Modeling DNA Sequence Based cis-Regulatory Gene Networks

Modeling DNA Sequence Based cis-Regulatory Gene Networks Hamid Bolouri and Eric H. Davidson Presented by Geoffrey

Introduction • Cis-Regulatory elements can be regarded as pieces of DNA sequences that have target site sequences recognized by binding proteins • They are genetically hardwired information processors and are linked together to form a huge network • Each element receives informational input that determines its activity and produces an informational output in the form of regulatory instructions (i.e. activates or inhibits other elements)

Introduction • Genetic regulatory apparatus remains unchanged in every cell. What it does will depend on the inputs that it receives at each point in time • Part of the inputs depends on prior transactions of genes that synthesize the necessary factors, and part on other events, such as extra-cellular signals

Cis-Regulatory Elements • Each element carries out some processing of its input information • Inputs are often multiple while the output is a unique function that informs the basal transcription apparatus how frequently to initiate transcription • Example of an element in diagram form (This diagram shows a gene whose expression is activated by Ubiquitous activator and inhibited by protein A)

Cis-Regulatory Elements in Development • Cis-Regulatory information processing is important in development because development depends fundamentally on spatial (which type of cells and where) and temporal (when) control of gene expression • These decisions result from logic functions carried out by the regulatory elements • For example, a given cis-regulatory element might lead to the expression of a gene when two inputs overlap (AND operation), resulting in the appearance of a new factor; or it might control the expression through the interplay between positive and negative inputs.

Cis-Regulatory Elements in Development • Hence thinking about cis-regulatory elements from an informational point of view leads to the mutable, measurable and regulatory properties of genomic DNA • The gene sequence of each element will dictate which input the element will listen to and the functions it is capable of processing • Each input hence indicates a target site sequence that can be tested and recognized via mutation or gene transfer

Illustration – Endo16 Model • The cis-regulatory system of the endo16 gene of the sea urchin has been studied in great detail • It has a modestly complex pattern of expression during its embryogenesis • It is activated in the vegetal plate of the embryo, specifically in the Veg2 lineage, at about the 8th cleavage • The Veg2 lineage consists of the progeny of eight 6th cleavage founder cells, and from it derives most of the endoderms

Illustration – Endo16 Model • The endo16 gene is transcribed in this endomesodermal field until gastrulation (process by which germ cells of the blastoderm are translocated to new positions in the embryo), during which it is expressed throughout the invaginating archenteron but no longer in the mesodermal domain • As the gut become regionalized, expression is extinguished in the foregut and hindgut but accelerated in the midgut where it continues to be expressed in the feeding larva

Illustration – Endo16 Model • Summary of the expression pattern of endo16 gene (shown in blue)

Illustration – Endo16 Model • The cis-regulatory system that controls the endo16 expression is about 2300 base pairs in length and it consists of several clusters of target sites that execute distinct functions, hence each can be thought of as separable modular regulatory elements • The basal transcription apparatus (Bp) has no regulatory activity on its own and is used to service regulatory elements expressed in every domain of the embryo

Illustration – Endo16 Model • Modules A and B carry out many interesting regulatory functions • They have altogether 17 target sites for factors that recognize and bind specifically at given sequences • A protein, SpGCF1, interacts at 5 sites of module A. The other 12 target sites are serviced by 9 different transcription factors where each interaction has a distinct and measurable functional meaning • The details of the interaction are shown in the box below. The target sites are indicated by boxes (blue for Module B and red for Module A). The arrows lead from the target site to the logic operations indicated in circles. The logic operation will then state how the factors will interact

Illustration – Endo16 Model • The complete model of the endo16 expression is shown in the figure below. The elements now are the individual genes that are involved in the expression • Details of the model can be seen here [click]

Logic Operation • The model specifies logic operations by which the inputs are processed and the altered values are carried forward • Common operations includes: • AND – when all the conditions are met, then the indicated operations on the value of the output at that node will take place • OR – when one (or some) of the conditions are met, then the indicated operations will take place

Logic Operation • There are direct physical implications of the logic operations. The ‘AND’ operator shows that the proteins binding at the respective sites are together necessary for the function to occur (e.g. formation of a huge functional complex by the transcriptional factors) • However, it does not necessary mean that it is an all-or-none output. Alternate outputs with values could be associated with inputs not being present by adding the ‘else’ portion • The point is that the model describes the functions that are mediated by each site, conditional on the inputs present. It does not attempt to describe the biochemistry of the proteins that contribute to this function • Simply put, they are just information processing constructs similar to those that can be found in normal programming languages

Continuous and Boolean Functions • Taking again the computational model as an example: • The fill in boxes with solid lines extending indicates inputs where the amplitude varies over time, e.g. UI, R, OTX • Open boxes with dashed lines indicate inputs that are often present in excess, and hence can be regarded as boolean inputs, i.e. either they are present, or they are not • Open boxes with thin lines indicate scalar operations on the inputs of the node

Continuous and Boolean Functions • Hence the endo16 model is not a kinetic model per se • It does not consist of a set of time based differential equations describing the kinetic reactions • Instead, it describes the logic functions mediated by the DNA target sites • Although it is not something new in other fields, say, engineering, but it does offer a refreshing way of modeling gene regulatory networks, which are predominantly based on differential equations

Models for Networks of cis-Regulatory Elements Symbolism and Significance • All major processes in animal development are driven forward by regulatory genes, i.e. genes that express transcription factors • Development events are not discrete and the regulatory networks that control development are often connected to other networks that control prior and surrounding processes in both the spatial and temporal domains • The model used for the cis-Regulatory elements can be used to model the beginning of the process for which the network displays the genetic program, as well as the end, which is the activation of gene batteries (a series of genes), e.g. endo16 which expresses an adhesion protein involved in the gastrulation of the sea urchin embryo

General Purposes of DNA sequence based Network Models • The objective of such a model is to: • State the key inputs and outputs of the cis-regulatory system • Explain why each gene runs where and when it does • How the spatial territories are being built up • Even incomplete models are informative as the interactions found always have some functional meaning • Each cis-regulatory system can also be considered as a ‘black box’ which can be connected to other systems

Genomic and Nuclear Views • A useful concept for DNA sequence-level network is the distinction between “View from Genome” and “View from Nucleus” • The VFG shows all the interactions that the system is capable of while the VFN focus on those sites that are occupied by the indicated inputs in any given nucleus at any given time, i.e. snapshot

Genomic and Nuclear Views • A simple illustration is shown in the figure. Here there are two spatial domains of an embryo – domain A, and the rest (~A) • The VFG shows that there is a ubiquitous positive activator needed for all three genes. But gene 1 also requires another positive input to be activated and it acts positively in domain A and negatively in others (~A) • This will then affect the expression of gene 2 and gene 3 • Hence in any development stage, either VFN(A) or VFN(~A) could be possible

Conclusion • Cis-Regulatory networks serve as a development biologist’s essential organizer for getting causal relationship between genes • They are essential due to the myriad of information and possible interactions that may occur • The models used are not actually genetic models although their key elements are genomic target site sequence elements • The relationship between the elements can be viewed from several angles, i.e. views – VFG, VFN, Black Box View (Bird’s eye view). No transformations are needed to transit from one view to another • The model serves also as a predictive tool, enabling developmental biologists to see what might happen to the regulatory system if a target site is mutated or experimentally altered

Modeling DNA Sequence Based cis-Regulatory Gene Networks