Promoters and Transcription Start Sites in Biotechnology Patent Claims

Biotechnology invention disclosures frequently refer to promoters and transcription start sites (TSSs). Unfortunately, these terms are not always used precisely. An inventor may identify a “promoter” without making clear what nucleotide sequence is intended to constitute the promoter, where the transcription start site is located, or whether the identified promoter extends across the TSS. In other cases, what is described as a promoter may actually be an experimentally determined transcription start site without a fully characterized promoter region.

These ambiguities may not matter greatly in an informal scientific discussion. They can matter considerably, however, when an invention disclosure is converted into a patent application and claims must be drafted.

A promoter and a transcription start site are closely related, but they are not the same thing. Understanding the distinction, and establishing exactly what relationship exists between them, can be important in determining what an inventor has actually discovered and what can appropriately be claimed.

Promoters and Transcription Start Sites

A transcription start site is the nucleotide at which synthesis of an RNA transcript begins. By convention, this nucleotide is designated +1. Nucleotides upstream of the TSS are commonly assigned negative numbers, while nucleotides downstream are assigned positive numbers. Thus, a sequence extending from −500 to +25 includes 500 nucleotides upstream of the TSS, the TSS itself, and 24 additional nucleotides downstream. There is no nucleotide designated 0 in this convention.

A promoter, in contrast, is a region of DNA involved in initiating transcription. It contains sequence features that permit or assist the binding and operation of RNA polymerase and associated transcription factors and can contribute to determining when, where, and how strongly a gene is expressed. The promoter should therefore not be thought of simply as a particular nucleotide position. Nor should it necessarily be thought of as a region that ends immediately before the TSS. Although much of a promoter commonly lies upstream of the transcription start site, a core promoter may encompass the TSS and include sequence extending downstream of it.

The relationship can become still more complicated because transcription does not invariably begin at one uniquely defined nucleotide. A gene may use several closely spaced start sites, with one serving as the predominant TSS. Different promoters or TSSs may also be used under different biological conditions or in different tissues. Thus, even a reference to “the transcription start site” or “the promoter of gene X” may require further explanation.

The Problem with Invention Disclosures

This biological complexity can present a very practical problem for the patent practitioner. An invention disclosure might state, for example, that the inventors have “identified the promoter of gene X.” That statement immediately raises additional questions. What experiments were actually performed? Was a transcription start site mapped? Was an upstream DNA fragment shown experimentally to drive transcription? Were smaller fragments tested to determine what sequence was necessary for promoter activity? Is the sequence designated as the promoter entirely upstream of the TSS, or does it extend across and beyond it? Thus, before a patent application is prepared, it is important to determine exactly what the inventors mean when they use the word “promoter.”

 The same care should be taken with the TSS. If transcription begins predominantly at one nucleotide but also begins at nearby positions, the specification should not necessarily describe the experimentally observed system as having a single invariant TSS. Where multiple transcription start sites have been observed, that fact may itself be important in defining the invention.

Defining the Relationship

When a promoter is part of the invention, the specification should, whenever possible, define its relationship to the TSS. One particularly useful approach in this regard is to describe the promoter by nucleotide coordinates relative to the transcription start site. For example: “The promoter extends from nucleotide −500 to nucleotide +25 relative to the transcription start site designated +1.”

This tells the reader considerably more than merely stating that a particular sequence is “the promoter of gene X.” It identifies the reference point, defines the boundaries of the disclosed promoter, and makes clear that the promoter includes the TSS and extends downstream from it.

Coordinates are not the only way to define a promoter. If the promoter has been sequenced, it can be identified by a SEQ ID NO. If particular functional portions have been characterized, the application can identify a core promoter or particular promoter elements. Frequently, the most informative disclosure will provide both sequence information and a description of promoter activity.

Care is especially important with expressions such as “the promoter of gene X.” Some genes can be transcribed from more than one promoter and can have alternative transcription start sites. Unless the context makes the meaning clear, referring simply to “the promoter” can leave uncertain which regulatory region is intended.

