An Integrated Approach to Discriminate Transcriptional Regulation underlining TRA expression in mTECs, using High Throughput Sequencing Data

Abstract

Thymus is one of the primary lymphoid organs and its epithelial cells hosts a phenomenon, promiscuous gene expression, through which all the peripheral transcripts of the body are ectopically expressed as self-antigens in them. The functional role of thymus is further extended to thymocytes, which on their course of development interacts with self-antigens through surface borne T cell receptors and co-receptors. The affinity of this interaction is monitored closely and in later stages of development, if it crosses a threshold, corresponding thymocytes either succumb to apoptosis or transform into thymic T regulatory cells by expressing Foxp3. Either fate fundamentally deals with autoimmunity and its prevention. The following study focuses on regulatory control of pGE; at transcriptional and chromatin configurational levels. For the purpose, contextspecific accessibility and transcriptomic datasets were combined to obtain regulatory element (RE), transcription factor (TF) and chromatin regulator (CR); responsible for regulatory control of each individual target gene (TG); by running a statistical model, termed as, Paired Expression and Chromatin Accessibility model. Building and observing a CR-TF-RE-TG regulatory network revealed a lot of interesting and novel information. The found TFs belong to various families, members of which have been mentioned in literature in relation to pGE. Most of the REs, as enhancers, were far away from the transcription start sites; from 10 kb to 1 Mb. These enhancers were involved in long range intra-chromosomal interactions with other enhancers and promoters. Furthermore, these interactions generally extended their control on distant genes, situated around 40-50 kb from them. Permissive histone marks, comparatively to repressive ones, were found more prevalent at the REs. Chromatin looping as a probable cause of these interactions were observed by looking into associated CRs and their modifications. Acetylation and deacetylation appeared as the main agents of post-transcriptional chromatin modification. The other observed modifications dealt with nucleosome positioning and permissive H3K4me3. The study recapitulates some of the regulatory relations mentioned in literature and offers new possibilities for future endeavours.