4.7 Article

Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

HYL1-CLEAVAGE SUBTILASE 1 (HCS1) suppresses miRNA biogenesis in response to light-to-dark transition

Hyun Ju Jung et al.

Summary: The protein HCS1 is identified as a cytoplasmic protease that degrades HYL1, which is important for miRNA biogenesis. The activity of HCS1 is regulated by light and darkness, with COP1 suppressing its activity in light and promoting its activity in darkness.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Dynamic Phosphorylation of miRNA Biogenesis Factor HYL1 by MPK3 Involving Nuclear-Cytoplasmic Shuttling and Protein Stability in Arabidopsis

Prakash Kumar Bhagat et al.

Summary: This study investigates the role of MAP kinase-mediated phosphorylation of AtHYL1 and its sub-cellular activity. The results show that AtHYL1 plays an important role in nuclear-cytosolic shuttling and can dimerize both in the nucleus and cytosol.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Biology

Functional characterization of a 'plant-like' HYL1 homolog in the cnidarian Nematostella vectensis indicates a conserved involvement in microRNA biogenesis

Abhinandan M. Tripathi et al.

Summary: The biogenesis of miRNAs in animals and plants depends on RNase III Dicer, but their partner proteins are considered distinct. However, a homolog of the plant-specific Dicer partner HYL1 has been discovered in the cnidarian phylum, challenging the idea that miRNAs evolved convergently in animals and plants. This study shows that the HYL1 homolog Hyl1La is crucial for development and miRNA biogenesis in the cnidarian model Nematostella vectensis, suggesting an early emergence of the miRNA system.

ELIFE (2022)

Article Biochemistry & Molecular Biology

Chromatin-associated microprocessor assembly is regulated by the U1 snRNP auxiliary protein PRP40

Agata Stepien et al.

Summary: This study discovered that PRP40 in Arabidopsis regulates the assembly of the microprocessor, playing a crucial role in the correct production of miRNA.

PLANT CELL (2022)

Article Plant Sciences

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

Lucia Gonzalo et al.

Summary: This study demonstrates that plant miRNA biogenesis occurs coupled to transcription, and both co-transcriptional and post-transcriptional processing mechanisms co-exist. R-loops formed near the transcription start site region of MIRNAs promote co-transcriptional pri-miRNA processing.

NATURE PLANTS (2022)

Article Biochemistry & Molecular Biology

HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing

Damian A. Cambiagno et al.

Summary: Studies have shown that HST plays a crucial role in the miRNA pathway in Arabidopsis by facilitating the stability of the DCL1-MED37 complex, thereby regulating the transcription and processing of primary miRNAs.

MOLECULAR PLANT (2021)

Article Biochemistry & Molecular Biology

DEAD-BOX RNA HELICASE 27 regulates microRNA biogenesis, zygote division, and stem cell homeostasis

Xiu-Li Hou et al.

Summary: Mutations in the RH27 gene affect zygote division and stem cell homeostasis in Arabidopsis, resulting in defects in embryogenesis and compromised functionality in the shoot and root apical meristems. RH27 is an important component of the microprocessor complex and plays a critical role in regulating zygote division and stem cell homeostasis.

PLANT CELL (2021)

Article Biochemistry & Molecular Biology

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

Mateusz Bajczyk et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana

Susheel Sagar Bhat et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Plant Sciences

Regulation of Plant Microprocessor Function in Shaping microRNA Landscape

Jakub Dolata et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Multidisciplinary Sciences

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs

Qiang Cai et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis

Zhonghui Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Genetics & Heredity

The SnRK2 kinases modulate miRNA accumulation in Arabidopsis

Jun Yan et al.

PLOS GENETICS (2017)

Article Plant Sciences

mirEX 2.0-an integrated environment for expression profiling of plant microRNAs

Andrzej Zielezinski et al.

BMC PLANT BIOLOGY (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Plant Sciences

Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

Maria Barciszewska-Pacak et al.

FRONTIERS IN PLANT SCIENCE (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana

Katarzyna Dorota Raczynska et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA

Xi Yang et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Structural Determinants of Arabidopsis thaliana Hyponastic Leaves 1 Function In Vivo

Paula Burdisso et al.

