A1BG regulatory elements and regions

Revision as of 23:20, 30 October 2020 by Marshallsumter (talk | contribs) (Created page with "It may be still fair to say that in the apparent present era of functional genomics, the challenge is to elucidate gene function such as that of A1BG, its likely regulatory ne...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

It may be still fair to say that in the apparent present era of functional genomics, the challenge is to elucidate gene function such as that of A1BG, its likely regulatory networks and signaling pathways.[1] "Since regulation of gene expression in vivo mainly occurs at the transcriptional level, identifying the location of genetic regulatory elements is a key to understanding the machinery regulating gene transcription. A major goal of current genome research is to identify the locations of all gene regulatory elements, including promoters, enhancers, silencers, insulators and boundary elements, and to analyze their relationship to the current annotation of human genes."[2][3] Although "many genome-wide strategies have been developed for identifying functional elements", "no method yet has the resolution to precisely identify all regulatory elements or can be readily applied to the entire human genome."[4]

"The experimental evidence demonstrates that genome binding specificity is achieved through the interplay of at least three factors: DNA sequence; DNA shape; and occlusion by chromatin."[5]

There is one CRISPRi-validated cis-regulatory element on 19q13.43: Gene ID: 116286197 LOC116286197. And, four Sharpr-MPRA regulatory regions: (1) Gene ID: 112553117 LOC112553117 Sharpr-MPRA regulatory region 1998, Gene ID: 112553119 LOC112553119 Sharpr-MPRA regulatory region 10473, Gene ID: 112577453 LOC112577453 Sharpr-MPRA regulatory region 7872, and Gene ID: 112577454 is Sharpr-MPRA regulatory region 9894.

Def. nucleotide "sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents", [that] "may be found in both promoter and enhancer regions"[6] are called response elements.

Heterodimers

Some bZIP proteins, "including LIP19, OsZIP-2a, and OsZIP-2b, do not bind to DNA sequences. Instead, these bZIP proteins form heterodimers with other bZIPs to regulate transcriptional activities (Nantel and Quatrano, 1996; Shimizu et al., 2005)."[7]

DNase I hypersensitive sites

"This genomic region represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the ZNF582 (zinc finger protein 582) gene on chromosome 19 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells."[8]

Gene ID: 116286197 CRISPRi-validated cis-regulatory element chr19.6329 is at NC_000019.10 (56186901..56187499).[8]

Gene ID: 147948 ZNF582 is at NC_000019.10 (56382751..56393585, complement).[9] The CRISPRi-validated cis-regulatory element chr19.6329 is (56382751 - 56186901) = 195850 nts from the beginning of ZNF582.

Transcriptional regulatory regions

"This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss)."[10]

"This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). It also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone)."[11]

"This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss)."[12]

"This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss)."[13]

"The growth hormone-regulated transcription factors STAT5 and BCL6 coordinately regulate sex differences in mouse liver, primarily through effects in male liver, where male-biased genes are upregulated and many female-biased genes are actively repressed."[14] "CUX2, a highly female-specific liver transcription factor, contributes to an analogous regulatory network in female liver. Adenoviral overexpression of CUX2 in male liver induced 36% of female-biased genes and repressed 35% of male-biased genes. In female liver, CUX2 small interfering RNA (siRNA) preferentially induced genes repressed by adenovirus expressing CUX2 (adeno-CUX2) in male liver, and it preferentially repressed genes induced by adeno-CUX2 in male liver. CUX2 binding in female liver chromatin was enriched at sites of male-biased DNase hypersensitivity and at genomic regions showing male-enriched STAT5 binding. CUX2 binding was also enriched near genes repressed by adeno-CUX2 in male liver or induced by CUX2 siRNA in female liver but not at genes induced by adeno-CUX2, indicating that CUX2 binding is preferentially associated with gene repression. Nevertheless, direct CUX2 binding was seen at several highly female-specific genes that were positively regulated by CUX2, including A1bg [A1BG in humans], Cyp2b9, Cyp3a44, Tox [TOX in humans], and Trim24 [TRIM24 in humans]."[14]

ABA-response elements

Main article: ABA-response element gene transcriptions

"The ABA responsive element (ABRE) is a key cis‐regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA‐induced genes in rice aleurone cells, suggesting other ABREs may exist."[15]

"Many ABA‐inducible genes in various species contain a conserved cis‐regulatory ABA responsive element (ABRE) with the consensus sequence ACGTG(G/T)C (Hattori et al. 2002; Shen et al. 2004)."[15]

ABRE core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: 5'-ACGTGGC-3' at 4344 and complement.

ABRE proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: 5'-ACGTGGC-3' at 4239 and complement.

ABRE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-CTGTGCA-3' at 3429 and complement.

Positive strand, positive direction: 5'-GACACGT-3' at 2960, 5'-ACGTGTC-3' at 1823 and complements.

Abf1 regulatory factors

Main article: Abf1 regulatory factors

Abfm regulatory factor distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: 5'-CGTTCTTTATGAT-3' at 352 and complement.

Positive strand, positive direction: 5'-CGTCACCGGTGAC-3' at 2073, 5'-CGTTCGGTGTGAC-3' at 346 and complements.

A boxes

Main article: A box gene transcriptions

"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box), GACGTC (C box), TACGTA (A box), AACGTT (T box), and a GCN4 motif, namely TGA(G/C)TCA (Landschulz et al., 1988;[16] Nijhawan et al., 2008[17])."[7]

"The human TGF-β1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."[18]

A box proximal promoters

Main article: Proximal promoter gene transcriptions

Negative direction: 5'-TACGTA-3' at 4246 and complement.

A box distal promoters

Main article: Distal promoter gene transcriptions

Positive direction: 5'-TACGTA-3' at 3071 and complement.

Box A distal promoters

Negative direction: 5'-TGACTCT-3' at 2788 and complement.

Positive direction: 5'-TCTCAGT-3' at 2613 and complement.

