GRNs of the cells can also be revealed through chromatin profiling assays ( Nikolaev et al, 2007 ). Accordingly, we first obtained cell-specific genes and cell-specific TFs and then preliminarily constructed cell-specific GRNs.…”

“…In recent years, chromatin accessibility profiling has become an important tool for studying genetic and epigenetic regulation ( Maezawa et al, 2018 ), allowing us to dissect the pangenomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin states and their corresponding TFs ( Ma and Zhang, 2020 ). Moreover, chromatin accessibility profiling is expected to be a powerful tool for the identification of regulatory DNA elements that gene regulatory networks (GRNs), and changes in chromatin accessibility can be interpreted in the context of these dynamic regulatory networks ( Nikolaev et al, 2007 ). The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and DNase I hypersensitive sites sequencing (DNase-seq) are a technology that maps the landscape of chromatin accessibility ( Shashikant and Ettensohn, 2019 ).…”

A New Technique for Selective Identification and Mapping of Enhancers Within Long Genomic Sequences

“…(1,2). Although the nucleotide sequences of the human and some other genomes are already known (35), the information about genomic location of these elements is rather scarce.…”