Debashish Ray
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View article: CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs
CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs Open
RNA-binding proteins (RBPs) are key mediators of post-transcriptional gene regulation, including splicing, transport, stability, and other facets of RNA metabolism. Many RBPs exert their function through sequence-specific protein–RNA inter…
View article: A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function
A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function Open
RNA-binding proteins (RBPs) are key regulators of gene expression; however, their RNA-binding specificities, that is, motifs, have not been comprehensively determined. Here we introduce Eukaryotic Protein–RNA Interactions (EuPRI), a freely…
View article: At‐ <scp>RS31</scp> orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with <scp>TOR</scp> ‐ <scp>ABA</scp> pathways
At‐ <span>RS31</span> orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with <span>TOR</span> ‐ <span>ABA</span> pathways Open
Summary Alternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants to boost functional diversity and fine‐tune responses to environmental and developmental cues. Arabidopsis thaliana At‐RS3…
View article: At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways
At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways Open
SUMMARY Alternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants to boost functional diversity and fine-tune responses to environmental and developmental cues. At-RS31, a plant-specific s…
View article: Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes
Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes Open
RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions) — a freely available resource of RNA motifs for 34,736 RBPs from 690 eukaryotes. EuPRI includes in vitro bind…
View article: Uncovering a mammalian neural-specific poly(A) binding protein with unique properties
Uncovering a mammalian neural-specific poly(A) binding protein with unique properties Open
The mRNA 3′ poly(A) tail plays a critical role in regulating both mRNA translation and turnover. It is bound by the cytoplasmic poly(A) binding protein (PABPC), an evolutionarily conserved protein that can interact with translation factors…
View article: RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific Open
Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)—proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have unchara…
View article: PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins Open
Modelling both primary sequence and secondary structure preferences for RNA binding proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure representations and can be difficult to interpret and evaluate. To ad…
View article: The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians
The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians Open
Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has undergone a striking process of evolutionary s…
View article: The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians
The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians Open
The eutherian placenta is a major site for parental genetic conflict. Here, we identify the X-linked Mbnl3 gene as a novel player in this dispute. Mbnl3 belongs to an RNA binding protein family whose members regulate alternative splicing a…
View article: Additional file 8 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 8 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 8: Table S7. Results of metabolic analysis U251 control vs. U251 SERBP1 knockdown.
View article: Additional file 7 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 7 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 7: Table S6. RNA-seq analysis of U251 control vs. SERBP1 knockdown samples. Sheet 1, summary of results; sheet 2, list of genes affected by SERBP1 knockdown; sheet 3, list of ncRNA affected by SERBP1 knockdown; sheet 4, gen…
View article: Additional file 11 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 11 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 11: Table S10. Gene set enrichment analysis (GSEA) of genes upregulated upon SERBP1 knockdown. Sheet 1, EZH2 and SUZ12 matches in ChEA 2016 datasets; sheet 2, EZH2 and SUZ12 matches in ENCODE 2015 datasets; sheet 3, genes w…
View article: Additional file 13 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 13 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 13: Table S12. Expression analyses of SERBP1 knockdown upregulated set in TCGA GBM vs. LGG and TCGA GBM vs. GTEx brain (cortex) samples.
View article: Additional file 16 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 16 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 16. Complete list of reagents.
View article: Additional file 5 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 5 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 5: Table S4. Characteristics of all glioma patients in the cohort from the Shanghai Changzheng Hospital.
View article: Additional file 6 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 6 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 6: Table S5. RIP-seq analysis of 293 T cells transfected with SERBP1-streptag. Sheet 1, summary of results; sheet 2, list of SERBP1 target genes; sheet 3, gene ontology analysis; sheet 4, metabolism terms enriched in the GO…
View article: Additional file 14 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 14 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 14: Table S13. List of primers used for cloning
View article: Additional file 10 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 10 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 10: Table S9. Gene expression correlation analysis. Genes showing positive and negative (anti-correlation) with SERBP1 in brain samples (Kang dataset) according to R2. Sheet 1, genes showing positive correlation with SERBP1…
View article: Additional file 3 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 3 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 3: Table S2. List of TCGA and CGGA glioma patients.
View article: Additional file 12 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 12 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 12: Table S11. Genes in SERBP1 knockdown upregulated set showing H3K27me3 sites in GBM cells according to [45].
View article: Additional file 15 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 15 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 15: Table S14. List of primers and probes used in qRT-PCR analyses
View article: Additional file 9 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Additional file 9 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation Open
Additional file 9: Table S8. Gene expression correlation analysis. Genes showing positive and negative (anti-correlation) with SERBP1 in TCGA GBM samples according to R2. Sheet 1, genes showing positive correlation with SERBP1 in TCGA GBM …
View article: ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development
ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development Open
Stress hormones bind and activate the glucocorticoid receptor (GR) in many tissues including the brain. We identified arginine and glutamate rich 1 (ARGLU1) in a screen for new modulators of glucocorticoid signaling in the CNS. Biochemical…
View article: The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans
The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans Open
Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and lim…
View article: A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)
A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B) Open
Mutations of EXOSC3 have been linked to the rare neurological disorder known as Pontocerebellar Hypoplasia type 1B (PCH1B). EXOSC3 is one of three putative RNA-binding structural cap proteins that guide RNA into the RNA exosome, the cellul…
View article: The TRIM-NHL protein NHL-2 is a Novel Co-Factor of the CSR-1 and HRDE-1 22G-RNA Pathways
The TRIM-NHL protein NHL-2 is a Novel Co-Factor of the CSR-1 and HRDE-1 22G-RNA Pathways Open
Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and lim…