Abscisic acid-responsive elements

Main article: Phosphate starvation-response transcription factor gene transcriptions

Abscisic acid-responsive elements (CACGTG).[19]

"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."[5]

The Pho4 homodimer binds to DNA sequences containing the bHLH binding site 5'-CACGTG-3'.[20]

The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of HIS4 and PHO5 regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].[21]

Phop core promoters

Main article: Core promoter gene transcriptions

Positive strand, negative direction: 5'-CACATT-3' at 4533 and complement.

Pho4 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, positive direction: 5'-CACGTG-3' at 570 and complement.

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTG-3' at 1219, and 5'-CACGTG-3' at 547 and complements.

Phop distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-TTACAC-3' at 4091, 5'-AACGTG-3' at 3288, 3'-CACGTT-5' at 2864, 3'-CACATT-5' at 2087, 5'-TTACAC-3' at 2064, 5'-AACGTG-3' at 1718, 3'-CACGTT-5' at 1536, 5'-AACGTG-3' at 1346, 5'-AACGTG-3' at 1338, 3'-CACATG-5' at 797, 3'-CACATT-5' at 612, and 3'-CACATG-5' at 324 and complements.

Positive strand, negative direction: 5'-CACATG-3' at 2667, 5'-CACGTT-3' at 343 and complements.

Negative strand, positive direction: 5'-CATGTG-3' at 3958, 5'-CACATG-3' at 3956, 5'-CATGTG-3' at 3902, 5'-CACATG-3' at 3742, 5'-CACATG-3' at 3707, 5'-CACATG-3' at 2031, 5'-CACGTG-3' at 570, 5'-AATGTG-3' at 229 and complements.

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTT-3' at 2801, 5'-CACGTT-3' at 2335, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547 and complements.

ACA boxes

Main article: H and ACA box gene transcriptions

The "3' end of mature hTR (45) has an ACA trinucleotide 3 nt upstream of its 3' end. In addition, the 3' region of hTR contains a single H box consensus sequence (5'-AGAGGA-3')."[22]

H and ACA box core promoters

Positive strand, negative direction: 5'-AGGACA-3' at 4468 and complements.

H and ACA box proximal promoters

Negative strand, positive direction: 3'-AGGACA-3' at 4252 and complements.

H and ACA box distal promoters

Negative strand, negative direction: 5'-AGGACA-3' at 1911 and complements.

Negative strand, positive direction: 5'-ACAGGA-3' at 3572, 3'-AGGACA-3' at 3131, 3'-AGGACA-3' at 2460 and complements.

Positive strand, negative direction: 5'-AGGACA-3' at 3756, 5'-AGGACA-3' at 3389, 5'-ACAGGA-3' at 2690 and complements.

Positive strand, positive direction: 5'-AGGACA-3' at 3622, 5'-ACAGGA-3' at 3620, 5'-AGGACA-3' at 144 and complements.

ACGT-containing elements

Main article: ACGT-containing element gene transcriptions
Main article: MYB recognition element gene transcriptions

A box proximal promoters

Negative direction: 5'-TACGTA-3' at 4246 and complement.

A box distal promoters

Positive direction: 5'-TACGTA-3' at 3071 and complement.

ABRE core promoters

Positive strand, positive direction: 5'-ACGTGGC-3' at 4344 and complement.

ABRE proximal promoters

Positive strand, negative direction: 5'-ACGTGGC-3' at 4239 and complement.

ABRE distal promoters

Negative strand, negative direction: 5'-GACACGT-3' at 3429 and complement.

Positive strand, positive direction: 5'-GACACGT-3' at 2960, 5'-ACGTGTC-3' at 1823 and complements.

ACE proximal promoters

Negative strand, negative direction: 5'-ACGTG-3' at 4339 and complement.

Positive strand, negative direction: 5'-ACGTG-3' at 4237 and complement.

ACE distal promoters

Negative strand, negative direction: 5'-CACGT-3' at 3429, 5'-ACGTG-3' at 3288, 5'-CACGT-3' at 2863, 5'-ACGTG-3' at 2760, 5'-ACGTG-3' at 2425, 5'-CACGT-3' at 2081, 5'-ACGTG-3' at 1999, 5'-ACGTG-3' at 1718, 5'-CACGT-3' at 1535, 5'-CACGT-3' at 1470, 5'-ACGTG-3' at 1346, 5'-ACGTG-3' at 1338 and complements.

Negative strand, positive direction: 5'-CACGT-3' at 3254, 5'-ACGTG-3' at 570, 5'-CACGT-3' at 569, and complements.

Positive strand, negative direction: 5'-CACGT-3' at 1772, 5'-CACGT-3' at 531, 5'-CACGT-3' at 342, and complements.

Positive strand, positive direction: 5'-CACGT-3' at 3960, 5'-ACGTG-3' at 3884, 5'-CACGT-3' at 3883, 5'-CACGT-3' at 3464, 5'-ACGTG-3' at 3342, 5'-ACGTG-3' at 3321, 5'-ACGTG-3' at 2961, 5'-CACGT-3' at 2960, 5'-CACGT-3' at 2800, 5'-CACGT-3' at 2681, 5'-CACGT-3' at 2334, 5'-CACGT-3' at 2326, 5'-CACGT-3' at 2063, 5'-ACGTG-3' at 1821, 5'-CACGT-3' at 1786, 5'-ACGTG-3' at 1471, 5'-ACGTG-3' at 1371, 5'-ACGTG-3' at 1219, 5'-CACGT-3' at 1218, 5'-CACGT-3' at 783, 5'-ACGTG-3' at 547, 5'-CACGT-3' at 546, and complements.

Activating transcription factor (Burton) distal promoters

Negative strand, positive direction: 5'-TGACGTAAG-3' at 2207 and complement.

cAMP response element proximal promoters

Negative strand, negative direction: 5'-TGACGTCA-3' at 4317.

C-box (Song) core promoters

Positive strand, positive direction: 5'-GACGTC-3' at 4316, and complement.

C-box (Song) proximal promoters

Negative strand, negative direction: 5'-GACGTC-3', 4316 and complement.

C-box (Song) distal promoters

Positive strand, positive direction: 5'-GACGTC-3' at 3280, 5'-GACGTC-3' at 3231, 5'-GACGTC-3' at 2858, 5'-GACGTC-3' at 1506, 5'-GACGTC-3' at 1120, 5'-GACGTC-3' at 532, 5'-GACGTC-3' at 437, 5'-GACGTC-3' at 193, and complements.

