Stochastic Capture of Chromatin Topological Domains by Nuclear Matrix Bound RNA Polymerase II Determines Monogenic Vκ Choice

Mono-specificity of antigen receptors (AgR) is dependent upon monoallelic expression of,V(D)J recombined AgR allele. By using combined DNA-RNA Fluorescent in situ Hybridization,(FISH) and single-cell RNA-sequencing, we report that in the context of Igκ, allelic choice for,recombination is determined by germline Vκ expression. Allelic choice is associated with,asymmetric localization of chosen allele within a rich niche of elongating RNA-Polymerase II,(e-Pol II) where Vκ germline expression is initiated upon downregulation of nuclear-matrix (nm) bound cyclin D3. This e-Pol II niche is cylindrical in shape, and allows efficient contraction between Vκ and Jκ compared to the alternate niche. Vκ transcription from the chosen allele occurs within CTCF-defined loops, whereby transcription is predicted to happen by random loop capture by fixed e-Pol II arrayed along the cylinder. Multiple Vκ segments can be active within a cell from the chosen allele, however, only one Vκ gene productively interacts with Jκ for recombination. Based on polymer chain simulation of Igκ within a cylindrical niche, the physical constrain imposed by e-Pol II niche both favors CTCF defined loops formation and positioning of loops that reflects observed preference for distal and proximal Vκ usage. Absence of cyclin D3 is also associated with expression of other monoallelic genes such as olfactory receptor (OR) genes, protocadherin genes and randomly monoallelic genes. We propose that in the context of monoallelic and monogenic genes, allelic choice for transcription is determined by asymmetric localization of single allele in rich niche of e-Pol II, whereas in the case of monoallelic but clustered genes, this asymmetric localization is followed by random loop capture transcription across the cluster, allowing monogenic choice for expression. Therefore, Igκ transcriptional regulation reported here, sheds light on mechanism of both monoallelic and monogenic choice.