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Functional regulatory elements
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Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the NaV1.1 sodium channel alpha subunit, is one such gene with two co-active promoters.
22p
vibransone
28-03-2024
5
2
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Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity— however, most predicted enhancer regions remain to be functionally tested.
25p
vibransone
28-03-2024
5
2
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Part 2 book "Avian embryology" includes content: Time lapse imaging of the early avian embryo, gain and loss of function approaches in the chick embryo, manipulation and electroporation of the avian segmental plate and somites in vitro, generating transgenic quail using lentiviruses, dissection of chick genomic regulatory regions, computational approaches to finding and analyzing cis regulatory elements.... and other contents.
199p
oursky05
20-09-2023
3
2
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Auxins play an important role in plant growth and development; the auxins responsive gene; auxin/ indole-3-acetic acid (Aux/IAA), small auxin-up RNAs (SAUR) and Gretchen Hagen3 (GH3) control their mechanisms. The GH3 genes function in homeostasis by the catalytic activities in auxin conjugation and bounding free indole-3- acetic acid (IAA) to amino acids.
17p
vihagrid
30-01-2023
8
3
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Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced following excessive oncogenic activity, is a major barrier against cancer transformation.
13p
vigalileogalilei
27-02-2022
10
1
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Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signatures is a powerful means to detect functional elements and clarify regulatory activities in human studies.
16p
vigalileogalilei
27-02-2022
11
1
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Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically identify the SNPs that affect gene expression by modulating activities of distal regulatory elements, we adapt the self-transcribing active regulatory region sequencing (STARR-seq) strategy, a high-throughput technique to functionally quantify enhancer activities.
14p
vialfrednobel
29-01-2022
6
0
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Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, because of genome size and complexity, these tools have yet to be applied to the whole human genome.
13p
vialfrednobel
29-01-2022
8
0
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Transposable elements are increasingly recognized as a source of cisregulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into functional enhancers regulating host gene expression.
26p
viarchimedes
26-01-2022
9
0
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Mammalian genomes contain millions of putative regulatory sequences, which are delineated by binding of multiple transcription factors. The degree to which spacing and orientation constraints among transcription factor binding sites contribute to the recognition and identity of regulatory sequence is an unresolved but important question that impacts our understanding of genome function and evolution.
19p
viarchimedes
26-01-2022
11
0
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Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat.
21p
viarchimedes
26-01-2022
10
1
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Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there are 10–100× more binding sites than differentially expressed genes.
26p
viarchimedes
26-01-2022
12
0
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The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments.
33p
viarchimedes
26-01-2022
10
0
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Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, studying lncRNA function has been a challenge due to their diverse biological roles and because lncRNA loci can contain multiple molecular modes that may exert function.
35p
viarchimedes
26-01-2022
9
0
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The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins.
15p
vilarryellison
29-10-2021
7
1
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Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range.
38p
vilarryellison
29-10-2021
10
1
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Identifying functional non-coding variation is critical for defining the genetic contributions to human disease. While single-nucleotide polymorphisms (SNPs) within cis-acting transcriptional regulatory elements have been implicated in disease pathogenesis, not all cell types have been assessed and functional validations have been limited. In particular, the cells of the peripheral nervous system have been excluded from genome-wide efforts to link non-coding SNPs to altered gene function.
19p
vilarryellison
29-10-2021
11
0
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Post-transcriptional regulation is crucial for the control of eukaryotic gene expression and might contribute to adaptive divergence. The three prime untranslated regions (3’ UTRs), that are located downstream of protein-coding sequences, play important roles in post-transcriptional regulation. These regions contain functional elements that influence the fate of mRNAs and could be exceptionally important in groups such as rapidly evolving cichlid fishes.
11p
vibeauty
23-10-2021
13
1
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A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57–74, 2012; Nat 507:462–70, 2014; Nat 507:455–61, 2014; Nat 518:317–30, 2015).
9p
vibeauty
23-10-2021
8
1
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With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements.
14p
vibeauty
23-10-2021
18
2
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