C/G-box hybrid (Song) distal promoters

Positive strand, positive direction: 5'-ACACGTCA-3' at 3962 and complement.

CRE box proximal promoters

Negative strand, negative direction: 5'-TGACGTCA-3', 4317, and complement.

Enhancer box distal promoters

Negative strand, positive direction: 5'-CACGTG-3' at 570 and complement.

Positive strand, positive direction: 5'-CACGTG-3' at 3884 5'-CACGTG-3' at 2961, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547, and complements.

Initiator element (YYANWYY) core promoters

Positive strand, positive direction: 5'-GACGTGG-3' at 4343 and complement.

Initiator element (YYANWYY) proximal promoters

Negative strand, negative direction: 5'-GACGTGA-3' at 4340, and complement.

Initiator element (YYANWYY) distal promoters

Negative strand, negative direction: 5'-TTACGTC-3' at 3772, 5'-AACGTGA-3' at 3289, 5'-GACGTGG-3' at 2761, 5'-GACGTGA-3' at 2426, 5'-CCACGTC-3' at 2082, 5'-GACGTGA-3' at 2000, 5'-TCACGTT-5' at 1536, 5'-TCACGTC-3' at 1471, 5'-AACGTGA-3' at 1347, 5'-AACGTGG-3' at 1339, 5'-GACGTAA-3' at 152, and complements.

Positive strand, negative direction: 5'-GACGTGG-3' at 4238, 5'-TCACGTC-3' at 1773, and complements.

Negative strand, positive direction: 5'-TCACGTC-3' at 3255, and complement.

Positive strand, positive direction: 5'-TCACGTC-3' at 3465, 5'-CTACGTC-3' at 3460, 5'-AACGTAG-3' at 3402, 5'-AACGTGA-3' at 3343, 5'-GACGTGG-3' at 3322, 5'-CCACGTT-3' at 2801, 5'-CCACGTT-3' at 2335, 5'-TCACGTC-3' at 2327, 5'-TCACGTC-3' at 2064, 5'-GACGTAA-3' at 2206, 5'-TCACGTC-3' at 1787, 5'-GACGTGA-3' at 1472, 5'-GACGTGA-3' at 1372, 5'-CCACGTC-3' at 784, and complement.

Initiator element (BBCABW) core promoters

Positive strand, positive direction: 5'-TGACGT-3' at 4341, 5'-TGACGT-3' at 4338, 5'-TGACGT-3' at 4330, 5'-ACGTCT-3' at 4317, and complements.

Initiator element (BBCABW) proximal promoters

Negative strand, negative direction: 5'-ACGTGA-3' at 4340, 5'-ACGTCA-3' at 4317, 5'-TGACGT-3' at 4315, and complements.

Initiator element (BBCABW) distal promoters

Negative strand, negative direction: 5'-TTACGT-3', 3771, 5'-ACGTCT-3' at 3431, 5'-ACACGT-3' at 3429, 5'-ACGTGA-3' at 3289, 5'-ACACGT-3' at 2863, 5'-TGACGT-3' at 2759, 53'-ACGTCA-3' at 2737, 5'-ACGTGA-3' at 2426, 5'-TGACGT-3' at 2424, 5'-ACGTCA-3' at 2402, 5'-ACGTCA-3' at 2083, 5'-ACGTGA-3' at 2000, 5'-TGACGT-3' at 1998, 5'-ACGTCA-3' at 1976, 5'-ACGTGT-3' at 1719, 5'-TCACGT-3' at 1535, 5'-TGACGT-3' at 1494, 5'-ACGTCA-3' at 1472, 5'-ACGTGA-3' at 1347, 5'-ACGTCA-3' at 1323, 5'-ACGTCA-3' at 1032, 5'-ACGTAA-3' at 152, and complements.

Positive strand, negative direction: 5'-AGACGT-3' at 4236, 5'-ACGTCT-3' at 1774, 5'-TCACGT-3' at 1772, 5'-ACGTAA-3' at 533, 5'-ACACGT-3' at 531, 5'-ACACGT-3' at 342, and complements.

Negative strand, positive direction: 5'-ACGTCT-3' at 3256, 5'-TCACGT-3' at 3254, 5'-ACACGT-3' at 569, and complements.

Positive strand, positive direction: 5'-ACGTCA-3' at 3962, 5'-ACACGT-3' at 3960, 5'-ACGTCT-3' at 3831, 5'-TCACGT-3' at 3464, 5'-ACGTCA-3' at 3461, 5'-ACGTGA-3' at 3343, 5'-TGACGT-3' at 3320, 5'-ACGTCA-3' at 3281, 5'-AGACGT-3' at 3279, 5'-AGACGT-3' at 3268, 5'-ACGTCA-3' at 3232, 5'-ACGTAA-3' at 3072, 5'-TTACGT-3' at 3070, 5'-AGACGT-3' at 3061, 5'-ACGTGT-3' at 2962, 5'-ACACGT-3' at 2960, 5'-ACGTCT-3' at 2859, 5'-AGACGT-3' at 2857, 5'-ACGTCT-3' at 2721, 5'-ACACGT-3' at 2681, 5'-ACGTCA-3' at 2328, 5'-TCACGT-3' at 2326, 5'-ACGTAA-3' at 2206, 5'-TGACGT-3' at 2204, 5'-ACGTCA-3' at 2065, 5'-TCACGT-3' at 2063, 5'-ACGTCT-3' at 1937, 5'-ACGTGT-3' at 1822, 5'-TCACGT-3' at 1786, 5'-TGACGT-3' at 1505, 5'-ACGTGA-3' at 1472, 5'-ACGTGA-3' at 1372, 5'-ACGTGT-3' at 1220, 5'-ACGTGT-3' at 548, 5'-ACGTCT-3' at 438, 5'-AGACGT-3' at 224, and complements.

MRE proximal promoters

Negative strand, negative direction: 5'-ACGTGAG-3' at 4341 and complement.

