Biology subjects

Yadavalli, A. D.

Publications and source records attributed to Yadavalli, A. D..

3 recordsLinked to original sources

bioRxiv2024

The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon

The computational modeling of chromatin structure is highly complex and challenging due to the hierarchical organization of chromatin, which reflects its diverse biophysical principles, as well as inherent dynamism, which underlies its complexity. The variety of methods for chromatin structure modeling, which are based on different approaches, assumptions and scales of modeling, suggests that there is a necessity for a comprehensive benchmark. This inspired us to conduct a project at the NIH-funded 4D Nucleome Hackathon on March 18-21, 2024 at The University of Washington in Seattle, USA. The hackathon provided an amazing opportunity to gather an international, multi-institutional and unbiased group of experts to discuss, understand and undertake the challenges of chromatin model comparison and validation. These challenges seem straightforward in theory, however in practice, they are challenging and ambiguous. To address them, we developed a bioinformatics workflow for chromatin model comparison and validation, in which we use distance matrices to represent chromatin models, and we calculate Spearman correlation coefficients between pairs of matrices to estimate correlations between models, as well as between models and experimental data. During the 4-day hackathon, we tested our workflow on several distinct software packages for chromatin structure modeling and we discovered several challenges that include: 1) different aspects of chromatin biophysics and scales complicate model comparisons, 2) expertise in biology, bioinformatics, and physics is necessary to conduct a comprehensive research on chromatin structure, 3) bioinformatic software, which is often developed in academic settings, is characterized by insufficient support and documentation. Therefore, our work constitutes a way to advance the modeling of the 3D organization of the human genome, while emphasizing the importance of establishing guidelines for software development and standardization.

genomics↗

bioRxiv2024

Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination

Somatic hypermutation (SHM) and class switch recombination (CSR) diversify immunoglobulin (Ig) genes and are initiated by the activation induced deaminase (AID), a single-stranded DNA cytidine deaminase that is thought to engage its substrate in the context of RNA polymerase II (RNAPII) transcription. Through a loss of function genetic screen, we identified numerous potential factors involved in SHM including ELOF1, a component of the RNAPII elongation complex that has been shown to function in DNA repair and transcription elongation. Loss of ELOF1 strongly compromises SHM, CSR, and AID targeting and alters RNAPII transcription by reducing RNAPII pausing downstream of transcription start sites and levels of serine 5 but not serine 2 phosphorylated RNAPII throughout transcribed genes. ELOF1 must bind to RNAPII to be a proximity partner for AID and to function in SHM and CSR. We propose that ELOF1 helps create the appropriate stalled RNAPII substrate on which AID acts. HighlightsO_LIA CRISPR knockout screen has identified numerous potential SHM factors. C_LIO_LISHM, CSR, and AID targeting are strongly compromised in the absence of ELOF1. C_LIO_LIELOF1 must interact with RNAPII to be an AID proximity partner and support AID targeting. C_LIO_LIELOF1 supports RNAPII pausing and generation of the substrate for AID action. C_LI

immunology↗

bioRxiv2020

Systematic hormone-metabolite network provides insights of high salinity tolerance in Pongamia pinnata (L.) pierre

Salinity stress results significant losses in plant productivity, and loss of cultivable lands. Although Pongamia pinnata is reported to be a salt tolerant semiarid tree crop, the adaptive mechanisms to saline environment are elusive. The present investigation describes alterations in hormonal and metabolic responses in correlation with physiological and molecular variations in leaves and roots of Pongamia at sea salinity level (3% NaCl) for 8 days. At physiological level, salinity induced adjustments in plant morphology, leaf gas exchange and ion accumulation patterns were observed. Our study also revealed that phytohormones including JAs and ABA play crucial role in promoting the salt adaptive strategies such as apoplasmic Na+ sequestration and cell wall lignification in leaves and roots of Pongamia. Correlation studies demonstrated that hormones including ABA, JAs and SA showed a positive interaction with selective compatible metabolites (sugars, polyols and organic acids) to aid in maintaining osmotic balance and conferring salt tolerance to Pongamia. At the molecular level, our data showed that differential expression of transporter genes as well as antioxidant genes regulate the ionic and ROS homeostasis in Pongamia. Collectively, these results shed new insights on an integrated physiological, structural, molecular and metabolic adaptations conferring salinity tolerance to Pongamia. High lightOur data, for the first time, provide new insights for an integrated molecular and metabolic adaptation conferring salinity tolerance in Pongamia. The present investigation describes alterations in hormonal and metabolic responses in correlation with physiological and molecular variations in Pongamia at sea salinity level (3% NaCl) for 8 days.

plant biology↗