A5088793206- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Cancer-related gene regulation
- RNA Research and Splicing
- Ubiquitin and proteasome pathways
- RNA and protein synthesis mechanisms
- Histone Deacetylase Inhibitors Research
- Metabolism and Genetic Disorders
- Biochemical Acid Research Studies
- Chromatin Remodeling and Cancer
- DNA Repair Mechanisms
- Mitochondrial Function and Pathology
- Enzyme Structure and Function
- Bacterial Genetics and Biotechnology
- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- Mechanisms of cancer metastasis
- CRISPR and Genetic Engineering
- Protein Degradation and Inhibitors
- Cancer Mechanisms and Therapy
- Diet and metabolism studies
- Cancer, Hypoxia, and Metabolism
- interferon and immune responses
- Computational Drug Discovery Methods
Stowers Institute for Medical Research
2017-2024
Southwestern Medical Center
2024
The University of Texas Southwestern Medical Center
2024
Advanced Centre for Treatment, Research and Education in Cancer
2014-2021
Tata Memorial Hospital
2014-2021
Homi Bhabha National Institute
2017-2021
Abstract Heterogeneous ribonucleoproteins (hnRNPs) are RNA binding molecules that involved in key processes such as splicing and transcription. One hnRNP protein, L, regulates alternative (AS) by to pre-mRNA transcripts. However, it is unclear what factors contribute L-regulated AS events. Using proteomic approaches, we identified several co-purify with L. We demonstrate one factor, the histone methyltransferase SETD2, specifically interacts L vitro vivo. This interaction occurs through a...
Abstract Background The histone H3K36me3 mark regulates transcription elongation, pre-mRNA splicing, DNA methylation, and damage repair. However, knowledge of the regulation enzyme SETD2, which deposits this functionally important mark, is very limited. Results Here, we show that poorly characterized N-terminal region SETD2 plays a determining role in regulating stability SETD2. This stretch 1–1403 amino acids contributes to robust degradation by proteasome. Besides, protein aggregate prone...
Abstract Paraspeckles are subnuclear RNA–protein structures that implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show interact with SWI/SNF chromatin‐remodeling complex. This specifically mediated by direct interaction of long‐non‐coding RNA NEAT1 ARID1B cBAF‐type Strikingly, depletion, addition to...
Serial capture affinity purification (SCAP) is a powerful method to isolate specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated Here, we applied SCAP dissect subpopulation WDR76 in complex SPIN1, histone reader that recognizes trimethylated H3 lysine4 (H3K4me3). In contrast previous analysis SPIN1:SPINDOC complex, histones H3K4me3 mark were enriched WDR76:SPIN1 Next,...
Abstract The RNA recognition motif (RRM) binds to nucleic acids as well proteins. More than one such domain is found in the pre-mRNA processing hnRNP While mode of by RRMs known, molecular basis their protein interaction remains obscure. Here we describe between L and LL with methyltransferase SETD2. We demonstrate that for occur, a leucine pair within highly conserved stretch SETD2 insert side chains hydrophobic pockets formed RRM2. Notably, structure also highlights RRM2 can form ternary...
The distinct functional effects of the replication-dependent histone H2A isoforms have been demonstrated; however, mechanistic basis non-redundancy remains unclear. Here, we investigated specific contribution isoform H2A1H, which differs from another H2A2A3 in identity only three amino acids. H2A1H exhibits varied expression levels different normal tissues and human cancer cell lines (H2A1C humans). It also promotes proliferation a context-dependent manner when exogenously overexpressed. To...
Aberrant changes in histone post-translational modifications are encountered frequently diseases like cancer. Although H3 have been extensively studied context of diseases, the functionally important H2A PTM H2A119ub (H2Aub) has not gained much attention. In this study, we report that H2Aub markedly decreases hepatocellular carcinoma. Usp21, a deubiquitinase, is probably responsible for decrease H2Aub. addition, levels showed an inverse correlation with H3S10 phosphorylation (H3S10p) and...
SETD2 is an important methyltransferase that methylates crucial substrates such as histone H3, tubulin, and STAT1 also physically interacts with transcription splicing regulators Pol II various hnRNPs. Of note, has a functionally uncharacterized extended N-terminal region, the removal of which leads to its stabilization. How this region regulates half-life unclear. Here we show consists multiple long disordered regions across length cumulatively destabilize protein by facilitating...