PLOS ONE (2014)

Article Multidisciplinary Sciences

COP1 E3 ligase protects HYL1 to retain microRNA biogenesis

Seok Keun Cho et al.

NATURE COMMUNICATIONS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Introns of plant pri-miRNAs enhance miRNA biogenesis

Dawid Bielewicz et al.

EMBO REPORTS (2013)

Article Biochemistry & Molecular Biology

Enhanced microRNA accumulation through stemloop-adjacent introns

Rebecca Schwab et al.

EMBO REPORTS (2013)

Article Biochemistry & Molecular Biology

Multiple RNA recognition patterns during microRNA biogenesis in plants

Nicolas G. Bologna et al.

GENOME RESEARCH (2013)

Article Biochemistry & Molecular Biology

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

Hongliang Zhu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Multidisciplinary Sciences

CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts

Shuxin Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Plant Sciences

Emerging roles for RNA polymerase II CTD in Arabidopsis

Mohsen Hajheidari et al.

TRENDS IN PLANT SCIENCE (2013)

Article Cell Biology

Drosha Regulates Gene Expression Independently of RNA Cleavage Function

Natalia Gromak et al.

CELL REPORTS (2013)

Article Biochemistry & Molecular Biology

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

Pablo A. Manavella et al.

Article Plant Sciences

Role of microRNAs and other sRNAs of plants in their changing environments

Katarzyna Kruszka et al.

JOURNAL OF PLANT PHYSIOLOGY (2012)

Article Biochemistry & Molecular Biology

mirEX: a platform for comparative exploration of plant pri-miRNA expression data

Dawid Bielewicz et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Biochemistry & Molecular Biology

The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana

Yun Ju Kim et al.

EMBO JOURNAL (2011)

Article Biochemistry & Molecular Biology

Identification of MicroRNA Processing Determinants by Random Mutagenesis of Arabidopsis MIR172a Precursor

Julieta L. Mateos et al.

CURRENT BIOLOGY (2010)

Article Multidisciplinary Sciences

Arabidopsis resistance protein SNC1 activates immune responses through association with a transcriptional corepressor

Zhaohai Zhu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

Structure of Arabidopsis HYPONASTIC LEAVES1 and Its Molecular Implications for miRNA Processing

Seong Wook Yang et al.

STRUCTURE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Phosphorylation of the Human MicroRNA-Generating Complex Mediates MAPK/Erk Signaling

Zain Paroo et al.

Article Biochemistry & Molecular Biology

Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs

Bogna Szarzynska et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

Complex regulation of the TIR1/AFB family of auxin receptors

G. Parry et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Multidisciplinary Sciences

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

Sascha Laubinger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1

Zhicheng Dong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Plant Sciences

Gateway-compatible vectors for plant functional genomics and proteomics

KW Earley et al.

PLANT JOURNAL (2006)

Article Biochemistry & Molecular Biology

Loss of SMEK, a novel, conserved protein, suppresses mek1 null cell polarity, chemotaxis, and gene expression defects

MC Mendoza et al.

MOLECULAR AND CELLULAR BIOLOGY (2005)

Article Multidisciplinary Sciences

TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing

TP Chendrimada et al.

NATURE (2005)

Article Plant Sciences

Expression of Arabidopsis MIRNA genes

ZX Xie et al.

PLANT PHYSIOLOGY (2005)

Review Biochemistry & Molecular Biology

MicroRNAs: Genomics, biogenesis, mechanism, and function

DP Bartel

Article Plant Sciences

Chromatin techniques for plant cells

C Bowler et al.

PLANT JOURNAL (2004)

Article Multidisciplinary Sciences

Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions

Y Kurihara et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Cell Biology

The Drosha-DGCR8 complex in primary microRNA processing

JJ Han et al.

GENES & DEVELOPMENT (2004)

Article Multidisciplinary Sciences

The Microprocessor complex mediates the genesis of microRNAs

RI Gregory et al.

NATURE (2004)

Article Multidisciplinary Sciences

Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases

H Koiwa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Multidisciplinary Sciences

Control of leaf morphogenesis by microRNAs

JF Palatnik et al.

NATURE (2003)

Article Cell Biology

MicroRNAs in plants

BJ Reinhart et al.

GENES & DEVELOPMENT (2002)