MRE distal promoters

Negative strand, negative direction: 5'-ACGTGAG-3' at 3290, 5'-CACACGT-3' at 2863, 5'-ACGTGGG-3' at 2762, 5'-ACGTGAG-3' at 2427, 5'-ACGTGAG-3' at 2001, 5'-CTCACGT-3' at 1470, 5'-ACGTGAG-3' at 1348, and complements.

Positive strand, negative direction: 5'-ACGTGGG-3' at 3323, 5'-ACGTGTG-3' at 2963, 5'-CTCACGT-3' at 1772, 5'-ACGTGAG-3' at 1473, 5'-ACGTGAG-3' at 1373, 5'-ACGTGTG-3' at 1221, 5'-ACGTGTG-3' at 549, 5'-CACACGT-3' at 531, and complements.

Positive strand, positive direction: 5'-CCCACGT-3' at 3883, 5'-CCCACGT-3' at 2800, 5'-CTCACGT-3' at 2326, 5'-CTCACGT-3' at 1786, 5'-CGCACGT-3' at 1218, 5'-CGCACGT-3' at 546, and complements.

Phop distal promoters

Negative strand, negative direction: 5'-AACGTG-3' at 3288, 3'-CACGTT-5' at 2864, 5'-AACGTG-3' at 1718, 3'-CACGTT-5' at 1536, 5'-AACGTG-3' at 1346, 5'-AACGTG-3' at 1338 and complements.

Positive strand, negative direction: 5'-CACGTT-3' at 343 and complements.

Negative strand, positive direction: 5'-CACGTG-3' at 570 and complement.

Positive strand, positive direction: 5'-CACGTG-3' at 3884, 5'-CACGTG-3' at 2961, 5'-CACGTT-3' at 2801, 5'-CACGTT-3' at 2335, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 547 and complements.

Z box distal promoters

Positive strand, positive direction: 5'-ACACGTGT-3' at 2962 and complement.

Activating protein 2

Main article: Activating protein gene transcriptions

"AP-2 proteins can bind to G/C-rich elements, such as 5’-[G/C]CCN(3,4)GG[G/C]-3’ (41, 42)."[23]

Consensus sequences for the Activating protein 2 (AP-2) are GCCTGGCC.[24]

Activating protein (Murata) core promoters

Negative strand, positive direction: 5'-CCCTGGGGC-3' at 4427, 5'-CCCTTGGGG-3' at 4302 and complement.

Activating protein (Murata) proximal promoters

Negative strand, positive direction: 5'-CCCATGGGG-3' at 4224, 5'-CCCCATGGG-3' at 4223, and complements.

Activating protein (Murata) distal promoters

Negative strand, negative direction: 5'-CCCTGCGGC-3' at 1154 and complement.

Negative strand, positive direction: 5'-GCCCTGGGC-3' at 3498, 5'-GCCAATGGG-3' at 2911, 5'-GCCTCTGGC-3' at 2884, 5'-CCCTTAGGG-3' at 2766, 5'-GCCACCGGC-3' at 1547, 5'-GCCACCGGC-3' at 1295, 5'-GCCAGCGGC-3' at 332, 5'-CCCTCAGGC-3' at 91, and complements.

Positive strand, negative direction: 5'-CCCAAGGGC-3' at 1820 and complement.

Positive strand, positive direction: 5'-CCCGTTGGC-3' at 3912, 5'-CCCTGTGGG-3' at 3533, 5'-GCCAACGGG-3' at 3493, 5'-CCCAGAGGC-3' at 1961, 5'-GCCGGTGGG-3' at 1852, 5'-GCCCGCGGG-3' at 1770, 5'-CCCGGCGGC-3' at 1758, 5'-GCCCCCGGC-3' at 1647, 5'-CCCGACGGC-3' at 483, 5'-CCCTCCGGG-3' at 372, and complements.

Activating protein (Cohen) distal promoters

Negative strand, negative direction: 5'-CCGGTCCG-3' at 4103, 5'-CGGACCGG-3' at 3130, 5'-CCGGTCCG-3' at 2520, 5'-CGGACCGG-3' at 1200, 5'-CCGGTCCG-3' at 649 and complements.

Negative strand, positive direction: 5'-GCCTGGCC-3' at 3681, 5'-GCCTGGCC-3' at 2990, 5'-GGCCAGGC-3' at 1176 and complements.

Activating protein (Cohen2) distal promoters

Positive strand, positive direction: 5'-TCCCCCGCCC-3' at 4440 and complement.

Activating protein (Yao1) proximal promoters

Positive strand, positive direction: 5'-CCCTTCT-3' at 4264 and complement.

Activating protein (Yao1) distal promoters

Negative strand, negative direction: 5'-TCTTCCC-3' at 1657, 5'-GGGAAGA-3' at 620 and complements.

Activating protein (Yao2) core promoters

Negative strand, negative direction: 5'-ACCCTC-3' at 4549, 5'-ACCCTC-3' at 4497 and complements.

Activating protein (Yao2) proximal promoters

Negative strand, negative direction: 5'-ACCCTC-3' at 4303, 5'-ACCCTC-3' at 4271, 5'-GAGGGT-3' at 4259, 5'-ACCCTC-3' at 4153 and complements.

Activating protein (Yao2) distal promoters

Negative strand, negative direction: 5'-ACCCTC-3' at 3989, 5'-ACCCTC-3' at 3752, 5'-ACCCTC-3' at 3714, 5'-ACCCTC-3' at 3080, 5'-ACCCTC-3' at 2221, 5'-ACCCTC-3' at 2104, 5'-ACCCTC-3' at 1962, 5'-ACCCTC-3' at 1930, 5'-ACCCTC-3' at 1795, 5'-ACCCTC-3' at 1018, 5'-ACCCTC-3' at 686, 5'-ACCCTC-3' at 550, 5'-ACCCTC-3' at 413, 5'-GAGGGT-3' at 389 and complements.

Negative strand, positive direction: 5'-CTCCCA-3' at 3333, 5'-CTCCCA-3' at 2532, 5'-CTCCCA-3' at 2396, 5'-CTCCCA-3' at 2383, 5'-TGGGAG-3' at 1782, 5'-CTCCCA-3' at 466 and complements.

