**Aneta Tarczewska and Beata Greb-Markiewicz \***

Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrze ˙ze Wyspia ´nskiego 27, 50-370 Wroclaw, Poland; aneta.tarczewska@pwr.edu.pl

**\*** Correspondence: beata.greb-markiewicz@pwr.edu.pl

Received: 30 September 2019; Accepted: 22 October 2019; Published: 24 October 2019

**Abstract:** The bHLH proteins are a family of eukaryotic transcription factors regulating expression of a wide range of genes involved in cell differentiation and development. They contain the Helix-Loop-Helix (HLH) domain, preceded by a stretch of basic residues, which are responsible for dimerization and binding to E-box sequences. In addition to the well-preserved DNA-binding bHLH domain, these proteins may contain various additional domains determining the specificity of performed transcriptional regulation. According to this, the family has been divided into distinct classes. Our aim was to emphasize the significance of existing disordered regions within the bHLH transcription factors for their functionality. Flexible, intrinsically disordered regions containing various motives and specific sequences allow for multiple interactions with transcription co-regulators. Also, based on in silico analysis and previous studies, we hypothesize that the bHLH proteins have a general ability to undergo spontaneous phase separation, forming or participating into liquid condensates which constitute functional centers involved in transcription regulation. We shortly introduce recent findings on the crucial role of the thermodynamically liquid-liquid driven phase separation in transcription regulation by disordered regions of regulatory proteins. We believe that further experimental studies should be performed in this field for better understanding of the mechanism of gene expression regulation (among others regarding oncogenes) by important and linked to many diseases the bHLH transcription factors.

**Keywords:** bHLH; IDP; IDR; LLPS; disorder prediction; LLPS prediction; transcription; phase separation
