Non-coding DNA – a brief review

doi:10.7324/jabb.2017.50507

Cited by 2 publications

(1 citation statement)

References 63 publications

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“…The non-coding regions of DNA not only maintain the structure of chromatin but also harbor important regulatory elements (Böhmdorfer & Wierzbicki, 2015;Shanmugam, Nagarajan & Pramanayagam, 2017). Almost all sgRNA design models and algorithms are trained on datasets that exclude non-coding regions from analysis because of their potential to give rise to non-effective sgRNAs despite realizing the importance of these regions.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome

Malik

Gul

Munir

et al. 2021

PeerJ

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The CRISPR-Cas9 system has recently evolved as a powerful mutagenic tool for targeted genome editing. The impeccable functioning of the system depends on the optimal design of single guide RNAs (sgRNAs) that mainly involves sgRNA specificity and on-target cleavage efficacy. Several research groups have designed algorithms and models, trained on mammalian genomes, for predicting sgRNAs cleavage efficacy. These models are also implemented in most plant sgRNA design tools due to the lack of on-target cleavage efficacy studies in plants. However, one of the major drawbacks is that almost all of these models are biased for considering only coding regions of the DNA while excluding ineffective regions, which are of immense importance in functional genomics studies especially for plants, thus making prediction less reliable. In the present study, we evaluate the on-target cleavage efficacy of experimentally validated sgRNAs designed against diverse ineffective regions of Arabidopsis thaliana genome using various statistical tests. We show that nucleotide preference in protospacer adjacent motif (PAM) proximal region, GC content in the PAM proximal seed region, intact RAR and 3rd stem loop structures, and free accessibility of nucleotides in seed and tracrRNA regions of sgRNAs are important determinants associated with their high on-target cleavage efficacy. Thus, our study describes the features important for plant sgRNAs high on-target cleavage efficacy against ineffective genomic regions previously shown to give rise to ineffective sgRNAs. Moreover, it suggests the need of developing an elaborative plant-specific sgRNA design model considering the entire genomic landscape including ineffective regions for enabling highly efficient genome editing without wasting time and experimental resources.

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Section: Introductionmentioning

confidence: 99%

Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome

Malik

Gul

Munir

et al. 2021

PeerJ

View full text Add to dashboard Cite

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The Role of Cells in Encoding and Storing Information: A Narrative Review of Cellular Memory

Flores,

Liester

2024

Cureus

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Memory, a fundamental aspect of human cognition and consciousness, is multifaceted and extends beyond traditional conceptualizations of mental recall. This review article explores memory through various lenses, including brain-based, body-based, and cellular mechanisms. At its core, memory involves the encoding, storage, and retrieval of information. Advances in neuroscience reveal that synaptic changes and molecular modifications, particularly in the hippocampus, are crucial for memory consolidation. Additionally, body memory, or somatic memory, highlights how sensory experiences and traumatic events are stored and influence behavior, underscoring the role of implicit memory. Multiple studies have demonstrated that memories can be encoded and stored in cells. Evidence suggests that these memories can then be transferred between individuals through organ transplantation. Additionally, observations in organisms that lack a nervous system, such as bacteria, fungi, and plants, expand traditional memory concepts. This review highlights and compiles novel research from the last few decades that explores information encoding and storage at a cellular level across a wide variety of disciplines. Our aim is to integrate these findings into a cohesive framework that helps explain the role of cellular processes in memory retention and transfer. By compiling research across diverse fields, this review aims to establish a foundation for future investigation into the physiological and psychological significance of cellular memory. Despite substantial progress, critical gaps persist in our understanding of how cellular memory interfaces with neural memory systems and the precise pathways through which information is encoded, stored, retrieved, and transferred at the cellular level. There has been a noticeable lack of research focused on cellular memory, and more rigorous investigations are needed to uncover how cells participate in memory and the extent to which these processes influence human behavior and cognition.

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Non-coding DNA – a brief review

Cited by 2 publications

References 63 publications

Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome

Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome

The Role of Cells in Encoding and Storing Information: A Narrative Review of Cellular Memory

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