Positive strand, positive direction: 5'-CTCCCA-3' at 3880, 5'-CTCCCA-3' at 2797, 5'-CTCCCA-3' at 182.

Activating transcription factors

Main article: Activating transcription factor gene transcriptions

"The ATF4 binding consensus sequence has been reported as (G/A/C)TT(G/A/T)C(G/A)TCA (38), which matches the ChIP-seq data."[25]

Combined consensus sequences are XTTXCATCA (where X = G, A or T), TTTTCATCA, and (G/A/C)TT(G/A/T)C(G/A)TCA to produce 5'-NTT(A/G/T)C(A/G)TCA-3'.

Copying the consensus for the ATF4: 5'-TTTTCA-3', 5'-CTTTCGTCA-3', or 5'-GTTTCA-3' 5'-GTTTCATC-3' 5'-ATTTCAT-3' (where X = G, A or T) and putting the sequence in "⌘F" finds no, no, no, no, no locations between ZSCAN22 and A1BG and no, one, no, no no, no locations between ZNF497 and A1BG as can be found by the computer programs.

Activating transcription factor (Burton) distal promoters

Positive strand, negative direction: 5'-ATTTCATCA-3' at 2888, 5'-TGACGAAAC-3' at 313 and complement.

Negative strand, positive direction: 5'-CTTGCGTCA-3' at 2423, 5'-TGACGTAAG-3' at 2207, 5'-TGATGAAAC-3' at 2147, 5'-CTTTCGTCA-3' at 1184 and complements.

Activating transcription factor (Kilberg) distal promoters

Positive strand, negative direction: 5'-ATTTCATCA-3' at 2888 and complement.

Negative strand, positive direction: 5'-TGATGAAAC-3' at 2147 and complement.

Adr1ps

Main article: Adr1p gene transcriptions

The upstream activating sequence (UAS) for Adr1p is 5'-TTGGGG-3' or 5'-TTGG(A/G)G-3'.[21]

Copying 5'-TTGGGG-3' in "⌘F" yields six between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

