TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS) DOI Creative Commons

Xiaobing Gu,

Mingdong Wang, Xiao‐Ou Zhang

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D322 - D333

Published: Nov. 13, 2023

Abstract Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function epigenetically regulated promoters, these TE-derived transcription start sites (TSSs) play a role regulating genes associated with specific functions, such cancer embryogenesis. However, lack of an accessible database that systematically gathers TSS data is current research gap. To address this, we established TE-TSS, integrated resource human mouse TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines developmental stages. From these, identified 5768 2797 TSSs, 47% 38% being experimentally validated, respectively. enables comprehensive exploration usage diverse samples, providing insights into tissue-specific gene expression patterns transcriptional Furthermore, compares regions across 15 mammalian species, enhancing our understanding their evolutionary functional aspects. The establishment facilitates further investigations roles shaping transcriptomic landscape offers valuable resources for comprehending involvement biological processes.

Language: Английский

Green biomanufacturing in recombinant collagen biosynthesis: trends and selection in various expression systems DOI
Zilong Zhao, Jianjun Deng, Daidi Fan

et al.

Biomaterials Science, Journal Year: 2023, Volume and Issue: 11(16), P. 5439 - 5461

Published: Jan. 1, 2023

The rapid development of synthetic biology allows us to perform a heterologous expression recombinant collagens in diverse systems (prokaryotic organisms, yeasts, plants, insects, mammalian and human cells, etc. ).

Language: Английский

Citations

31
Basic Epigenetic Mechanisms DOI
James Davie, Hedieh Sattarifard, S Sudhakar

et al.

Sub-cellular biochemistry/Subcellular biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 49

Published: Jan. 1, 2025

Language: Английский

Citations

0
Decoding Local Adaptation in the Exploited Native Marine Mussel Mytilus chilensis: Genomic Evidence from a Reciprocal Transplant Experiment DOI Open Access
Marco Yévenes, Gonzalo Gajardo, Cristian Gallardo‐Escárate

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(3), P. 931 - 931

Published: Jan. 23, 2025

Local adaptations are important in evolution as they drive population divergence and preserve standing genetic diversity essential for resilience under climate change human impacts. Protecting locally adapted populations is aquaculture species. However, high larval connectivity frequent translocations challenge this Chilean blue mussel (Mytilus chilensis) aquaculture, a world-class industry Chiloé Island. This study examined local two ecologically distinct natural beds, Cochamó (northernmost inner sea of Chiloé) Yaldad (southernmost tip), through 91-day reciprocal transplant experiment genomic evidence. mussels grew faster their native environment (0.015 g/day) than (0.004 g/day), though growth declined upon transplantation. Mussels transplanted within between beds displayed distinctive adaptive transcriptomic responses, with differentially expressed genes involved immune function, osmoregulation, metabolism, cellular balance. Additionally, 58 known outlier SNPs mapped over the species’ genome sequence were linked oxidative stress, oxygen management, revealing selection-targeted specific regions. highlights how affect response M. chilensis impact environments counterbalancing its connectivity, concluding that differences should be monitored conserved sustainable practices.

Language: Английский

Citations

0
Harnessing promoter elements to enhance gene editing in plants: perspectives and advances DOI Creative Commons
Nikita Gondalia, Luis Felipe Quiroz, Linyi Lai

et al.

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Summary Genome‐edited plants, endowed with climate‐smart traits, have been promoted as tools for strengthening resilience against climate change. Successful plant gene editing (GE) requires precise regulation of the GE machinery, a process controlled by promoters, which drives its transcription through interactions factors (TFs) and RNA polymerase. While constitutive promoters are extensively used in constructs, their limitations highlight need alternative approaches. This review emphasizes promise tissue/organ specific well inducible enable targeted spatiotemporal manner no effects on other tissues. Advances synthetic biology paved way creation offering refined control over expression augmenting potential GE. The integration these novel systems presents significant opportunities conditional genome editing. Moreover, advent bioinformatic artificial intelligence is revolutionizing characterization regulatory elements, enhancing our understanding roles plants. Thus, this provides insights into strategic use promoter to enhance precision, efficiency specificity GE, setting stage innovative crop improvement strategies.

Language: Английский

Citations

0
Cut from the same cloth: RNAs transcribed from regulatory elements DOI
Ekaterina M. Stasevich,

Anna Šimonová,

Е. А. Богомолова

et al.

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Journal Year: 2024, Volume and Issue: 1867(3), P. 195049 - 195049

Published: July 3, 2024

Language: Английский

Citations

2
Fundamentals for predicting transcriptional regulations from DNA sequence patterns DOI Creative Commons
Masaru Koido, Kohei Tomizuka, Chikashi Terao

et al.

