Dr. Surya Chhetri 

In humans, three billion base pairs long DNA, “the blueprint of life,” contains the instruction and recipe codes for every cell in our body- translating the directives for which proteins to make, in what quantity, and when.
These highly coordinated events, wherein the information flows from DNA (Deoxyribonucleic Acid) to RNA (Ribonucleic Acid) to functional product protein as a function of precise spatio-temporal genetic regulation, enables our cells to work in a modus operandi fashion and maintain its cellular identity.

A Regulated Process
In this remarkably regulated process, out of the total 20-25000 known human protein-coding genes, only a subset of genes are committed at any given time in any given cell type to form the basis of its cell-type specificity, work, and function.
To better understand the cellular specificness and how cells work we need to understand the process of gene regulation that is central to the normal function and development of the cells.
When deviated, it can also lead to aberrant cellular phenotypes and various forms of diseases, including cancers and developmental disorders. It turns out, there are millions of DNA regions in the genome acting as “genetic switches,” called cis-regulatory elements, responsible for the turning “on” and “off” genes in a highly sophisticated and concerted effort of gene regulation.
And, as a field, scientists are still trying to understand how and what proteins control those genetic switches for the controlled modulation of genes. Identification of such proteins can illuminate our understanding of transcriptional gene regulatory networks and associations, vital for achieving cell-specific functions and targeted gene expression programmes. Such proteins can be alluded to as DNA (Chromatin) associated proteins or CAPs. They can turn the genes “on” and “off” by acting on such genetic switches, either independently or in coordination with many other proteins, including Transcription Factors, Cofactors, and Chromatin regulators. These proteins can decode the underlying DNA sequence of those switches to make the cells into a liver cell, a neuronal cell, or a cancer cell, thereby controlling when and where the subset of genes express to give that required cell-type specificity. To that end, it’s of immense importance for us to have a sharp catalog of such DNA-associated proteins if we are to have a fuller and comprehensive pictorial view of how genes are controlled and regulated inside the cell system.

Findings of Study
Hence, in this study, with the human liver cell line as a model, we made a significant effort to identify and understand the genome-wide occupancy maps of such 208 DNA associated proteins (including 171 Transcription Factors and 37 Chromatin regulators) involved in transcriptional gene regulation — at an unprecedented scale — as a part of the Encyclopedia of DNA Elements (ENCODE) consortium effort.
It is a project funded by the National Institute of Health (NIH), National Human Genome Research Institute (NHGRI), the most extensive collaborative effort of its kind aiming to study, identify and create a catalog of functional DNA elements in the human and mouse genome.
This study of 208 DNA (Chromatin) associated proteins or CAPs, at an unmatched level of coverage is nearly a quarter of all the factors physiologically expressed within a single human cell-type system. It enabled us to discover and gain many novel gene regulatory insights and principles, otherwise impossible, from a survey of few individual binding maps.
The study identified and expanded novel DNA sequence motifs, wherein protein binds to, important for protein-DNA interactions inside the cell. The research uncovered novel protein associations with the NuRD complex, previously unidentified, including liver pioneer and critical transcription factors (FOXA3, SOX13, ARID5B) co-localizing with GATAD2A, supporting the imputations of pivotal contacts in highly dimensional Chromatin associated protein networks. We also gain new insights into the “genomic-flavors” of individual Chromatin associated proteins suggesting epigenetic and chromatin state preference of each protein, including their association to promoters and enhancers regions. It highlights the proximal and distal gene-regulatory pathways existing parallel to the cell system.
One of the intriguing findings and highlights of this study is the High occupancy target (HOT) regions in the genome. We identified more than 5000 of such sites, mostly the promoters and enhancers, at which many transcription factors associate. In this study, we manifest most HOT sites being driven by a few strong and specific TF-DNA interactions and non-specific recruitment of other factors.

Extensive Evidence
With extensive evidence presented in the study, this leads us to propose a model in which HOT regions are nucleated by the anchoring DNA motifs and their cognate transcription factors. They would serve as a core for other non-sequence specific CAPs to aggregate likely through both protein complexes and binding to degenerate motifs, and possibly, linking together multiple distal cis-regulatory regions or “switches” through CAPs interactions.
An outcome not possible by the study of a few Chromatin associated protein maps only. Also, the research here presents a vital resource for the scientific community for various other studies. Further, it demonstrates a proof-of-concept example, accentuating the importance of building toward a complete catalogue of CAPs interactions in an individual cell type to generating meaningful hypotheses.

(Dr. Chhetri is engaged in understanding the mechanisms and impact of functional genetic variants on gene regulation, human health, and disease as a postdoctoral scholar at Johns Hopkins University, USA)