Response element negative results

Response elements not occurring in promoters near A1BG
Name of elements Consensus sequences Testing Notes
ABA-response elements 5'-GATCGATC-3', 5'-CGATCGAT-3', 5'-ACGTGTCC-3', 5'-GATCGAT-3' 16 ABREN, CGATCGAT motif, ABRE, and core of ABREN and CGATCGAT motif.[15]
Abf1 regulatory factors 5'-CGTCCTCTACG-3' 16 5'-CGTNNNNNACGAT-3'[5]
Activating proteins 5'-GCCCACGGG-3' 16 Activating protein 2 (AP-2)[23]
Activating proteins 5'-GGCCAA-3' 16 Activating protein 2 (AP-2)[26]
Alpha-amylase conserved elements 5'-TATCCA-3' ⌘F 5'-TATCCATCCATCC-3'[19]
Amino acid response elements 5'-ATTGCATCA-3' ⌘F AARE1 (5'-ATTGCATCA-3')[27]
Amino acid response elements 5'-TTTGCATCA-3' ⌘F 5'-TTTGCATCA-3'.[28][29]
AARE-like 5'-TGGTGAAAG-3' ⌘F AARE-like sequence (5′- TGGTGAAAG-3′, named AARE3)[27]
Androgen response elements 5'-GGTACA-3' ⌘F 5′-GGTACACGGTGTTCT-3′[30]
Androgen response elements 5'-TGATTCGTGAG-3' ⌘F 5'-(A/T)(A/G)(A/C/G)(C/T)(C/G/T)(A/C/G)(C/G)(A/C/T)(A/C/G)(A/T)G(A/G/T)(A/G)(C/G)(A/C/T)-3'[31]
Antioxidant-electrophile responsive elements 5'-GTGAGGTCGC-3' ⌘F 5'-GTGAGGTCGC-3'[32] or 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3'[33], an antioxidant response element (ARE)
CAAT boxes 5'-(C/T)(A/G)(A/G)CCAATC(A/G)-3' 16 consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT
Calcineurin-responsive transcription factor gene transcriptions (Crz1ps) 5'-TGCGCCCC-3' ⌘F 5'-TG(A/C)GCCNC-3'[21]
Calcium-response elements 5'-CTATTTCGAG-3' ⌘F CaRE1 5'-CTATTTCGAG-3'[34]
Cat8ps 5'-CGGTCCGC-3' ⌘F 5'-CGGNBNVMHGGA-3', 5'-CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA-3'
Cbf1 regulatory factors 5'-TCACGTGA-3' 8 strongly bound Cbf1 motifs enriched at both ends with a "T" on the 5′ and "A" on the 3′ end
C-boxes 5'-GAGGCCATCT-3' 16 5'-GAGGCCATCT-3'[35]
C/A hybrid boxes 5'-TGACGTAT-3' 16 5'-TGACGTAT-3'[36]
C/T hybrid boxes 5'-TGACGTTA-3' 16 5'-TGACGTTA-3'[36]
C/EBP boxes 5'-TTAGGACAT-3', or 5'-TAGCATT-3' ⌘F CCAAT-enhancer-binding site (C/EBP) is TAGCATT
Cell cycle regulation 5'-CCCAACGGT-3' ⌘F tomato genome-wide analysis
CENP-B boxes 5'-TTTCGTTGGAAGCGGGA-3' 16 specifically localized at the centromere
Circadian control elements 5'-CAACTTTA-3' ⌘F CCE
CCCTC-binding factors (CTCF) 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3' 16 5′-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3′[37]
DAF-16-associated elements 5'-TGATAAG-3' ⌘F DAF-16-associated element (DAE)[38]
DAF-16 binding elements 5'-GTAAACA-3' ⌘F DAF-16 binding element (DBE)[38]
D boxes 5'-GTTGTATAAC-3' ⌘F 5′-CTTATGTAAA-3′[39]
D-boxes 5'-TCTCACA-3' ⌘F TCTCACATT(A/C)AATAAGTCA is a D-box.[35]
Defense and stress-responsive elements 5'-ATTTTCTTCA-3' ⌘F Defense and stress-responsive elements (DREs)
DNA damage response elements (DREs) 5'-TAGCCGCCG-3' or 5'-TTTCAAT-3' ⌘F in the upstream repression sequence (URS)
DNA replication-related elements 5'-TATCGATA-3' ⌘F DNA replication-related element (DRE)[40]
DREB boxes 5'-TACCGACAT-3' 16 CRT/DREB box
EIF4E basal elements 5'-TTACCCCCCCTT-3' 16 poly(C) motif
Endoplasmic reticulum stress response elements 5'-CCAAT-3' ⌘F 5'-CCAATGGGCTGAAAC-3' between ZNF497 and A1BG
Estrogen response elements 5'-AGGTTA-3' or 5'-GGTCAGGAT-3' ⌘F 5'-AGGTTATTGCCTCCT-3' or 5'-GGTCAGGATGAC-3'
Forkhead boxes 5'-(A/G)(C/T)AAA(C/T)A-3' ⌘F 5'-GTAAACAA-3' FOXO1
Gal4ps 5'-CGGACCGC-3' ⌘F 5'-CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG-3'
G boxes 5'-(G/T)CCACGTG(G/T)C-3' ⌘F no "perfect palindrome" G boxes in either promoter
GCN4 motifs 5'-TGACTCA-3', 5'-TGAGTCA-3' ⌘F ACGT motif
Gcn4ps 5'-ATGACTCTT-3' ⌘F GCN4 motifs
GLM boxes 5′-(G/A)TGA(G/C)TCA(T/C)-3′ 16 GCN4-like motif
γ-interferon activated sequences (GAS) 5'-TTCCTAGAA-3' ⌘F ALS-GAS1 between nt −633 and nt −625