The methyltransferase SETD2 regulates cryptic transcription, alternative splicing, and the DNA damage response. It is mutated in a variety of cancers believed to be tumor suppressor. Counterintuitively, despite its important role, robustly degraded by proteasome keeping levels low. Here we show that accumulation results non-canonical deposition functionally H3K36me3 histone mark, which includes reduced enrichment over gene bodies exons. This perturbed epigenetic landscape associated with...
The pyruvate dehydrogenase complex (PDC) is a multienzyme that plays key role in energy metabolism by converting to acetyl-CoA. An increase of nuclear PDC has been shown be correlated with an histone acetylation requires reported form ~ 10 MDa macromolecular machine proficient performing sequential catalytic reactions via its three components. In this study, we show the displays size versatility ionic strength-dependent manner using exclusion chromatography yeast cell extracts. Biochemical...
Histones, the structural unit of chromatin, must be assembled/dissembled to preserve or change chromatin organization in accordance cellular needs. Initially, function histone chaperones was thought only “histone carriers/vehicles”, but now with accumulating evidences they are known key actors metabolism. With this outburst knowledge, placed at center gene regulation, having roles play DNA replication, repair and transcription. This review will focus on current knowledge we have about role...
Epigenetics have witnessed a renewed interest over the past decade and assays with recombinant histones has become an important tool for uncovering various aspects of histone biology. However, at times absence accumulation in bacteria is encountered which also commonly observed many eukaryotic proteins general. In this study, we investigated effect multiple parameters on heterologous expression proteins. We show that there marked variability H2A.2, H2B.1, H3.2 H4 host, possibly owing to...
Cells are capable of adapting their metabolism in response to changes nutrient availability, and this can cause gene expression. Recent studies have revealed that certain metabolic enzymes, such as acetyl-CoA synthetase Acs2, present the nucleus. Acs2 plays a vital role producing from acetate, which is crucial for histone acetylation, an epigenetic mark activates transcription. However, importance local production nucleus not fully understood. Our research aims determine nuclear by exploring...
SUMMARY Heterogeneous ribonucleoproteins (hnRNPs) are RNA binding molecules that involved in key processes such as splicing and transcription. One hnRNP protein, L, regulates alternative (AS) by to pre-mRNA transcripts. However, it is unclear what factors contribute L-regulated AS events. Using proteomic approaches, we identified several co-purify with L. We demonstrate one factor, the histone methyltransferase SETD2, specifically interacts L vitro vivo . This interaction occurs through a...
ABSTRACT The histone H3K36me3 mark regulates transcription elongation, pre-mRNA splicing, DNA methylation, and damage repair. However, knowledge of the regulation enzyme SETD2, which deposits this functionally important mark, is very limited. Here we show that poorly characterized N-terminal region SETD2 plays a determining role in regulating stability SETD2. This stretch 1-1403 amino acids contributes to robust degradation by proteasome. Besides, protein aggregate-prone forms insoluble...
WDR76 is a multifunctional protein involved in many cellular functions. With diverse and complicated interaction network, dissecting the structure function of specific complexes needed. We previously demonstrated ability Serial Capture Affinity Purification (SCAP) method to isolate by introducing two proteins interest as baits at same time. Here, we applied SCAP dissect subpopulation complex with SPIN1, histone marker reader that specifically recognizes trimethylated H3 lysine4 (H3K4me3). In...
ABSTRACT The pyruvate dehydrogenase complex (PDC) is a multienzyme that plays key role in energy metabolism by converting to acetyl-CoA. An increase of nuclear PDC has been shown be correlated with an histone acetylation requires reported form ~ 10 MDa macromolecular machine proficient performing sequential catalytic reactions via its three components. In this study, we show the displays size versatility ionic strength-dependent manner using exclusion chromatography yeast cell extracts....
With the identification of increasing number chromatin modifiers, histone variants, post-translational modifications and their cross-talk, it is essential to validate these findings interactions in vitro for which pure complexes are required. Although, production such has been described earlier but still remains a challenge non-specialist lab. Here we describe protocol quickly obtain large quantities highly histones using bacterial expression system GST pull-down reconstitution experiments....