CRISPRi Screen Uncovers lncRNA Regulators of Human Monocyte Growth DOI Creative Commons

Cristina Flores-Arena,

Eric Malekos, Sergio Covarrubias

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 25, 2024

Abstract Long noncoding RNAs are emerging as critical regulators of biological processes. While there over 20,000 lncRNAs annotated in the human genome we do not know function for majority. Here performed a high-throughput CRISPRi screen to identify those that important viability monocytes using cell line THP1. We identified total 38 hits from and validated characterized two top intergenic hits. The first is lncRNA neighboring macrophage transcription factor IRF8 ( RP11-542M13 . 2 hereafter referred long RNA regulator monocyte proliferation, LNCRMP ) second called OLMALINC (oligodendrocyte maturation-associated intervening non-coding RNA) was previously found be oligodendrocyte maturation. Transcriptional repression severely limited their proliferation capabilities. RNA-seq analysis knockdown lines showed regulated proapoptotic pathways while impacted genes associated with cycle. Data supports both functioning cis regulate proteins also essential THP1 growth. This research highlights importance screening powerful tool quickly discovering functional (lncRNAs) play vital role regulating viability.

Language: Английский

Finding functional microproteins DOI
Sikandar Azam,

Fengping Yang,

Xuebing Wu

et al.

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

1
Genome modeling and design across all domains of life with Evo 2 DOI Creative Commons
Garyk Brixi, Matthew G. Durrant, Ja‐Lok Ku

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Abstract All of life encodes information with DNA. While tools for sequencing, synthesis, and editing genomic code have transformed biological research, intelligently composing new systems would also require a deep understanding the immense complexity encoded by genomes. We introduce Evo 2, foundation model trained on 9.3 trillion DNA base pairs from highly curated atlas spanning all domains life. train 2 7B 40B parameters to an unprecedented 1 million token context window single-nucleotide resolution. learns sequence alone accurately predict functional impacts genetic variation—from noncoding pathogenic mutations clinically significant BRCA1 variants—without task-specific finetuning. Applying mechanistic interpretability analyses, we reveal that autonomously breadth features, including exon–intron boundaries, transcription factor binding sites, protein structural elements, prophage regions. Beyond its predictive capabilities, generates mitochondrial, prokaryotic, eukaryotic sequences at genome scale greater naturalness coherence than previous methods. Guiding via inference-time search enables controllable generation epigenomic structure, which demonstrate first scaling results in biology. make fully open, parameters, training code, inference OpenGenome2 dataset, accelerate exploration design complexity.

Language: Английский

Citations

1
Evaluation of Cas13d as a tool for genetic interaction mapping DOI Creative Commons

Ghanem El Kassem,

Jasmine Hillmer,

Michael Boettcher

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 14, 2025

Abstract Mapping genetic interactions (GIs) is crucial for understanding network complexity. In this study, we investigate the utility of Cas13d, a CRISPR system targeting RNA, GI mapping and compare it to Cas9 Cas12a, two DNA nucleases commonly used mapping. We find that Cas13d induces faster target gene perturbation generates more uniform cell populations with double perturbations than or Cas12a. then encounter gRNA-gRNA interference when concatenating gRNAs different genes into one gRNA array, which overcome by dual promoter expression strategy. Moreover, three same are able maximize Cas13d-mediated knockdown effects. Combining these strategies enhances proliferation phenotypes while reducing library size facilitates reproducible quantification GIs in oncogenic signaling pathways. Our study highlights potential mapping, promising advancements therapeutically relevant drug response

Language: Английский

Citations

0
Emerging Roles of Long Non‐Coding RNAs in Cardiovascular Diseases DOI Creative Commons

Xiangyue Kong,

Fengjuan Li, Yuan Wang

et al.