Grainy head transcription factor binding sites 5'-AACCGGTT-3' ⌘F also 5'-GACTGGTT-3'
GT boxes 5'-GGGGTGGGG-3' ⌘F (-78 to -69)
Hac1ps 5'-CAGCGTG-3' ⌘F Regulates the unfolded protein response
Heat-responsive elements 5'-AAAAAATTTC-3' ⌘F four nGAAn motifs
Hex sequences 5'-TGACGTGGC-3' ⌘F the Hex sequence (TGACGTGGC)[36]
HMG boxes 5'-(A/T)(A/T)CAAAG-3' ⌘F two or more HMG boxes
Hybrid C, A boxes 5'-TGACGTAT-3' ⌘F A at the 12 position
Hybrid C, G boxes 5'-TGACGTGT-3' ⌘F G at the 12 position
Hybrid C, T boxes 5'-TGACGTTA-3' ⌘F T at the 12 position
Hypoxia-inducible factors 5'-GCCCTACGT-3' ⌘F composed of HIF-1α and HIF-1β
I boxes 5'-GATAAG-3' ⌘F 5'-GGATGAGATAAGA-3'
Inositol, choline-responsive element 5'-TYTTCACATGY-3' ⌘F 5'-TCTTCAC, TCTTCACAT-3'
Kozak sequences 5'-(GCC)GCC(A/G)CCATGG-3' ⌘F 5'-GAAAATGG-3'.[41]
L boxes 5'-TAAATG(A/C/G)A-3' ⌘F L1 box
MAREs 5'-TGCTGA(G/C)TCAGCA-3' ⌘F and 5'-TGCTGA(GC/CG)TCAGCA-3'
M boxes 5'-GTCATGTGCT-3' ⌘F upstream of the TATA box
Mcm1 regulatory factors 5'-(A/C/T)(A/C/T)NC(C/T)(A/C/T)(A/C/T)(A/T)(A/C/T)(A/C/T)N(A/G)(C/G/T)(A/C/T)-3' ⌘F Genome-wide determinant search
Met31ps 5'-AAACTGTGG-3' ⌘F Sulfur amino acid metabolism [72]
Middle sporulation elements 5'-C(A/G)CAAA(A/T)-3' ⌘F 5'-ACACAAA-3' (2017)
Motif ten elements 5'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-3' 16 Gene ID: 6309
Ndt80ps 5'-TCCGCA-3' ⌘F 5'-DNCRCAAAW-3'
Nuclear factor Y 5'-TACCGACAT-3' ⌘F NF-Y is a trimeric complex
Nutrient-sensing response element 1 5'-GTTTCATCA-3' ⌘F only one nucleotide difference between the SESN2 CARE and the ASNS
Oaf1ps 5'-(A/C/G/T)(A/C/G/T)(A/C/G/T)T(A/C/G/T)A(A/C/G/T)-3' ⌘F 5'-CGG(A/C/G/T)3T(A/C/G/T)A(A/C/G/T)9-12CCG-3'
Pdr1p/Pdr3ps 5'-TCCGCGGA-3' ⌘F Pdr1p/Pdr3p response element (PDRE)
Polycomb response elements 5'-CGCCATTT-3' ⌘F closely resembles the extended Pho-Phol consensus sequence
Rap1 regulatory factors 5'-C(A/C/G)(A/C/G)(A/G)(C/G/T)C(A/C/T)(A/G/T)(C/G/T)(A/G/T)(A/C/G)(A/C)(A/C/T)(A/C/T)-3' ⌘F Rap1 (CCCACCAACAAAA) none
Rgt1ps 5'-CGGACCA-3' ⌘F Glucose-responsive transcription factor
Rlm1ps 5'-CTATATATAG-3' ⌘F CTA(T/A)4TAG
Rox1ps 5'-GGGTAA-3' ⌘F Heme-dependent repressor of hypoxic genes [78]
Rpn4ps 5'-GGTGGCAAA-3' ⌘F proteasome genes
Seed-specific elements 5'-CATGCATG-3' ⌘F SRE consensus: 5'-CAGCAGATTGCG-3' is none
Shoot specific elements 5'-GATAATGATG-3' ⌘F SRE consensus: 5'-CAGCAGATTGCG-3' is none
Sip4ps 5'-CCGTCCGT-3' ⌘F 5'-CC(C/G)T(C/T)C(C/G)TCCG-3'
Smp1ps 5'-ACTACTA-3' ⌘F 5-ACTACTA(T/A)4TAG-3'
Sterol response elements 5'-TCGTATA-3' ⌘F perhaps plant specific
TATCCAC boxes 5'-TATCCAC-3' 16 GA responsive complex component
TCCACCATA elements 5'-TCCACCATA-3' ⌘F adjacent co-dependent regulatory element of POLLEN1
Tec1ps 5'-GAATGT-3' ⌘F Ste12p cofactor
Tetradecanoylphorbol-13-acetate response elements (TREs) 5'-TGA(G/C)TCA-3' 16 cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40
TGF-β control elements (TCEs) 5'-GAGTGGGGCG-3' ⌘F in mouse and rat, 5'-GCGTGGGGGA-3' in humans
TGF-β inhibitory elements (TIEs) 5'-GAGTGGTGA-3' 16 in the rat transin/stromelysin promoter
Thyroid hormone response elements (TREs) 5'-AGGTCA-3' ⌘F See VDREs, X boxes
Unfolded protein response elements (UPREs) 5'-TGACGTG(G/A)-3' ⌘F XBP1 binds to UPRE
Vhr1ps 5'-AATCA-N8-TGA(C/T)T-3' ⌘F Response to low biotin [71] concentrations
Vitamin D response elements (VDREs) 5'-(A/G)G(G/T)(G/T)CA-3' ⌘F 5'-AGGTCA-3' not ⌘F
X boxes 5'-GTTGGCATGGCAAC-3' 16 X2 box is 5'-AGGTCCA-3' not ⌘F
Xbp1ps 5'-GcCTCGA(G/A)G(C/A)g(a/g)-3' ⌘F Transcriptional repressor
Xenobiotic response elements (XREs) 5'-(T/G)NGCGTG(A/C)(G/C)A-3' ⌘F contains the core sequence 5'-GCGTG-3'
Yap1p,2ps 5'-TTACTAA-3' ⌘F Yap1p binding sites
Y boxes 5'-(A/G)CTAACC(A/G)(A/G)(C/T)-3' 16 inverted CAAT box
Zap1ps 5'-ACCCTCA-3' ⌘F 5'-ACC(C/T)(C/T)(A/C/G/T)AAGGT-3'

