bims-micpro 2023-05-21 papers

Issue of 2023‒05‒21
five papers selected by
Thomas Farid Martínez
University of California, Irvine

bioRxiv. 2023 May 06. pii: 2023.05.04.539399. [Epub ahead of print]

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.

A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a step-wise approach to employ multiple CRISPR-Cas9 screens to elucidate functional non-canonical ORFs implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream open reading frames (uORFs) exhibited selective functionality independent of the main coding sequence. One of these, ASNSD1-uORF or ASDURF, was upregulated, associated with the MYC family oncogenes, and was required for medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future cancer genomics studies seeking to define new cancer targets.Highlights: Ribo-seq reveals widespread translation of non-canonical ORFs in medulloblastomaHigh-resolution CRISPR tiling reveals uORF functions in medulloblastomaASNSD1-uORF controls downstream pathways with the prefoldin-like complexASNSD1-uORF is necessary for medulloblastoma cell survival.

DOI: https://doi.org/10.1101/2023.05.04.539399

Bioinformatics. 2023 May 15. pii: btad323. [Epub ahead of print]

uORF4u: a tool for annotation of conserved upstream open reading frames.

Artyom A Egorov, Gemma C Atkinson.

SUMMARY: Upstream open reading frames (uORFs, often encoding so-called leader peptides) can regulate translation and transcription of downstream main ORFs (mORFs) in prokaryotes and eukaryotes. However, annotation of novel functional uORFs is challenging due their short size of usually less than 100 codons. While transcription- and translation-level next generation sequencing (NGS) methods can be used for genome-wide functional uORF identification, this data is not available for the vast majority of species with sequenced genomes. At the same time, the exponentially increasing amount of genome assemblies gives us the opportunity to take advantage of evolutionary conservation in our predictions of functional ORFs.Here we present a tool for conserved uORF annotation in 5' upstream sequences of a user-defined protein of interest or a set of protein homologues. It can also be used to find small conserved ORFs within a set of nucleotide sequences. The output includes publication-quality figures with multiple sequence alignments, sequence logos and locus annotation of the predicted conserved uORFs in graphical vector format.AVAILABILITY: uORF4u is written in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program and additional customisation. Source code is available from the GitHub page: github.com/GCA-VH-lab/uorf4u Detailed documentation that includes an example-driven guide available at the software home page: gca-vh-lab.github.io/uorf4u. A web version of uORF4u is available at server.atkinson-lab.com/uorf4u.

DOI: https://doi.org/10.1093/bioinformatics/btad323

J Adv Res. 2023 May 17. pii: S2090-1232(23)00142-X. [Epub ahead of print]

Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton.

Ghulam Qanmber, Qi You, Zhaoen Yang, Liqiang Fang, Zhibin Zhang, Mao Chai, Baibai Gao, Fuguang Li, Zuoren Yang.

INTRODUCTION: The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement.OBJECTIVES: Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored.
METHODS: We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton.
RESULTS: Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6, a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels.
CONCLUSION: Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.

Keywords: Cotton fiber; LncRNA; ORFs; Transcriptome; Translational regulation; Translatome

DOI: https://doi.org/10.1016/j.jare.2023.05.004

Elife. 2023 May 16. pii: e82249. [Epub ahead of print]12

linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells.

Valerie A Tornini, Liyun Miao, Ho-Joon Lee, Timothy Gerson, Sarah E Dube, Valeria Schmidt, François Kroll, Yin Tang, Katherine Du, Manik Kuchroo, Charles E Vejnar, Ariel Alejandro Bazzini, Smita Krishnaswamy, Jason Rihel, Antonio J Giraldez.

Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode micropeptides. However, systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here, we show that two putative lincRNAs (linc-mipep, also called lnc-rps25, and linc-wrb) encode micropeptides with homology to the vertebrate-specific chromatin architectural protein, Hmgn1, and demonstrate that they are required for development of vertebrate-specific brain cell types. Specifically, we show that NMDA receptor-mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes - evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions, with implications for neurodevelopmental disorders and disease.

Keywords: behavior; cell identity; developmental biology; gene regulation; micropeptides; neurodevelopment; neuroscience; single cell analyses; zebrafish

DOI: https://doi.org/10.7554/eLife.82249

Front Physiol. 2023 ;14 1149120

Role of MOTS-c in the regulation of bone metabolism.

Xuejie Yi, Guangxuan Hu, Yang Yang, Jing Li, Junjie Jin, Bo Chang.

MOTS-c, a mitochondrial-derived peptide (MDP), is an essential regulatory mediator of cell protection and energy metabolism and is involved in the development of specific diseases. Recent studies have revealed that MOTS-c promotes osteoblast proliferation, differentiation, and mineralization. Furthermore, it inhibits osteoclast production and mediates the regulation of bone metabolism and bone remodeling. Exercise effectively upregulates the expression of MOTS-c, but the specific mechanism of MOTS-c regulation in bone by exercise remains unclear. Therefore, this article reviewed the distribution and function of MOTS-c in the tissue, discussed the latest research developments in the regulation of osteoblasts and osteoclasts, and proposed potential molecular mechanisms for the effect of exercise on the regulation of bone metabolism. This review provides a theoretical reference for establishing methods to prevent and treat skeletal metabolic diseases.

Keywords: MOTS-c; bone; metabolism; movement presentation; osteoblast; osteoclast

DOI: https://doi.org/10.3389/fphys.2023.1149120