Brian D. Gregory
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View article: Expansion of human hematopoietic stem cells by inhibiting translation
Expansion of human hematopoietic stem cells by inhibiting translation Open
Hematopoietic stem cell (HSC) transplantation using umbilical cord blood (UCB) is a potentially life-saving treatment for leukemia and bone marrow failure but is limited by the low number of HSCs in UCB. The loss of HSCs after ex vivo mani…
View article: Arabidopsis DXO1 is an evolutionarily diverged homolog that impacts ribosome loading and mRNA surveillance
Arabidopsis DXO1 is an evolutionarily diverged homolog that impacts ribosome loading and mRNA surveillance Open
The Rai1/Dxo1/DXO protein family are involved in eukaryotic 5′-end RNA quality control by hydrolyzing non-canonical mRNA cap structures, such as the NAD + 5′-cap. The plant DXO1 ortholog shows distinct biochemical properties, compared to i…
View article: Epitranscriptomic modifications in plant RNAs
Epitranscriptomic modifications in plant RNAs Open
A plethora of new and exciting findings have dramatically widened the horizons of plant RNA-related research. Despite being identified decades ago, RNA modifications were largely ignored owing to the immense difficulty in studying them wit…
View article: HAMRLNC: A Comprehensive Pipeline for High-throughput Analysis of Modified Ribonucleotides and Long Non-Coding Ribonucleic Acids
HAMRLNC: A Comprehensive Pipeline for High-throughput Analysis of Modified Ribonucleotides and Long Non-Coding Ribonucleic Acids Open
Summary As sequencing technologies advance and costs decline, there has been a surge in the application of RNA sequencing (RNA-seq) in understanding biological processes. In addition to the typical uses of RNA-seq for transcriptomics, gene…
View article: Global analysis of excitotoxicity-induced alterations in RNA structure and RNA-protein binding in neurons
Global analysis of excitotoxicity-induced alterations in RNA structure and RNA-protein binding in neurons Open
View article: Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes
Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes Open
View article: The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress
The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress Open
RNA Covalent Modifications (RCMs) are post-transcriptional chemical alterations that influence RNA stability and translation efficiency, thus play critical roles in eukaryotic growth and development. However, their role in regulating plant…
View article: The Nuclear Cap-Binding Complex Regulates Subcellular RNA Processing and Surveillance of Coding and Non-Coding RNAs
The Nuclear Cap-Binding Complex Regulates Subcellular RNA Processing and Surveillance of Coding and Non-Coding RNAs Open
View article: <scp>mRNA ADENOSINE METHYLASE</scp> promotes drought tolerance through <scp>N<sup>6</sup></scp>‐methyladenosine‐dependent and independent impacts on <scp>mRNA</scp> regulation in Arabidopsis
<span>mRNA ADENOSINE METHYLASE</span> promotes drought tolerance through <span>N<sup>6</sup></span>‐methyladenosine‐dependent and independent impacts on <span>mRNA</span> regulation in Arabidopsis Open
Summary Among many mRNA modifications, adenine methylation at the N 6 position (N 6 ‐methyladenosine, m 6 A) is known to affect mRNA biology extensively. The influence of m 6 A has yet to be assessed under drought, one of the most impactfu…
View article: Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants
Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants Open
View article: Comparative analyses uncover a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants
Comparative analyses uncover a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants Open
Background In recent years, covalent modifications on RNA nucleotides have emerged as pivotal moieties influencing the structure, function, and regulatory processes of RNA Polymerase II transcripts such as mRNAs and lncRNAs. However, our u…
View article: Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing
Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing Open
Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod…
View article: Academia Molecular Biology and Genomics: A repository of information for all areas of Genomics and Molecular Biology Research
Academia Molecular Biology and Genomics: A repository of information for all areas of Genomics and Molecular Biology Research Open
View article: RNA N6-Methyladenosine Affects Copper-Induced Oxidative Stress Response in Arabidopsis thaliana
RNA N6-Methyladenosine Affects Copper-Induced Oxidative Stress Response in Arabidopsis thaliana Open
Recently, post-transcriptional regulation of mRNA mediated by N6-methyladenosine (m6A) has been found to have profound effects on transcriptome regulation during plant responses to various abiotic stresses. However, whether this RNA modifi…
View article: PELOTA and HBS1 suppress co‐translational messenger RNA decay in Arabidopsis
PELOTA and HBS1 suppress co‐translational messenger RNA decay in Arabidopsis Open
Various messenger RNA (mRNA) decay mechanisms play major roles in controlling mRNA quality and quantity in eukaryotic organisms under different conditions. While it is known that the recently discovered co‐translational mRNA decay (CTRD), …
View article: Expansion of human hematopoietic stem cells by inhibiting translation
Expansion of human hematopoietic stem cells by inhibiting translation Open
Hematopoietic stem cell (HSC) transplantation using umbilical cord blood (UCB) is a potentially life-saving treatment for leukemia and bone marrow failure but is limited by the low number of HSCs in UCB. The loss of HSCs after ex vivo mani…
View article: Pathogen-induced m6A dynamics affect plant immunity
Pathogen-induced m6A dynamics affect plant immunity Open
Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the p…
View article: Systematic Sampling of the Female Reproductive System for Molecular Characterization
Systematic Sampling of the Female Reproductive System for Molecular Characterization Open
As part of the National Institutes of Health Human BioMolecular Atlas Program to develop a global platform to map the 37 trillion cells in the adult human body, we are generating a comprehensive molecular characterization of the female rep…
View article: Transferable deep learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing
Transferable deep learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing Open
RNA modifications play crucial roles in various biological processes. Current methods for epitranscriptome profiling using nanopore direct RNA sequencing (DRS) are unable to simultaneously identify multiple types of modifications. Here, we…
View article: Table S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Table S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
Antibody List
View article: Table S3 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Table S3 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
shRNA
View article: Modified protocol for genome-wide mapping of uncapped transcripts (GMUCT) in eukaryotes v2
Modified protocol for genome-wide mapping of uncapped transcripts (GMUCT) in eukaryotes v2 Open
This is a modified protocol to construct a sequencing library for genome-wide mapping of uncapped and cleaved transcripts (GMUCT; Willmann et al, 2014 Methods, 10.1016/j.ymeth.2013.07.003).
View article: Table S3 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Table S3 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
shRNA
View article: Table S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Table S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
Antibody List
View article: Supplementary Figure S3 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Supplementary Figure S3 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
LIN28B-S in Huh7.5 cells
View article: Data from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Data from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
The RNA-binding protein LIN28B plays an important role in development, stem cell biology, and tumorigenesis. LIN28B has two isoforms: the LIN28B-long and -short isoforms. Although studies have revealed the functions of the LIN28B-long isof…
View article: Supplementary Figure S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Supplementary Figure S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
LIN28B mRNA expression in human CRC samples
View article: Supplementary Figure S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Supplementary Figure S2 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
LIN28B mRNA expression in human CRC samples
View article: Data from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Data from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
The RNA-binding protein LIN28B plays an important role in development, stem cell biology, and tumorigenesis. LIN28B has two isoforms: the LIN28B-long and -short isoforms. Although studies have revealed the functions of the LIN28B-long isof…
View article: Table S1 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions
Table S1 from Differential Regulation of <i>LET-7</i> by LIN28B Isoform–Specific Functions Open
qPCR primers