Hypotheses

  1. Downstream core promoters may work as transcription factors even as their complements or inverses.
  2. In addition to the DNA binding sequences listed above, the transcription factors that can open up and attach through the local epigenome need to be known and specified.
  3. Each DNA binding domain serving as a transcription factor for the promoter of any immunoglobulin supergene family member, also serves or is present in the promoters for A1BG.
  4. The function of A1BG is the same as other immunoglobulin genes possessing the immunoglobulin domain cl11960 and/or any of three immunoglobulin-like domains: pfam13895, cd05751 and smart00410 in the order and nucleotide sequence: cd05751 Location: 401 → 493, smart00410 Location: 218 → 280, pfam13895 Location: 210 → 301 and cl11960 Location: 28 → 110.

See also

References

  1. ↑ Francis S Collins, Eric D Green, Alan E Guttmacher, Mark S Guyer (24 April 2003). "A vision for the future of genomics research". Nature. 422 (6934): 835–47. doi:10.1038/nature01626. PMID 12695777. Retrieved 9 August 2020.
  2. ↑ The ENCODE Project Consortium (22 October 2004). "The ENCODE (ENCyclopedia of DNA Elements) Project". Science. 306 (5696): 636–640. doi:10.1126/science.1105136. PMID 15499007. Retrieved 9 August 2020.
  3. ↑ The ENCODE Project Consortium (14 June 2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. doi:10.1038/nature05874. PMID 17571346. Retrieved 9 August 2020.
  4. ↑ Ya-Mei Wang, Ping Zhou, Li-Yong Wang, Zhen-Hua Li, Yao-Nan Zhang, and Yu-Xiang Zhang (10 August 2012). "Correlation Between DNase I Hypersensitive Site Distribution and Gene Expression in HeLa S3 Cells". PLoS One. 7 (8): e2414. doi:10.1371/journal.pone.0042414. PMID 22900019. Retrieved 9 August 2020.
  5. ↑ 5.0 5.1 5.2 Invalid <ref> tag; no text was provided for refs named Rossi
  6. ↑ MeSH (8 July 2008). "Response Elements". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894: National Institutes of Health, Health & Human Services. Retrieved 2 September 2020.
  7. ↑ 7.0 7.1 ZG E, YP Z, JH Zhou and L W (16 April 2014). "Roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137. Vancouver style error: punctuation (help)
  8. ↑ 8.0 8.1 RefSeq (November 2019). "LOC116286197 CRISPRi-validated cis-regulatory element chr19.6329 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 July 2020.
  9. ↑ RefSeq (February 2016). "ZNF582 zinc finger protein 582 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 28 May 2020.
  10. ↑ RefSeq (June 2018). "LOC112553117 Sharpr-MPRA regulatory region 1998 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 25 July 2020.
  11. ↑ RefSeq (June 2018). "Sharpr-MPRA regulatory region 10473 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 16 July 2020.
  12. ↑ RefSeq (June 2018). "Sharpr-MPRA regulatory region 7872 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 1 August 2020.
  13. ↑ RefSeq (June 2018). "Sharpr-MPRA regulatory region 9894 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 16 July 2020.
  14. ↑ 14.0 14.1 Tara L. Conforto, Yijing Zhang, Jennifer Sherman, and David J. Waxman (November 2012). "Impact of CUX2 on the Female Mouse Liver Transcriptome: Activation of Female-Biased Genes and Repression of Male-Biased Genes" (PDF). Molecular and Cellular Biology. 32 (22): 4611–4627. doi:10.1128/MCB.00886-12. PMID 22966202. Retrieved 8 August 2020.
  15. ↑ 15.0 15.1 15.2 Kenneth A. Watanabe, Arielle Homayouni, Lingkun Gu, Kuan‐Ying Huang, Tuan‐Hua David Ho, Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.
  16. ↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
  17. ↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
  18. ↑ Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.
  19. ↑ 19.0 19.1 Invalid <ref> tag; no text was provided for refs named Sharma
  20. ↑ Dalei Shao, Caretha L. Creasy, Lawrence W. Bergman (1 February 1998). "A cysteine residue in helixII of the bHLH domain is essential for homodimerization of the yeast transcription factor Pho4p". Nucleic Acids Research. 26 (3): 710–4. doi:10.1093/nar/26.3.710. PMC 147311. PMID 9443961.
  21. ↑ 21.0 21.1 21.2 Invalid <ref> tag; no text was provided for refs named Tang
  22. ↑ James R. Mitchell, Jeffrey Cheng, ang Kathleen Collins (January 1999). "A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End" (PDF). Molecular and Cellular Biology. 19 (1): 567–576. doi:10.1128/mcb.19.1.567. PMID 9858580. Retrieved 5 November 2018.
  23. ↑ 23.0 23.1 Takayuki Murata, Chieko Noda, Yohei Narita1, Takahiro Watanabe, Masahiro Yoshida, Keiji Ashio, Yoshitaka Sato, Fumi Goshima, Teru Kanda, Hironori Yoshiyama, Tatsuya Tsurumi, and Hiroshi Kimura (27 January 2016). "Induction of Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (LMP1) by Transcription Factors Activating Protein 2 (AP-2) and Early B Cell Factor (EBF)" (PDF). Journal of Virology. doi:10.1128/JVI.03227-15. Retrieved 4 October 2020.
  24. ↑ Isabelle R. Cohen, Susanne Grässel, Alan D. Murdoch, and Renat V. Iozzo (1 November 1993). "Structural characterization of the complete human perlecan gene and its promoter" (PDF). Proceedings of the National Academy of Sciences USA. 90 (21): 10404–10408. doi:10.1073/pnas.90.21.10404. PMID 8234307. Retrieved 6 September 2020.
  25. ↑ Thomas D. Burton, Anthony O. Fedele, Jianling Xie, Lauren Sandeman and Christopher G. Proud (22 May 2020). "The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4" (PDF). Journal of Biological Chemistry. 295 (21): 7418. doi:10.1074/jbc.RA119.011864. PMID 32312748 Check |pmid= value (help). Retrieved 5 September 2020.
  26. ↑ Invalid <ref> tag; no text was provided for refs named Yao
  27. ↑ 27.0 27.1 Ryuto Maruyama, Makoto Shimizu, Juan Li, Jun Inoue & Ryuichiro Sato (24 March 2016). "Fibroblast growth factor 21 induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region". Bioscience, Biotechnology, and Biochemistry. 80 (5): 929–934. doi:10.1080/09168451.2015.1135045. Retrieved 4 October 2020.
  28. ↑ Angelika Bröer, Gregory Gauthier-Coles, Farid Rahimi, Michelle van Geldermalsen, Dieter Dorsch􏰀, Ansgar Wegener􏰀, Jeff Holst, and Stefan Bröer (March 15, 2019). "Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells" (PDF). Journal of Biological Chemistry. 294 (11): 4012–4026. doi:10.1074/jbc.RA118.006378. Retrieved 4 October 2020.
  29. ↑ Alisa A. Garaeva, Irina E. Kovaleva, Peter M. Chumakov & Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.
  30. ↑ S Kouhpayeh, AR Einizadeh, Z Hejazi, M Boshtam, L Shariati, M Mirian, L Darzi, M Sojoudi, H Khanahmad and A Rezaei (1 July 2016). "Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line" (PDF). Cancer Gene Therapy. 23: 254–257. doi:10.1038/cgt.2016.26. Retrieved 3 October 2020.
  31. ↑ Stephen Wilson, Jianfei Qi & Fabian V. Filipp (14 September 2016). "Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines". Scientific Reports. 6: 32611. doi:10.1038/srep32611. Retrieved 3 October 2020.
  32. ↑ Akihito Otsuki, Mikiko Suzuki, Fumiki Katsuoka, Kouhei Tsuchida, Hiromi Suda, Masanobu Morita, Ritsuko Shimizu, Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.
  33. ↑ Sarah E. Lacher, Daniel C. Levings, Samuel Freeman, Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.
  34. ↑ Xu Tao, Anne E. West, Wen G. Chen, Gabriel Corfas, Michael E. Greenberg (2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33: 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226. Retrieved 2 September 2020.
  35. ↑ 35.0 35.1 Invalid <ref> tag; no text was provided for refs named Johnson
  36. ↑ 36.0 36.1 36.2 Invalid <ref> tag; no text was provided for refs named Song
  37. ↑ Hideharu Hashimoto, Dongxue Wang, John R. Horton, Xing Zhang, Victor G. Corces and Xiaodong Cheng (1 June 2017). "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA". Molecular Cell. 66 (5): 711–720.e3. doi:10.1016/j.molcel.2017.05.004. PMID 28529057. Retrieved 28 August 2020.
  38. ↑ 38.0 38.1 Yan-Hui Li and Gai-Gai Zhang (12 April 2016). "Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans". Oncotarget. 7 (15): 19185–19192. doi:10.18632/oncotarget.8313. PMID 2702736. Retrieved 27 August 2020.
  39. ↑ Philipp Mracek, Cristina Santoriello, M. Laura Idda, Cristina Pagano, Zohar Ben-Moshe, Yoav Gothilf, Daniela Vallone, Nicholas S. Foulkes (December 6, 2012). "Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression". PLoS ONE. 7 (12): e51278. doi:10.1371/journal.pone.0051278. Retrieved 10 February 2019.
  40. ↑ Fumiko Hirose, Masamitsu Yamaguchi, Akio Matsukage (September 1999). "Targeted Expression of the DNA Binding Domain of DRE-Binding Factor, a Drosophila Transcription Factor, Attenuates DNA Replication of the Salivary Gland and Eye Imaginal Disc". Molecular and Cellular Biology. 19 (9): 6020–6028. doi:10.1128/MCB.19.9.6020. PMID 10454549. Retrieved 4 September 2020.
  41. ↑ Invalid <ref> tag; no text was provided for refs named Matsumoto

External links

{{Phosphate biochemistry}}

Retrieved from "https://www.wikidoc.org/index.php?title=A1BG_regulatory_elements_and_regions&oldid=1673086"