Two-zero Textures of the Majorana Neutrino Mass Matrix and Current Experimental Tests

In view of the latest T2K and MINOS neutrino oscillation data which hint at a relatively large theta_13, we perform a systematic study of the Majorana neutrino mass matrix M_nu with two independent texture zeros. We show that three neutrino masses (m_1, m_2, m_3) and three CP-violating phases (delta, rho, sigma) can fully be determined from two neutrino mass-squared differences (delta m^2, Delta m^2) and three flavor mixing angles (theta_12, theta_23, theta_13). We find that seven patterns of M_nu (i.e., A_{1,2}, B_{1,2,3,4} and C) are compatible with current experimental data at the 3-sigma level, but the parameter space of each pattern is more strictly constrained than before. We demonstrate that the texture zeros of M_nu are stable against the one-loop quantum corrections, and there exists a permutation symmetry between Patterns A_1 and A_2, B_1 and B_2 or B_3 and B_4. Phenomenological implications of M_nu on the neutrinoless double-beta decay and leptonic CP violation are discussed, and a realization of those texture zeros by means of the Z_n flavor symmetries is illustrated.Comment: 41 pages, including 4 tables and 14 figures, more discussions added, to appear in JHE

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

While it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then mRNAs encoding transcription factors dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously over-represented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

10.1038/s41467-021-23143-7Nature Communications121329