Journal of Cellular and Molecular Medicine, Journal Year: 2025, Volume and Issue: 29(5)

Published: March 1, 2025

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Over past decade, studies have demonstrated that circulating long non-coding RNAs (lncRNAs)-recognised for their stability ease detection-serve as crucial regulators potential biomarkers in multiple diseases. LncRNAs regulate key processes, including endothelial function, vascular remodelling, myocardial hypertrophy, all which influence CVD progression. Additionally, lncRNAs display cell-, tissue-, disease-specific expression patterns, making them ideal therapeutic targets or tools. This review presents a comprehensive overview current understanding CVDs, examining mechanisms action recent research advances. It also addresses use diagnostic prognostic markers, well applications RNA therapeutics novel treatment strategies.

Language: Английский

Citations

0
Long noncoding RNA as an emerging regulator of endoderm differentiation: progress and perspectives DOI Creative Commons
Jie Yang, Donghui Zhang, Wei Jiang

et al.

Cell Regeneration, Journal Year: 2025, Volume and Issue: 14(1)

Published: March 26, 2025

Abstract Accumulated studies have demonstrated that long noncoding RNAs (lncRNAs) play crucial regulatory roles in diverse biological processes, such as embryonic development and cell differentiation. Comprehensive transcriptome analysis identifies extensive lncRNAs, gradually elucidating their functions across various contexts. Recent highlighted the essential role of lncRNAs definitive endoderm differentiation, underscoring importance early development. In this review, we analyzed features overlapping, proximal, desert classified by genomic location, pluripotent stem cells (PSCs) differentiation derivatives. Furthermore, focus on lineage review latest advancements lncRNA identification distinct mechanisms. By consolidating current knowledge, aim to provide a clearer perspective how contribute different manners.

Language: Английский

Citations

0
High throughput CRISPR approaches: New solutions for challenging problems DOI

Gargi Bindal,

Chitra Seetharam Misra,

Mandeep Singh

et al.

TrAC Trends in Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 118245 - 118245

Published: March 1, 2025

Language: Английский

Citations

0
Next-Generation Sequencing: a powerful multi-purpose tool in cell line development for biologics production DOI Creative Commons
Luigi Grassi, Claire Harris, Jie Zhu

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Within the biopharmaceutical industry, cell line development (CLD) process generates recombinant mammalian lines for expression of therapeutic proteins. Analytical methods extensive characterisation protein product are well established; however, over recent years, next-generation sequencing (NGS) technologies have rapidly become an integral part CLD workflow. NGS can be used different applications to characterise genome, epigenome and transcriptome lines. The resulting datasets, especially when integrated with systems biology models, give comprehensive insights that applied optimize lines, media, fermentation processes. also provides monitor genetic variability during CLD. High coverage experiments indeed ensure integrity plasmids, identify integration sites, verify monoclonality This review summarises role in advancing production safety efficacy

Language: Английский

Citations

0
Unveiling roles of non‐coding RNAs in cancer through advanced technologies DOI Open Access

Runhao Wang,

Leng Han

Quantitative Biology, Journal Year: 2025, Volume and Issue: 13(4)

Published: April 20, 2025

Language: Английский

Citations

0
CRISPRi Screen Uncovers lncRNA Regulators of Human Monocyte Growth DOI Creative Commons

Cristina Flores-Arena,

Eric Malekos, Sergio Covarrubias

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 25, 2024

Abstract Long noncoding RNAs are emerging as critical regulators of biological processes. While there over 20,000 lncRNAs annotated in the human genome we do not know function for majority. Here performed a high-throughput CRISPRi screen to identify those that important viability monocytes using cell line THP1. We identified total 38 hits from and validated characterized two top intergenic hits. The first is lncRNA neighboring macrophage transcription factor IRF8 ( RP11-542M13 . 2 hereafter referred long RNA regulator monocyte proliferation, LNCRMP ) second called OLMALINC (oligodendrocyte maturation-associated intervening non-coding RNA) was previously found be oligodendrocyte maturation. Transcriptional repression severely limited their proliferation capabilities. RNA-seq analysis knockdown lines showed regulated proapoptotic pathways while impacted genes associated with cycle. Data supports both functioning cis regulate proteins also essential THP1 growth. This research highlights importance screening powerful tool quickly discovering functional (lncRNAs) play vital role regulating viability.

Language: Английский

Citations

0