Biology subjects

Prinjha, R.

Publications and source records attributed to Prinjha, R..

5 recordsLinked to original sources

bioRxiv2023

Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause

Exposure of unicellular or multicellular organisms to adverse environmental conditions, including nutrient deprivation, may induce a state of suspended animation or diapause. The diapause minimizes the organisms reliance on external energy sources and ensures survival. Among different forms of diapause, embryonic diapause, caused by a limited supply of nutrients to the growing embryos, is particularly challenging for the organism. Diapause embryos stop developing at the peak of pluripotent cell differentiation and maintain this undifferentiated yet entirely vital state despite the overall reduction in anabolic processes and genome-wide transcriptional repression. Using ES cells commonly employed to study the mechanism of embryonic diapause, we solve the paradox of the cell maintenance in an undifferentiated ES cell state during diapause. We find that broad transcriptional repression by long-term inhibition of the bromodomain and extra-terminal (BET) proteins causes diapause. These diapause ES cells upregulate a functionally linked group of genes encoding negative regulators of MAP kinase signaling (NRMKS), which play a crucial role in ES cell differentiation. We find that elevated NRMKS expression is a hallmark of the diapause cells and cells exposed to diapause-inducing conditions, including mTOR inhibition, and is required for the maintenance of ES cell pluripotency during diapause. Mechanistically, exposure of ES cells to diapause-inducing conditions leads to rapid decline of the Capicua transcriptional repressor (CIC) at the NRMKS gene promoters, followed by transcriptional upregulation of NRMKS genes. The mTOR and BET-dependent transcriptional switch supporting the undifferentiated state of the diapause ES cells suggests a broader usage of this mechanism in maintaining the undifferentiated state of metabolically dormant stem- or stem-like cells in different tissues.

cell biology↗

bioRxiv2022

Epigenetic and transcriptional plasticity of myeloid cells in Cystic Fibrosis

The relative contributions of acute and chronic inflammatory mechanisms in diseases characterised by persistent bacterial infection are unclear, despite important consequences for the development of novel anti-inflammatory therapies. Here, we examined longitudinal transcriptional and epigenetic changes in patients with Cystic Fibrosis (CF), a genetic condition characterised by persistent bacterial lung infections that drive progressive inflammatory lung damage. We find that sudden clinical deteriorations in lung health, termed Acute Pulmonary Exacerbations (APEs), are linked to innate immune signalling driven by bacterial components, and accompanied by changes in macrophage function. Treatment of patients with intravenous antibiotics results in rapid modification of myeloid cell gene expression and epigenetic state, towards that of healthy volunteers, suggesting that repeated acute inflammatory episodes play an important role in CF inflammatory lung damage.

immunology↗

bioRxiv2022

Essential bromodomain TcBDF2 as a drug target against Chagas disease

Trypanosoma cruzi is a unicellular parasite that causes Chagas disease, which is endemic in the American continent but also worldwide distributed by migratory movements. A striking feature of trypanosomatids is the polycistronic transcription associated with post-transcriptional mechanisms that regulate the levels of translatable mRNA. In this context, epigenetic regulatory mechanisms have been revealed of great importance, since they are the only ones that would control the access of RNA polymerases to chromatin. Bromodomains are epigenetic protein readers that recognize and specifically bind to acetylated lysine residues, mostly at histone proteins. There are seven coding sequences for BD-containing proteins in trypanosomatids, named TcBDF1 to TcBDF7, and a putative new protein-containing a bromodomain that was recently described. Using the Tet regulated overexpression plasmid pTcINDEX-GW and CRISPR/Cas9 genome editing we were able to demonstrate the essentiality of TcBDF2 in T cruzi. This bromodomain is located in the nucleus, through a bipartite nuclear localization signal. TcBDF2 was shown to be important for host cell invasion, amastigote replication, and differentiation from amastigotes to trypomastigotes. Overexpression of TcBDF2 diminished epimastigote replication. Also, some processes involved in pathogenesis were altered in these parasites, such as infection of mammalian cells, replication of amastigotes, and the number of trypomastigotes released from host cells. In in vitro studies, TcBDF2 was also able to bind inhibitors showing a specificity profile different from that of the previously characterized TcBDF3. These results, point to TcBDF2 as a druggable target against T. cruzi.

cell biology↗

bioRxiv2021

Bromodomain factor 5 is an essential transcriptional regulator of the Leishmania genome.

Leishmania are unicellular parasites that cause human and animal disease. Alongside other organisms in kinetoplastida, they have evolved an unusual genome architecture that requires all RNA polymerase II transcribed genes to be expressed constitutively, with transcriptional start regions denoted by histone variants and histone lysine acetylation. However, the way these chromatin marks are interpreted by the cell is not understood. Seven predicted bromodomain factors (BDF1-7), the reader modules for acetyl-lysine, were identified across Leishmania genomes. Using L. mexicana as a model, Cas9-driven gene deletions indicate that BDF1-5 are essential for promastigote survival, whilst DiCre inducible gene deletion of the dual bromodomain factor BDF5 identified it to be essential for both promastigotes and amastigotes. ChIP-seq assessment of BDF5s genomic distribution revealed it as highly enriched at transcriptional start sites. Using an optimised proximity proteomic and phosphoproteomic technique, XL-BioID, we defined the BDF5-proximal environment to be enriched for other bromodomain factors, histone acetyltransferase 2, and proteins essential for transcriptional activity and RNA processing. Inducible deletion of BDF5, led to a disruption of pol II transcriptional activity and global defects in gene expression. Our results indicate the requirement of Leishmania to interpret histone acetylation marks for normal levels of gene expression and thus cellular viability.

cell biology↗

bioRxiv2019

Histone methyltransferase MMSET/NSD2 is essential for generation of B1 cell compartment in mice

Humoral immunity in mice and man relies on the function of two developmentally and functionally distinct B cell subsets - B1 and B2 cells. While B2 cells are responsible for most of the adaptive response to environmental antigens, B1 cells, which are comprised of phenotypically distinct B1a and B1b cells, are carriers of the innate humoral immunity that relies on production of poly-reactive and low affinity antibodies. The molecular mechanism of B cell specification into different subsets is not well established. Here we identified lysine methyltransferase MMSET/NSD2 as a critical regulator of the B1 cell population. We show that NSD2 deficiency in B cell precursors prevents generation of the B1 cell compartment, while having a minor impact on B2 cells. Our data revealed MMSET/NSD2, which catalyzes histone H3 lysine 36 di-methylation, as the first in class epigenetic master regulator of a major B cell lineage in mice.

immunology↗