Journal of Human Genetics, Journal Year: 2024, Volume and Issue: 69(10), P. 499 - 504

Published: May 10, 2024

Abstract Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information the elements. These identified cell types pathways genetically associated with human complex traits. However, our understanding detailed allelic effects on these elements’ activities on-off states remains incomplete, hampering interpretation study results. This review introduces machine learning methods to learn sequence-dependent transcriptional regulation mechanisms from DNA sequences for predicting such (not associations). We provide a concise history machine-learning-based approaches, requirements, key computational processes, focusing primers learning. Convolution self-attention, pivotal modern deep-learning models, are explained geometrical interpretations using dot products. facilitates concept why been used sequences. will inspire further research this genetics genomics field.

Language: Английский

Citations

1
Epigenetic insights into Fragile X Syndrome DOI Creative Commons

Liangqun Xie,

Huiying Li,

MengLiang Xiao

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 12

Published: Aug. 16, 2024

Fragile X Syndrome (FXS) is a genetic neurodevelopmental disorder closely associated with intellectual disability and autism spectrum disorders. The core of the disease lies in abnormal expansion CGG trinucleotide repeat sequence at 5′end FMR1 gene. When repetition exceeds 200 times, it causes silencing gene, leading to absence encoded mental retardation protein 1 (FMRP). Although detailed mechanism by which triggers gene yet be fully elucidated, known that this process does not alter promoter region or coding This discovery provides scientific basis for potential reversal through interventional approaches, thereby improving symptoms FXS. Epigenetics, regulation depend on changes DNA sequence, has become new focus FXS research modulating expression reversible manner. latest progress molecular genetics revealed epigenetics plays key role pathogenesis pathophysiological processes article compiles existing findings aim deepening understanding identify targets therapeutic strategies.

Language: Английский

Citations

0
An overview of progress in the application of recombinant collagen in cosmetics DOI Creative Commons
Chen‐Li Cheng,

Y.J Zhang,

Jingbo Yang

et al.

Deleted Journal, Journal Year: 2024, Volume and Issue: 1(4), P. 100059 - 100059

Published: Nov. 29, 2024

Language: Английский

Citations

0
An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation DOI Creative Commons
Jill E. Moore, Henry Pratt, Kaili Fan

et al.

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

Published: Dec. 26, 2024

Abstract Mammalian genomes contain millions of regulatory elements that control the complex patterns gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues integrated these data to develop a Registry 0.9 million human 300 thousand mouse candidate cis-Regulatory Elements (cCREs) annotated with potential functions 1 . We have expanded include 2.35 927 cCREs, leveraging new datasets enhanced computational methods. This covers hundreds unique tissue types, providing comprehensive understanding regulation. Functional characterization from assays like STARR-seq, MPRA, CRISPR perturbation, transgenic now cover over 90% revealing functions. identified thousands novel silencer cCREs demonstrated their dual enhancer/silencer roles in different cellular contexts. Integrating other annotations facilitates genetic variation interpretation trait-associated identification, exemplified by discovering KLF1 as causal for red blood traits. is valuable resource studying genome its impact on health disease.

Language: Английский

Citations

0
Uncovering the cis-regulatory program of early human B-cell commitment and its implications in the pathogenesis of B-cell acute lymphoblastic leukemia DOI Creative Commons
Núria Planell,

Xabier Martinez‐de‐Morentin,

Daniel Mouzo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 2, 2023

ABSTRACT Dysregulation of the early stages B-cell lymphopoiesis, orchestrating development cellular immunity, may induce malignant transformations. Therefore, it is essential to characterize gene regulatory network (GRN) driving lymphopoiesis in healthy individuals uncover malignancy mechanisms. To this end, we generated a dataset that included paired human data for chromatin accessibility and expression eight precursor stages, providing first deep characterization including identification elements reconstruction GRN. Using data, recapitulated well-known revealed new regulons, such as ELK3, enriched pro-B cells with putative role cell cycle progression. Moreover, single-cell multi-omics analysis validated enhanced resolution landscape recovered by bulk revealing MYBL2 ZNF367 specific regulons cycling states, CEBPA associated lymphoid multipotent progenitors (LMPPs). Importantly, enabled us acute lymphoblastic leukemia (B-ALL) triggers. We identified different origins transformation depending on B-ALL subtype, association ETV6-RUNX1 increased ELK3 ALL subtype. Overall, our provides most comprehensive atlas date regulation (B-rex; https://translationalbio.shinyapps.io/brex/ ), facilitating further understanding differentiation health disease.

Language: Английский

Citations

0