How These Distinctions Affect Claims

The distinction between a promoter and a TSS becomes particularly important when claims are drafted because the invention can be claimed in several quite different ways. An invention may concern only a transcribed nucleic acid sequence. For example, it may be directed to a particular RNA, cDNA, coding sequence, or nucleic acid encoding a specified protein. Such a claim need not refer to a promoter at all. Nor must every such claim necessarily encompass the transcription start site. A coding sequence, for example, may begin downstream of the TSS because the RNA transcript contains a 5′ untranslated region preceding the coding region.

If the invention resides in a newly identified or engineered promoter, the promoter itself may be defined by sequence. A simplified claim might recite: “A nucleic acid comprising the nucleotide sequence of SEQ ID NO: 1.” The specification could then identify SEQ ID NO: 1 as a promoter and describe its transcriptional activity. A sequence-defined claim has the advantage of making the physical boundaries of the claimed molecule clear. Its disadvantage is that it may provide comparatively narrow protection if other sequence variants retain the same promoter activity.

In other cases, the promoter or regulatory region can be defined by its position relative to the TSS. For example: “A nucleic acid comprising nucleotides −500 to +25 relative to the transcription start site of gene X.” Here the TSS is not itself being claimed as though it were a separate molecular structure. Instead, it provides the reference point used to define the claimed region. This type of claim illustrates particularly well why the application should identify the TSS accurately. If the location of +1 is uncertain, the boundaries of a region defined relative to +1 may also become uncertain.

Frequently, the commercially significant invention is not the promoter by itself but an expression construct in which the promoter controls another sequence. A claim might therefore be directed to: “A nucleic acid comprising promoter P operably linked to a nucleic acid encoding protein X.” Here the relationship between the promoter and the transcribed sequence becomes part of the invention.

 Depending upon what has actually been developed, claims can be directed to the particular promoter, the promoter in combination with a coding sequence, an expression vector containing the construct, a transformed host cell, or methods employing the construct.

An inventor may also wish to obtain protection extending beyond one exact promoter sequence. Claims might therefore refer to sequence variants having a specified degree of sequence identity and retaining a defined promoter activity. Such claims potentially provide broader protection, but broader claiming places greater importance on the disclosure. If the specification identifies only a single promoter sequence, questions can arise as to how broadly the applicant can claim other sequences on the basis of their function.

The important point is that identifying the relevant promoter precisely in the specification does not necessarily require limiting every claim to one exact sequence. Rather, a precise disclosure provides the foundation from which different types and degrees of claim breadth can be considered.

What the Patent Application Should Establish

Promoters and transcription start sites therefore illustrate a broader principle of biotechnology patent drafting: terminology that is perfectly adequate for communication among scientists may not be sufficiently precise for defining patent rights. Where promoters and TSSs are relevant to an invention, the patent practitioner should try to determine:

-  where transcription actually begins and whether there is one TSS or more than one;

-  what sequence the inventors regard as constituting the promoter;

-  how the promoter was identified or functionally characterized;

-  whether the promoter lies entirely upstream of the TSS or encompasses and extends downstream of it;

-  whether particular portions of the promoter have been shown to be necessary or sufficient for activity;

-  whether the invention resides in the promoter itself, its activity, its relationship to another nucleic acid, or a larger construct containing it; and

-  how much sequence variation the experimental work reasonably supports.

Obtaining this information at the invention-disclosure stage is important. Once the application has been filed, it is too late to add sequence boundaries, functional relationships, or experimental findings that were understood by the inventors but never included in the original disclosure.

Conclusion

A promoter and a transcription start site describe different biological features. The TSS is the position at which transcription begins. A promoter is a functional DNA region involved in initiating that transcription, and the promoter may lie upstream of, encompass, and sometimes extend downstream of the TSS.

Disclaimer: This piece is provided for general informational purposes only and does not constitute legal advice. Patent issues are often complex and highly fact-specific, and no one should act on general information of this kind without consulting qualified patent counsel regarding the particular circumstances involved.